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2,16,18,219,251,257,343,344,345,350,495,519,524],"var":[3,11,12,178,358,376,508,524],"void":[4,6,7,8,41,181,225,244,500],"while":[1,3,9,11,12,13,17,74,75,115,152,161,176,189,203,208,217,229,231,235,247,248,253,254,255,257,263,271,294,307,308,312,314,318,348,378,386,393,399,410,416,458,459,480,482,485,492,495,506,511,518],__main__:495,__pthread_key_cr:12,_boundingbox:204,_compute_group_group:154,_compute_heat_flux:154,_compute_t:8,_j1m1m1:152,_j2m2m2:152,_manifold_rattl:519,_pair_lj:9,_serial:12,_wirnsberg:238,a10:360,a123:360,a12:460,a2m:[6,99],a_0:[257,347,399],a_0_real:257,a_1:347,a_2:347,a_3:347,a_4:347,a_c:407,a_cc:407,a_f:482,a_ij:399,a_pi:399,a_sigma:399,a_ss:407,aat:185,aatom1:[68,126],aatom2:[68,126],aatom3:[68,126],ab_23_cd:360,abbrevi:12,abc:[3,12,360,495,524],aberdeen:[88,89,240,322],abf:230,abf_integr:13,abi:208,abil:[3,229,271,304,317,418],abl:[3,8,9,11,12,39,94,203,208,228,237,245,287,343,350,393,495,524,528],ablat:347,abort:512,about:[0,1,3,6,8,9,11,12,13,15,16,39,41,42,63,65,82,119,126,127,130,172,178,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,235,236,237,238,239,243,244,245,246,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,270,276,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,331,332,333,335,336,338,339,340,341,342,343,344,345,346,347,349,350,351,352,354,355,356,357,358,375,378,382,385,386,388,393,398,404,409,426,455,459,488,495,498,499,504,505,507,512,516,519,524,527,529],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,35,37,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,59,65,66,71,74,75,76,77,80,81,94,95,97,98,99,103,104,106,107,123,125,127,128,130,152,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,176,177,178,180,181,184,185,186,187,188,189,190,191,192,193,195,196,197,199,203,204,205,206,207,210,211,212,213,214,218,219,220,222,223,225,228,229,231,232,237,241,244,246,250,252,254,255,256,260,270,271,276,300,303,305,310,316,317,318,323,331,335,338,339,340,341,358,360,361,362,363,364,365,366,367,368,370,372,378,380,383,387,388,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,448,449,450,451,453,455,456,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,491,492,493,494,495,497,498,499,500,501,504,505,506,507,508,511,512,515,518,519,524,525,528,529],abscissa:[450,451,478,479],absenc:214,absent:518,absolut:[3,207,217,230,231,235,318,323,337,377,378,386,423,431,498],absorb:347,absoult:378,abstol:318,ac3:177,academ:246,acc:342,acceler:0,accelri:[6,13],accept:[7,12,95,176,178,207,228,231,246,318,342,403,435,505,512,519],acceptanc:217,acceptor:425,access:[0,3,6,7,8,9,11,12,15,38,40,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,93,96,97,98,99,100,101,102,103,105,106,109,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,128,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,173,174,175,176,177,200,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,236,237,238,239,243,244,245,246,247,248,249,250,251,252,254,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,276,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,307,308,309,310,311,313,314,315,316,317,319,320,321,323,328,331,332,333,334,335,336,337,338,339,340,341,343,344,345,346,347,349,350,351,352,353,354,355,356,357,373,377,393,395,421,423,425,426,443,458,459,468,494,495,498,503,515,516,524],accident:519,accidenti:370,accler:[9,12],accommod:215,accomod:271,accompani:8,accomplish:[15,231,258,288],accord:[6,66,75,88,133,139,142,160,206,217,226,227,242,257,271,287,299,307,323,325,344,345,347,352,353,355,356,357,389,418,423,434,437,456,463,465,466,468,470,471,473,474,475,511,524],accordingli:[11,112,156,157,171,176,182,389,440,441,475],account:[3,6,95,130,160,176,177,186,198,220,222,236,238,251,252,254,271,277,278,279,291,292,294,296,298,302,308,317,319,321,331,333,334,335,338,339,340,343,347,350,366,387,409,414,423,431,435,440,441,443,446,466,494,511,519,525],accuml:[3,317,343,350],accumul:[6,8,14,75,88,154,210,220,221,254,317,323,349,375,393,503,523],accur:[1,3,6,9,14,16,37,41,56,161,225,269,312,317,318,321,335,343,350,356,358,378,399,418,422,423,448,460,476,478,479,480,482,511,516,524],accuraci:[1,3,6,12,41,202,203,207,225,238,248,271,309,321,348,358,377,378,385,395,418,448,450,451,458,459,478,479,486,506,511,516,518,524,528],accuractli:516,ach:377,achiev:[1,3,6,9,10,15,16,17,28,41,225,238,246,248,271,272,287,299,300,307,377,426,506],achiv:17,acid:9,ackland1:416,ackland2:416,ackland:2,acknowledg:0,acml:12,aco:524,acolor:[206,207],acoust:299,acquir:[3,6,60,63,64,181,182,227,229,231,271,454,490,502,518],across:[1,2,3,6,9,12,13,14,41,59,63,68,71,73,75,84,102,119,126,128,166,180,182,219,222,225,236,250,317,318,319,324,343,347,350,356,360,388,393,492,497,500,501,505,514,516],act:[3,6,73,119,129,163,235,249,252,253,254,255,257,260,270,317,328,342,344,345,347,356,357,358,386,401,412,422,423,425,460,475],acta:[130,177,394],actinid:[9,446],action:[2,6,11,12,75,247,252,345,518],activ:[5,8,11,12,13,15,55,61,95,176,230,247,251,254,260,266,270,297,317,318,326,346,375,439,476,506,518,521,524],active:[266,491],actual:[1,3,6,8,12,56,64,134,161,203,204,207,211,212,224,226,227,235,254,255,294,298,303,304,312,315,323,335,338,339,340,342,348,357,358,377,389,422,424,429,434,440,441,475,494,495,506,507,515,524],actualli:337,adam:[377,378],adapt:[2,3,6,9,95,172,210],adapti:298,adaptiv:[9,230,395],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,40,42,75,95,99,112,125,128,129,131,176,178,179,203,204,205,206,210,211,212,213,214,216,218,219,220,222,223,227,230,235,237,238,244,248,249,250,252,254,256,257,261,269,270,271,272,273,274,275,276,277,278,279,291,292,294,295,296,298,306,316,317,320,321,331,332,334,338,340,341,345,346,347,349,351,352,356,358,378,380,385,387,395,400,402,405,409,418,426,431,443,448,449,453,459,461,495,497,498,503,505,507,509,516,518,519],add_molecul:216,add_speci:216,add_to_nodeset:216,added:[498,519],addforc:[2,3,210],adding:[8,213,237,316,519],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,235,237,238,241,242,246,248,249,250,254,257,271,272,273,274,275,276,277,278,279,289,291,292,294,295,296,298,306,317,320,321,322,324,348,351,352,356,362,368,371,373,378,380,388,390,393,394,395,399,400,402,404,406,408,409,412,414,415,416,417,418,419,423,424,426,427,428,430,431,439,441,442,443,444,445,446,448,450,451,452,453,456,458,459,461,466,467,476,477,478,479,480,481,482,485,489,492,497,498,499,504,505,506,509,511,518,519,520,522,524,527,528,529],addition:[0,4,6,8,11],additionali:204,addres:9,address:[7,8,11,206,253,519],addtorqu:2,adequ:[263,335,348,377,388,506],adher:28,adhikari:257,adiabat:0,adiam:[206,207],adjac:[39,176,178,238,388,448,478,479,480,511,512],adjiman:447,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,251,254,258,262,267,268,271,272,276,294,298,301,303,304,307,308,309,310,315,317,318,326,335,339,343,348,350,351,352,354,355,357,377,378,386,388,393,395,415,440,441,466,482,507,525],adjust_radiu:326,adjust_radius_factor:326,admiss:276,adof:[158,219],adopt:[316,518],adp:[2,3,7],adri:[9,313,458,459],adust:172,advanc:[3,15,251,399,492,503],advantag:[1,6,8,11,17,39,40,41,225,393,417,506,511],advect:[3,6,335],advertis:8,advis:[318,388,457,516],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,231,232,238,244,250,252,254,260,266,268,272,273,274,275,277,278,279,285,291,292,294,296,317,319,333,347,357,370,377,384,385,386,388,389,390,393,418,440,441,448,494,495,497,499,500,502,505,507,516],affin:[15,16,17,231,393,408],affiniti:393,afile:248,aforement:17,afresh:[305,505,524],afshar:413,after:[2,3,5,6,8,11,12,14,20,21,32,39,40,41,44,50,59,60,61,63,65,75,156,157,158,159,160,161,162,165,166,167,168,170,171,178,179,181,182,185,186,191,197,202,203,204,205,206,207,208,210,211,212,216,217,219,220,225,226,227,228,229,231,235,246,257,258,259,260,261,267,268,269,271,277,278,279,285,291,292,294,296,299,303,307,315,317,318,321,330,332,336,338,339,340,342,343,344,345,346,350,352,354,358,361,362,368,376,383,384,386,387,389,391,392,393,394,395,399,406,408,416,417,418,419,420,426,427,428,439,440,441,443,444,445,446,450,451,452,456,458,459,466,467,476,477,479,480,481,482,485,492,494,496,497,498,499,500,502,503,505,507,509,511,514,515,516,518,519,523,524,525,527,528,529],afterrun:505,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,231,238,250,303,361,376,388,440,441,492,494,495,497,499,504,511,513,524,527],against:[11,12,13,66,232,388,458,459],aggreg:[6,12,68,71,73,84,102,119,126,250,267,315,317,333,492,525],aggress:[238,250,511],agilio:[9,13],agre:[3,8,199,386,395,428,459],agreement:[5,7],ahd:425,ahead:354,aidan:[0,5,7,9,13,380],aij:13,aim:6,airebo:[2,3,7,226,227,314],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,251],aktulga:[7,9,310,459],al2o3:466,al2o3_001:[130,319],al3:177,ala:[257,466],alain:9,alat:[298,443],albe:[456,480,482],albeit:316,albert:9,alchem:[95,172],alcohol:350,alcu:[394,399],alcu_eam:456,alderton:412,alejandr:[271,272],alessandro:13,algebra:446,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,231,238,250,257,259,260,285,300,308,317,321,322,342,343,347,350,355,384,385,386,390,393,414,418,441,446,463,465,492,494,511],alia:[9,15],alias:[1,378],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,252,380,497,500,518],alkali:418,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,263,264,266,267,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,330,331,332,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,366,371,373,375,376,377,378,379,380,383,386,387,388,389,390,392,393,394,395,396,398,399,400,402,403,404,405,406,408,409,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,507,508,509,510,511,512,514,515,516,518,519,523,524,525,527,528,529],allen:[28,95,412,422],allentildeslei:95,allign:3,allindex:359,alloc:[3,5,6,8,9,11,12,62,244,349,387,389,393,454,459,497,505],allocat:3,alloi:[2,3,12,13,394,399,409],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,236,237,244,246,247,248,249,251,252,254,257,260,261,266,268,271,272,289,298,302,303,304,305,306,307,309,311,316,317,318,319,320,321,323,325,326,330,331,332,333,334,335,342,343,344,345,347,348,349,350,351,352,356,358,360,362,371,373,377,378,380,386,387,388,389,392,393,395,396,399,400,401,402,403,404,409,416,418,423,424,425,426,431,435,440,441,446,448,456,459,460,463,465,466,475,483,486,488,490,492,495,497,499,500,501,502,503,504,507,509,510,511,514,515,519,524,525],almost:[2,3,12,15,62,252,307,347,378,390,393,475],alo:409,alon:[6,7,228,313,458,459,495],alond:13,along:[6,8,12,28,40,74,75,95,130,176,177,178,202,203,206,219,228,238,252,257,258,262,263,268,270,307,317,321,323,327,331,333,342,346,347,353,356,358,380,382,384,385,386,388,409,412,423,426,429,431,435,443,458,459,478,479,497,500,507,508,524],alonso:[444,445],alpha:[6,12,51,211,257,307,308,312,386,394,397,400,409,413,414,416,417,419,420,425,430,431,443,449,455,481,483,515,518],alpha_c:439,alpha_i:467,alpha_lj:439,alphabet:[2,3,21,36,44,55,65,186,198,210,362,371,387,406,476,497],alphanumer:[3,65,210,306,314,360,387,524],alreadi:[3,7,8,9,12,16,17,42,57,178,179,181,205,215,219,225,227,231,261,305,307,335,358,359,387,388,413,424,426,433,441,475,486,489,493,497,498,502,507,523,524],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,28,35,36,37,39,40,41,42,44,54,55,56,60,61,63,65,69,74,75,76,77,79,81,86,87,88,89,95,97,98,100,103,113,114,115,116,117,118,120,121,123,125,127,128,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,198,199,201,202,203,204,205,206,207,208,210,211,212,213,215,218,219,220,221,222,223,224,225,226,227,228,229,231,232,237,240,241,242,244,245,246,247,248,250,251,254,255,256,257,266,268,269,271,272,273,274,275,276,277,278,279,284,288,289,291,292,294,295,296,298,299,300,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,327,328,331,333,335,338,339,340,341,342,346,347,348,349,351,353,356,358,359,360,362,368,371,375,377,378,380,381,383,386,387,388,389,390,392,393,399,403,404,406,410,411,412,413,416,417,418,422,423,425,426,427,435,439,440,443,446,448,452,454,455,456,457,459,460,461,463,470,471,473,474,476,477,478,479,480,481,482,483,485,492,494,495,496,497,498,499,500,501,502,504,505,506,507,509,510,511,512,514,515,516,517,518,519,520,522,523,524,525,527,529],alter:[3,6,8,9,11,12,41,61,155,156,157,158,159,161,164,165,166,167,170,171,178,182,203,204,206,208,211,212,219,226,227,228,229,231,270,271,312,315,317,320,328,335,343,350,357,385,388,426,497,502,504,507,524,525,529],altern:[1,6,8,9,11,12,15,16,17,99,178,203,210,220,231,240,251,255,271,306,317,318,342,343,350,363,367,377,385,386,394,395,409,414,416,417,419,428,431,439,443,444,445,452,456,457,467,477,480,482,485,495,497,498,510,512,515],alternat:[386,518],although:[15,28,42,199,260,271,304,308,317,342,376,504,518,529],aluminum:489,alwai:[0,6,11,12,15,16,17,54,59,65,75,176,207,21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,11,14,40,86,95,96,124,130,177,178,203,204,208,210,211,212,217,232,237,246,306,308,309,310,314,337,350,377,378,387,400,402,408,409,411,412,416,418,419,426,431,435,439,453,458,459,466,476,482,483,485,486,488,489,497,498,502,507,509,518,523,524],charmm2lammp:13,charmm:[0,2,3,5],chartreus:207,cheap:335,cheaper:[236,422,460],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,199,200,217,225,226,227,232,243,246,252,253,303,316,321,335,343,345,350,358,360,373,376,386,387,388,389,390,393,415,427,430,448,459,490,492,494,495,497,505,511,514,515,516,524],checkf:199,checkout:519,checkqeq:459,checku:199,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,221,230,235,238,247,248,255,257,270,271,272,289,294,295,300,304,307,309,317,322,323,335,338,339,342,343,344,345,352,361,370,372,377,378,385,388,395,400,404,405,408,409,410,412,413,414,418,421,422,424,425,431,435,436,439,443,447,448,450,451,453,466,475,483,506,509,511,518],chemic:[9,40,88,89,130,172,177,203,204,216,217,246,308,313,314,342,378,420,451,458,459,471,479],chemistri:[307,308,310,395,399,418,458,459],chen:347,cheng:408,chenoweth:[458,459],chenoweth_2008:[458,459],chi:[102,167,202,298,308,310,373,419,422,525],chiefli:457,child:8,chip:[7,9,16,17,393,510],chipot:230,chiral:370,chmod:[11,12],cho:443,chocol:[7,207],choic:[3,6,9,12,14,15,17,40,41,54,74,95,153,156,157,171,182,197,199,219,225,228,231,232,248,254,257,269,271,300,304,308,317,342,353,371,378,384,385,388,390,393,426,439,448,454,459,497,506,507,510,511,517,518,523],choos:[1,3,6,7,8,9,12,16,17,28,39,54,95,128,168,169,206,226,227,228,229,232,243,254,257,269,271,273,274,275,276,277,278,279,303,304,322,335,339,353,377,378,385,486,492,494,506,512],chose:[480,482],chosen:[2,3,6,12,16,152,178,181,190,199,206,212,217,229,232,243,246,247,255,257,269,271,276,300,303,314,335,339,342,343,348,350,351,357,378,379,385,393,414,418,423,430,433,461,480,492,506,511,512,518],chri:176,christian:[7,9,16],christoph:7,chunk:[0,2,3],chunkid:[69,79,86,98,103,114,116,125,158,173,175,219,332],chute:[4,9,10,249],ciccotti:321,cieplak:[6,184,509],cii:220,cij:220,circl:[42,75,330],circular:[3,6,156,201],circumst:17,circumv:[100,117,312],citat:0,cite:[3,7,8,12,254,466],civ:9,cl1:177,clarendon:[28,412],clarifi:[7,480,482],clariti:360,clark:453,class2:[2,3],classic:[0,3,5,6,7,8,9,15,244,300,307,312,347,372,418],classifi:[476,485],claus:495,clean:[6,12,14,16,505],cleanli:[496,515,528],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:501,click:[2,11,21,36,44,55,178,186,198,206,251,362,371,388,406,476,519],client:[251,253],climb:[270,388,511],clinic:[7,13],clo:[167,202,525],clock:[12,492,511,516],clockwis:[184,353],clone:519,close:[3,6,11,12,13,39,41,70,75,153,181,203,227,228,229,248,255,257,271,287,294,317,321,353,356,376,378,381,384,385,388,393,395,399,409,410,429,443,448,450,451,458,462,464,478,482,501,507,518,519,521],closer:[3,10,41,127,176,202,203,225,229,233,344,388],closest:[227,298,317,350,422,460,475,486],cloud:[466,518],clovertown:17,clsuter:76,clump1:[302,317],clump2:[302,317],clump3:[302,317],clump:317,cluster:[2,3,6,7,12,15,63,65,75],clutter:3,cmap:497,cmatrix:248,cmax:443,cmd:[11,12,300,508],cmdarg:11,cmin:443,cmm:7,cmoput:145,cn1:220,cn2:220,cna:[2,3,7,65,74],cnn:220,cnr:13,cnrs:9,cnt:[426,501],co2:[40,177,318,321,387,420],coars:[7,9,10,28,35,40,54,190,242,302,317,318,335,420,424,451,461,479,506,509],coarser:[378,524],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,197,361,362,368,406,426,430,448,463,465,468,497,526],coeffcient:497,coeffici:[0,2,3,4],coefficienct:413,coefficient0:416,coefficient1:416,coeffieci:[6,397,429],coeffincientn:416,coexist:[246,418],cohes:[6,419,443],coincid:[134,356,404,440,441,492],colberg:205,cold:[6,163,246,250,389,518],coldest:343,coleman8:9,coleman:[9,130,177,319],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,260,267,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[236,335,357],colliex:177,collinear:[3,302],collis:[3,257,335,353,357,415,423,489],colllis:335,colloid:[2,3,4,6,7],colombo:39,colon:[208,358,498,516],color1:207,color2:207,color:[3,9,41,203,206,207,225,247,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,74,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,260,268,269,307,317,336,337,347,357,395,421,425,458,459,498,512,514,515,524],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,14,42,65,75],comamnd:231,comand:228,comannd:393,comb3:[2,3],comb:[2,3,4,7,9,210,308],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,238,246,251,260,263,271,287,293,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[0,2,3],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,205,251,253,254,378,388,393,413,448,455,478,479,499],comm_modifi:[2,3,6,39],comm_modift:63,comm_styl:[2,3,41,63],comm_world:11,command:[0,1],comment:[2,4,7,11,12,37,56,184,199,203,241,242,255,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,295,429,491,492,494,511,528],common:[0,1],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,231,251,253,257,259,260,261,271,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,205,253,254,287,293,321,378,388,418,448,455,460,474,478,479,481],compact:[65,210,406,476],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,235,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:0,compart:382,compass:[7,9,20,21,36,43,44,55,185,186,198,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,238,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,226,227,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,207,208,251,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,207,225,230,260,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,257,287,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,217,246,495],complier:12,compon:[3,6,8,12,63,65,69,70,74,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,237,238,244,249,253,254,257,260,262,263,267,268,270,271,272,276,277,278,279,291,292,294,296,297,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,217,257,416],compound:[408,418,419,485],compres:[75,125,219],compress:[3,6],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[0,1],computation:[3,6,226,227,347,399],computational:518,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,65],compute_peratom:8,compute_sa:[130,319],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,528],concav:356,concentr:[75,242,318,416,420,451,479],concept:[6,158,168,219,506],conceptu:[3,6,75,166,229,231,388,409,426,443,502],concern:[6,77,95,205,247],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:500,confer:[15,446],confid:[3,511],config:[12,203,494],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,231,232,236,246,253,254,285,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,515,519],confin:[497,511],confirm:516,conflict:[3,12,40,204,448,495,519],conform:[3,6,13,61,228,229,270,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,254,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,254,257,261,285,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,228,251,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,207,211,212,232,251,252,409,431,435,492,498,500],consequ:[1,6,217,347,430,511],conserv:[3,9,28,210,217,228,235,236,247,250,254,256,257,261,267,269,271,285,287,289,317,318,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,232,258,272,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,254,255,338,339,340,393,459,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,235,237,244,247,254,255,256,268,271,273,274,275,276,277,278,279,280,281,283,284,285,286,289,290,291,292,294,295,296,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:216,consit:317,constant:[0,3,4],constantli:238,constitu:[3,6,260,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,232,238,246,247,252,260,263,265,287,293,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[3,5],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,271,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:[15,459],consum:[1,312,454,524],consumpt:375,contact:[0,2,3,4,5,8,9,12,13,40,42,65],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,232,237,241,242,248,252,253,254,257,269,285,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,15,16,127,128,207,226,227,232,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,238,246,247,248,250,251,252,254,255,256,262,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,216,347,463,465],contour_integr:216,contract:[61,229,231,271,304,317],contradictori:3,contrain:321,contraint:285,contrari:[248,255],contrast:[1,6,42,55,66,160,163,204,231,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,246,254,257,260,261,266,272,294,295,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230,231,250,251,254,255,271,273,274,275,276,277,278,279,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:216,controlfil:459,convect:99,conveni:[6,12,28,203,208,223,319,380,467,483,516,519,524],convent:[3,8,28,189,196,198,204,207,316,331,359,416,418,524],converg:[3,6,41,96,203,204,206,208,213,225,228,229,237,244,276,287,293,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511,516],convers:[3,8,152,206,207,217,220,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,269,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,238,250,315],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:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,231,232,235,237,238,239,244,246,249,250,251,252,253,254,255,268,270,271,273,274,275,277,278,279,294,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,219],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,206,347,388,406,458,495,519],copper:489,coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:207,core:[0,1,3,4],core_shel:160,cores:518,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,509],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:[3,6,40,124,206,356,357,380,484,497,519],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,231,238,246,248,254,271,272,294,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,232,237,244,255,265,271,272,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[2,3,6,99,100,152,174,210,219],correpond:[241,242],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,238,239,242,244,245,249,254,257,258,267,268,269,271,273,274,275,276,277,278,279,280,281,285,289,291,292,294,296,298,299,300,304,309,310,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[2,6,7,21],cosineshift:26,cosmo:[248,253],cossq:2,cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,243,271,289,309,318,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,15,96,248,389],couett:4,coul:[2,3,6,9,15,35,45,46,76,95,118,127,172,184,211,212,348,378,386],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,244,253,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,232,237,243,246,252,271,285,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:246,counterbal:[238,250],counterbalanc:28,counterclockwis:184,counterpart:[203,492],counterproduct:17,coupl:[0,3,4],couple:[4,6,11,12],courant:324,cours:[3,8,15,138,140,172,203,211,212,247,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:248,cover:[6,12,75,199,207,216,257,418,484],coverag:75,cpc:253,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,244,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,235,255,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuinfo:15,cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,389,518],craympi:393,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:302,criteria:[3,127,179,206,207,226,227,228,266,386,455,484,499,502,524],criterion:[12,41,133,178,181,217,225,228,246,285,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,269,342,347,386],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,231,268,270,294,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,15,74,77,117,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,15,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[2,3,210],cst:416,cstherm:6,cstyle:494,csvr:[2,3,6,210],ctcm:[394,416],ctemp_core:235,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,235,356,380,518],cubes:[41,225],cubic:[2,3,37,56,117,199,241,257,298,335,378,380,416],cuda:[1,3,7,9,12,14,16,393,510,524],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:399,cummul:[3,6,223,226,227,228,230,243,248,254,256,335,338,339,340,341,343,350,425,515],cumul:[6,217,219,222,236,246,254,269,271,276,285,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,236,237,238,244,246,248,251,252,254,260,266,268,271,272,277,278,279,285,287,291,292,293,294,296,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,246,287,293,299],curvatur:[422,460,489],custom:[0,2,3,6],cut0:495,cut1:506,cut2:506,cut:[1,2,3,6,9,12,14,15,16,17,18,41],cuthi:[298,310],cutinn:[401,440,441],cutlo:[298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,233,241,242,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[2,7,15,362],cwiggl:[3,268,352,355,357,524],cyan:[2,206,207],cycl:[3,246,269,271,272,276],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,252,293,303,353,356,382,500],cylinder_d:382,cylindr:[6,252,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:257,d3q19:257,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,203,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:294,damag:[2,3,9,65],dammak:312,damp:[3,6,210,215,254,255,256,261,271,272,276,293,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:255,damp_drud:255,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,246,358,413,515],dangl:181,daniel:9,darden:[378,412],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:308,dash:[423,514],dat:[6,99,199,216,493],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:[12,13,319],dataset:319,datatyp:3,date:[0,4,6,12,13,202,458,459,524],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:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dcd:[3,6,7,203,205,206,207,208,300,498,502],dcs:9,ddim:202,deactiv:439,dealt:253,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[2,3,7,211,212,312],decai:[100,409,489],decid:[3,6,12,15,75,268,306,317,348,512,519],decipher:380,deck:306,declar:205,declin:335,decod:206,decompos:[95,467],decomposit:[3,5,7,17,64,216,300,322],decoupl:[6,518],decreas:[3,15,203,204,213,214,221,228,231,237,238,244,246,254,346,377],decrement:323,dedic:[15,393],deepli:374,deeppink:207,deepskyblu:207,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:2,defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,235,236,237,240,242,244,245,246,249,252,253,254,255,256,257,266,268,270,271,272,273,274,275,276,277,278,279,281,282,283,286,289,290,291,292,294,295,296,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,240,252,276,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[2,3,6,7,8,40,42,59,61,63,65,85,122,134,138,139,153],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,235,246,248,249,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:199,degress:[158,219],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,243,246,271,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],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:[318,495,524],dellago:[6,238],deloc:[272,418,466],delr:443,delt_lo:511,delta:[2,21],delta_1:399,delta_3:399,delta_7:399,delta_conf:3,delta_ij:[443,456],delta_pi:399,delta_r:456,delta_sigma:399,deltah_f:242,delx:202,delz:202,demand:312,demo:11,demon:297,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,257,259,260,261,299],denomin:[7,183],denot:[130,235,238,255,299,310,312,409,424,426,459,463,465],dens:[75,228,318,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,231,244,257,260,264,265,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[269,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,231,237,239,242,245,248,249,250,252,254,255,257,259,260,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,298,309,310,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:232,deposit:[2,3,4,112,180,210,217],deprec:[3,308,458],deprect:219,depth:[51,156,206,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,238,246,254,268,271,273,274,275,276,277,278,279,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:298,descend:207,descent:[7,385],descib:[40,206,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,234,235,241,242,247,248,251,252,253,254,255,256,257,259,260,261,266,270,271,272,276,284,295,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[2,3,6,8,9,11,12,13,17],descriptor:[152,203,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,234,235,271,272,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,244,246,247,254,255,256,260,271,294,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,206],despit:518,destabil:399,destre:370,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,238,244,246,247,248,249,251,252,254,256,257,261,268,269,270,271,272,273,274,275,276,277,278,279,283,285,291,292,294,295,296,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,382,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,245,303,346,388,408,425,430,492,494,497,508,511,524],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,119,123,126,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,231,232,235,237,242,246,249,250,252,254,255,260,266,268,269,271,277,278,279,291,292,294,296,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,251,276,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[269,276,298,421],deviator:9,devic:[1,3,12,14,16,251,393],device_typ:393,devin:[309,408],devis:445,dfactor:206,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,202,231,303],dhug:[269,307],dhugoniot:[269,307],dia:443,diag:318,diagnost:[2,5],diagon:[3,6,91,129,152,153,154,229,271,304,317,350,463,465],diagonalstyl:467,diagram:[41,84,130,177,198,225,300],diallo:425,diam:[206,207,303,387],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,254,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:268,dictat:[217,269],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:2,dielectr:2,diff:[3,6,12,15,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,235,238,241,245,246,247,248,249,250,251,254,255,257,268,271,272,273,274,275,277,278,279,281,283,286,289,290,291,292,296,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,199,318,377,409,456,481],difficult:[229,300,393,425,506,516],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[0,4],diffuse:[4,6],digit:[2,3,207,360,446,524],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:418,dij:321,dilat:[2,3,61,63,65,82],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,231,252,353,380,443,500,523,524,525],dimdim:524,dimems:299,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:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,270,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:207,dimstr:[41,225],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[0,2,3,4],dipolar:[4,28,40,203,204,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,269,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[2,3,6,7,12,13,15,28,59,74,75,117,130,152,176,177,178,184,202,203,206,210,213,214,215,231,232],directli:[3,6,8,9,11,12,95,124,129,152,154,203,204,205,206,213,237,248,252,257,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directori:[0,1,2,3],disabl:[3,12,15,347,393,430,495,510,524],disadvantag:[6,225],disallow:[203,231,271],disappear:499,discard:[2,3,41,75,221,225,348,356,494,499,500],discontinu:[199,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,206,207,254,257,293],discuss:[0,1,2,3],disk:[6,92,93,100,171,201,232,246,303,495],disloc:[74,446],disord:[39,74,446],disp:[0,2,3],dispar:460,disperion:[412,435],dispers:[3,6,7,9,176,299,377,378,403,412,435,440,448,459,478,485],displac:[2,3,6,7,12,42,61,65],displace_atom:[2,3,7,113],displace_box:61,displacemet:500,displai:[11,13,21,36,44,55,186,198,203,206,362,371,406,476],dispters:3,disregard:446,dissip:[6,9,40,88,89,240,247,254,299,322,344,345,401,413,414,423,440,441,476],dissolut:226,dist:[6,73,99,119,128,203,300,316,415,475,492,525],distanc:[2,3,6,7,8,9,12,19,20,39,43,45,46,47,48,49,51,53,54,55,56,57,58,60,61,63,65,66,69,73,75,76,77,78,79,80,81,86,87,94,97,98,100,103,113,114,115,116,117,119,125,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,202,203,204,206,207,215,219,226,227,228,229,231,232,233,236,238,246,252,257,268,269,270,271,276,285,298,299,303,307,308,315,316,317,321,323,327,331,332,333,334,335,342,343,345,346,347,350,352,353,354,355,356,357,361],distinct:[6,235,314,377,460],distinguish:[6,94,152,260,418,496,524],distort:[176,394],distrbut:394,distribut:[0,2,4,5,6],distro:[122,406,455,456],ditto:[8,12,14,16,17,42,126,227,317,489,495],div:[8,15],divd:128,diverg:[3,12,39,317,345,395,499,518,527],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,231,298,343,350,355,377,386,388,419,459,466,485,506,514,524],divis:[6,197,257,399,429,439,494,515,524],dl_poly:[6,7],dlambda:172,dlammps_async_imd:251,dlammps_bigbig:[12,39,207],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,346,497,498,502],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:507,dlm:[271,289],dlmp_intel_offload:[9,15],dlo:[61,202,231,303],dlopen:6,dlvo:[7,407,488],dm_lb:257,dmax:[335,384],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,84,86,95,98,102,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,232,246,254,255,266,271,272,277,278,279,283,291,292,294,295,296,303,306,317,331,335,338,339,340,349,353,356,358,360,362,371,376,382,386,387,388,393,394,395,398,406,408,409,416,417,419,425,426,428,429,443,444,445,448,452,455,456,457,467,476,477,480,482,484,485,495,497,498,499,500,502,505,506,507,514,515,519,524,525,527,528],docuement:460,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,235,237,238,241,242,243,246,247,250,252,254,255,257,260,267,271,272,273,274,275,277,278,279,291,292,293,294,295,296,304,305,306,310,312,315,317,335,338,340,342,343,347,350,351,352,355,356,357,358,363,364,365,367,368,370,376,377,378,379,380,387,388,389,394,395,396,397,398,399,401,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,426,427,428,429,430,433,434,436,437,438,440,441,443,444,445,446,448,450,451,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,493,494,495,497,498,499,500,501,504,505,507,508,509,510,511,514,515,518,519,524,529],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,331,387,389,393,395,408,417,428,458,459,477,480,481,482,485,497,499],dof:[3,8,123,156,157,158,171,219,317,525],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[387,497],doi:[6,230,298],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,231,232,250,253,257,271,272,300,312,317,322,347,352,353,377,378,388,393,415,448,492,494,497,501,514],domin:[1,418,511],don:[0,8,9,12,13,15,127,181,213,237,255,356,443,466,495,497,519],donadio:339,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,241,242,244,246,251,252,254,255,262,271,277,278,279,291,292,294,296,297,299,300,301,303,306,314,317,319,321,335,338,339,340,342,344,345,358,360,376,377,378,386,388,389,392,393,395,403,416,426,427,428,435,441,442,443,448,450,451,458,475,478,479,484,492,493,494,495,498,501,502,505,515,516,518,519,524,525],donor:425,dot:[153,174,213,237,249,270],doti:[399,456],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,231,244,305,356,360,376,378,392,393,399,419,424,446,458,459,493,497,501,505,510,524,525],dover:216,down:[3,6,7,8,11,39,75,229,246,254,335,351,418,448,466,496,516],downhil:[384,385],download:[5,7,8,9,11,12,13,16,251,427,457],downsid:6,downward:314,dozen:[8,9,12,118,210,458,459],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[2,3,6,7],dpde:264,dpdtheta:[40,88,89,414],dpdtheta_i:[240,241,242],dproduct:396,dr_ewald:[130,319],drag:[2,6,99,210],dragforc:257,drai:[206,269,307],drain:[250,351,386],dramat:[9,61,202,226,227,228,229,231,271,335,338,339,378,448,466,494],drautz:399,draw:206,drawback:306,drawn:[42,203,206,207,247,492],drayleigh:[269,307],dreid:[2,3,4,6,9],drei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,50,51,53,54,55,56,62,63,64,66,70,82,85,88,89,91,95,96,106,107,108,109,110,111,115,118,122,123,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,160,162,164,165,169,170,172,176,177,184,185,187,188,189,190,191,192,193,195,196,198,199,203,204,205,207,208,210,211,212,213,214,215,217,221,224,226,227,228,230,231,232,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,263,264,265,266,267,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,289,290,291,292,293,294,295,296,298,299,300,302,303,307,308,309,310,311,312,313,314,316,317,318,320,321,322,323,324,325,326,327,328,330,331,332,334,335,341,342,343,344,345,347,348,350,352,353,354,355,356,359,361,363,364,366,367,368,370,371,372,378,386,388,392,393,394,395,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,448,449,450,451,452,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,489,495,498,499,500,504,506,516,524,529],enclos:[2,6,12,180,203,207,305,360,443,466,493,495,505,514,524],encod:[13,39,42,203,206,207,306,426],encompass:[3,6,40,42,59,61,127,179,330,349,476,500],encount:[3,8,12,61,117,222,392,502,524],encourag:[7,8,311,318,333],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,181,182,185,202,203,204,206,207,208,211,212,220,222,223,228,231,238,247,252,254,256,270,271,272,285,293,304,316,317,318,323,335,338,339,340,341,343,346,347,350,354,357,358,376,377,387,388,392,393,413,416,422,429,442,446,460,463,465,467,468,486,492,495,497,498,499,500,502,504,505,509,513,515,518,524,529],end_of_step:8,endbondtors:[3,185,191,497],endif:8,energet:[228,395,459],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:466,energy_update_freq:459,enforc:[6,9,59,60,114,202,203,204,205,206,208,210,217,228,231,271,297,299,309,317,321,360,377,431,494,524,525],enforce2d:[2,3,6,201,210],eng:[11,68,73,119,203,244,358,360,408,445],eng_previ:360,engiliti:9,engilitycorp:9,engin:231,engineer:[216,302,323,344,416],enginer:444,enhanc:[212,216,238,492],enlarg:[61,206],enough:[3,40,63,94,178,179,181,182,225,255,303,307,312,317,348,352,353,356,389,393,409,454,497,501,502],enpub:416,ensembl:6,ensight:6,ensur:[3,6,152,203,204,217,221,229,246,247,271,324,346,378,399,415,439,477,485],enter:[59,168,419,446,485,511],enthalpi:[135,273,274,275,318,416,514,515,524],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,130,153,158,177,178,207,210,211,212,219,225,228,230,238,243,246,247,250,254,255,267,271,273,274,275,276,277,278,279,298,300,302,315,317,318,333,347,349,360,393,412,435,448,478,479,497,505,506,514],entireti:484,entiti:[6,8,40,42,203,317],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,130,139,142,143,144,145,146,148,149,150,176,199,204,207,211,222,230,241,242,307,358,387,399,417,443,450,451,452,459,467,477,478,479,480,481,482,485,524],entries:207,entropi:511,entry1:[37,56,207,406,450,451,478,479],entry2:207,entryn:207,enumer:[179,203,490],enumuer:6,env:393,environ:[1,3,6,11,12,15,16,17,206,248,253,298,393,394,399,406,408,417,418,456,480,494,508,524],eos:[9,241,242],epair:[118,207,395,421,425,458,459,515],epen:[458,459],epfl:[248,253],epp:412,epq:412,eps0:488,eps14:439,eps:[455,476],epsilon0:482,epsilon:[3,6,35,45,46,50,53,54,95,184,211,212,246,317,335,352,356,384,386,398,404,405,407,409,410,411,412,420,422,424,425,426,429,430,431,432,433,434,435,436,437,438,439,442,447,453,460,461,471,477,483,484,487,488,506,518,523],epsilon_0:489,epsilon_14:404,epsilon_:460,epsilon_d:410,epsilon_i:[422,448,460],epsilon_i_:460,epsilon_i_a:[422,460],epsilon_i_b:[422,460],epsilon_i_c:[422,460],epsilon_ij:448,epsilon_j:[422,448,460],epsilon_j_:460,epsilon_j_a:[422,460],epsilon_j_b:[422,460],epsilon_j_c:[422,460],epsilon_lj:460,epton:455,eqch:173,eqeq:[458,459],eqp:412,eqq:412,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,131,153,156,172,174,176,178,202,206,207,210,211,212,213,214,217,220,221,222,223,224,225,229,231,232,237,246,247,249,250,252,254,255,257,260,261,268,269,276,287,288,298,300,303,305,307,308,309,312,314,316,317,318,320,323,328,330,338,339,340,343,344,345,347,349,350,352,355,357,358,360,376,380,386,388,389,390,392,393,395,408,413,414,421,422,425,429,440,446,447,456,458,459,460,462,463,464,466,467,468,478,479,484,485,489,493,494,495,497,499,500,504,505,508,511,513,515,524,525],equat:[3,6,7,8,9,99,117,123,130,177,186,198,210,229,235,236,238,240,241,242,248,254,255,257,260,269,270,271,272,276,294,298,300,307,308,312,318,321,322,335,343,347,350,352,353,355,357,377,378,382,407,412,413,414,418,419,420,423,428,440,441,443,448,451,460,463,465,470,471,473,474,479,489,518],equation:[248,298,370],equi:272,equidist:270,equil:[3,308,381,504,529],equilater:507,equilibr:[3,4,5,6,7,9,61,99,178,210,217,220,228,229,246,269,271,272,294,295,304,307,308,309,310,343,344,345,350,408,409,458,459,493,507],equilibria:350,equilibribum:[226,227],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,229,231,246,247,248,255,257,271,276,294,307,308,312,316,321,323,331,335,342,343,345,350,361,363,367,370,408,443,452,466,518],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:216,equival:[6,12,13,28,61,63,128,136,137,145,150,176,180,203,207,218,219,220,222,223,229,231,246,254,271,294,304,316,317,355,395,413,418,466,480,482,483,497,500,505,506,515,518],equlibrium:6,equliibr:[308,310],er3:177,eradiu:[40,124,204,418,497],eras:[320,344],erat:[231,441],erc:409,erfc:[409,431,448],erforc:[124,204],erg:523,erhart:[217,416,480,482],ermscal:396,ernst:9,eror:3,eros:443,erose_form:443,erot:[2,3,6,9,65],errata:[480,482],erratum:352,erron:3,error:[0,1,2],erta:423,ervel:[124,204,497],escap:[232,518],especi:[8,15,166,178,210,217,225,246,307,312,315,316,393,494,516],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,299,351,378,395,409,431,482,502,515],essential:[8,276],essex:28,establish:[95,250],estim:[1,3,6,10,12,37,41,56,74,99,153,216,225,236,269,318,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,257,271,307,308,310,351,417,419,422,456,481,485,523],eta_dot:271,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:271,etap_dot:271,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,231,232,244,246,247,254,271,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,207,235,255,269,307,514,515],eu2:177,eu3:177,euler:[318,386,388],eulerian:216,euqat:469,europhi:257,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,237,247,249,250,252,253,254,255,299,305,308,318,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,294],evanseck:[6,19,184,404,509],evapor:[2,3,9,59,112,210,217],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,231,232,235,238,252,255,269,271,272,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,199,225,257,429,486],event:[2,3,6,8,65],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,253,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,238,243,244,246,248,250,251,252,257,258,267,271,272,276,287,293,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[238,248,257,300,492],evolv:[257,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,247,248,254,255,256,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,231,236,241,247,254,255,256,272,284,285,295,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,228,299,318],examp:[495,524],exampl:[0,1,2,3],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,231,236,243,271,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,225,231,271,335,459,505],excel:418,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,231,239,245,246,249,252,254,256,271,272,273,274,275,276,277,278,279,280,281,284,285,289,291,292,294,295,296,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[221,418],exchang:[2,3,6,8,63,64,210,216,217,238,246,250,254,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,258,267,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[271,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,251,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:247,exemplifi:418,exert:[6,252,255,287,312,354,355,356,378],exhaust:[216,392,524],exhibit:[100,238,250,271,385,418,506],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,232,246,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,203,225,376,392,495,496,505,514,515,516,524],exlanatori:3,exp6:2,exp:2,expand:[2,3,44],expans:[12,152,197,203,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,237,246,248,268,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,207,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,224,232,251,260,270,304,316,317,384,388,413,448,506,511],experienc:[6,12,15,259,260],experiment:[16,246,377,393,511],expert:12,expertis:7,expir:[515,516],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,231,271,287,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,203,204,219,270,298,426,491,494,495,497,506],explanatori:[3,8,128,203,204,218,219,222,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,231,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,231,239,245,247,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,306,307,309,310,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,459,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,318,420,456,477,485,489,511,524],expos:11,exposit:[216,413,415],express:[6,152,164,178,211,212,229,268,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[0,3,6,7],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,233,237,238,244,245,246,248,249,250,252,254,256,269,271,276,285,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,210,515],extent:[1,3,41,42,45,59,75,176,180,203,215,225,252,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[2,3,9,94,95,176,206,210,224,229,237],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,271,305,306,307,317,335,386,387,390,391,393,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,231,271,345,418,481,518],extrema:439,extreme:418,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,266,337,349,515,524],f_ij:456,f_indent:223,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:269,f_r:[255,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,215,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,248,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,231,232,238,246,251,254,256,257,269,271,272,276,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,229,232,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:251,fall:[3,6,207,222,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,232,271,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:254,farrel:[480,482],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,232,246,248,252,268,269,271,273,274,275,276,277,278,279,288,291,292,294,295,296,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,15,16,39,203,204,282,307,318,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,231,239,245,249,253,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,304,308,309,310,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:228,favorit:7,fbmc:342,fcc:[2,3,6,7,66,74,77,99,117,210],fcm:[288,524],fcold:238,fdirect:235,fdotr:427,fdt:[2,9,240,241,242,318,322],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[0,3,5,6],fecr:416,feedback:[7,251],feel:[7,251,252,260,298,356,358,388,448],fehlberg:318,felling:445,felt:356,femtosecond:523,fene:[2,3,6,7,10,15,44],fennel:[409,431],fep:[0,2],ferguson:[6,184,509],fermi:[1,9,10,12,14,164,393,482],fermion:418,fernando:442,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,238,255,271,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,260,506],fewest:3,fextern:244,feynman:300,fff:495,ffield:[408,419,458,459,466],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:238,ficiti:475,fictiti:[6,213,214,237,244,248,300,316,409,431,435,475],field1:[498,502],field2:498,field:[0,2,3,5],fifth:[6,331,420,452],figshar:298,figur:[1,3,8,12,15,307,494,495,519],fij:412,file0:298,file1:[11,13,242,298,346,360,387,502,504,508],file2:[11,13,242,346,360,387,502,504,508],file:[0,1,2,3,4],file_from:205,filen:387,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,241,242,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,203,204,207,499,504,529],filepo:314,fill:[7,9,178,206,303,347,380,389,399,446,459,500,519],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,241,242,243,246,270,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,213,237,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,202,268,500],finish:[6,11,41,225,360,374,376,377,390,392,393,484,502,524,525],finit:[0,3,4],finni:[7,416,476],finverse:235,fiorin:[9,230],fire:[2,3,210],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,74,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,241,242,246,247,252,257,268,269,270,271,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,199,241,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[0,1],fix_deposit:3,fix_flux:216,fix_heat:238,fix_id:[3,229,269,271,273,274,275,276,277,278,279,304,307],fix_manifoldforc:519,fix_modifi:[2,3,6,8,120,121,160,163,210],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[229,271],fixextern:244,fixid:[206,216],fji:412,flag1:[234,391],flag2:[234,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,234,251,254,258,260,267,268,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:234,flagvf:[401,440,441],flat:[6,15,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,206,219,230,248,272,343,350,418,481,515],flip:[3,6,231,271,354,355],floor:524,flop:12,floralwhit:207,flow:[4,5],fluctuat:[6,66,95,229,246,247,254,257,271,276,298,299,304,322,345,347,370,414],fluid:[2,6,7,9,10,40,69,79,86,96,103,116,127,128,158,173,175,229,231,249],fluid_veloc:261,flush:[3,207,514],flux:[2,3,6,65],flv:206,fly:[7,9,12,41,206,210,216,221,232,235,317,321,348,399,446,515,518],fmackai:9,fmag:233,fmass:300,fmax:[386,515],fmomentum:235,fmsec:[2,207,254,255,268,271,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:235,fnve:238,fnvt:235,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,298,467],fold:[15,333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,235,236,240,241,242,244,246,247,248,251,253,254,255,257,260,269,271,276,277,278,279,291,292,294,296,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,203,206,244,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,17],forc:[0,1,2,3,5],force_uvm:16,forceatom:260,forcefield:[316,425],forcegroup:257,forcezero:384,ford:412,forestgreen:207,forev:75,forget:[255,518],forgiv:271,fork:[12,203,519],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,128,152,153,172,173,182,186,203,207,210,211,212,218,219,220,222,223,227,247,248,254,256,260,268,294,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,515,518,524],formal:[6,82,85,99,247,248,254,271,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,241,242,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:242,former:[6,12,39,41,207,225,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,213,237,254,271,294,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,237,249,250,252,254,255,268,298,299,305,314,320,328,333,335,338,339,340,349,352,353,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,244,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,203,228,230,238,246,251,257,263,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,269,347,370,387,388,446,492],fourier:[2,6,12],fourth:[6,15,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:253,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,202,206,207,217,226,227,228,229,269,303,307,314,315,318,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,251,314],fraig:42,frame:[91,152,207,216,269,307,354,422],framer:[206,207],framework:[5,248,394,467],franc:9,frattl:238,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,211,212,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,219,228,235,246,248,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,206],freez:[2,3,6,210,215],frenkel:[6,238,246,345],freq:215,frequenc:[3,6,15,39,113,207,221,285,299,300,307,312,318,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,207,226,227,238,243,343,350,448,483,504,516],fri:[269,307],friction:[4,5,6,9,10,42,210,248,254,307,312,317,347,351,353,423,507],friedrich:324,from:[0,1,2,3,5],front:[269,307,354],frontend:[206,311],frozen:[6,123,182,245,247,255,389,421],fs2:[6,99],fscale:251,fstr:524,fstring:495,fstyle:353,ftol:[386,388,492,511],fuchsia:207,fuction:409,fudg:321,fugac:246,fugacity_coeff:246,fulfil:6,full:[1,2,3,6,9,12,15,16,37,39,40,99,206,220,221,230,238,257,298,318,377,378,393,399,416,418,419,422,459,483,497,499,504,505,509,511,516,518,528],full_energi:[3,246],fuller:386,fulli:[3,6,82,248,253,298,386,388,409,456,457,497,519,526,527],fulton:416,fumi:400,func:[495,524],funcfl:416,functionaliri:230,fund:[0,7],fundament:[335,523],funnel_flow:330,funrol:446,further:[3,4,6,8,12,13,63,65,67,72,75,83,94,101,115,118,127,206,207,210,219,222,223,226,232,236,257,261,300,308,319,322,324,335,347,349,358,378,384,386,387,388,389,394,398,408,446,466,492,511,512,524],furthermor:[26,187,238,318,414,418],furthest:63,futher:3,futur:0,g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:456,g_p:347,ga3:177,gaa:399,gahler:385,gai:[3,422,476],gain:[15,342],gainsboro:207,galindo:447,game:251,gamma0:28,gamma:[3,6,28,254,257,261,299,307,308,310,312,351,413,414,417,422,443,447,470,473,474,477,480,482,485,515],gamma_:[3,347,353],gamma_ijk:480,gamma_n:[353,423],gamma_p:[3,347],gamma_t:[353,423],gammaa:447,gammafactor:257,gammar:447,gan:[456,477,480,482,485],gan_sw:456,gan_tersoff:456,ganzenmuel:[7,9],ganzenmul:9,gao:[6,19,184,404,509],gap:[199,440,441,457,467],gap_2014_5_8_60_17_10_38_466:457,gap_exampl:457,gaseou:7,gass:246,gather:[11,505],gather_atom:11,gather_scatter_loop_unrol:9,gathert_atom:11,gauch:190,gaug:12,gauss:[2,3,118,172,211,212,410],gaussian:[6,40,65,99,113,115,232,247,248,254,300,316,335,339,357,377,413,415,418,421,457,476,492,524,525],gave:[3,448],gavhan:15,gaybern:[2,3,6,7,9,15,156,386],gcc:16,gcmc:[2,3,7,9,210,217],gcores:235,gd3:177,gdot:441,gdrudes:235,ge4:177,gec:[480,482],gen:[271,272],gener:0,genom:7,gentler:[352,355,357],gentli:417,geom:[6,377,415,492,525],geometr:[3,6,7,8,42,59,61,75,86,129,168,169,178,180,203,207,213,224,225,232,237,250,271,277,278,279,291,292,294,296,317,320,328,338,339,340,356,358,377,380,388,398,401,405,407,409,412,418,420,422,424,431,432,433,434,435,436,437,438,439,440,441,442,447,448,451,460,468,479,483,484,487,488,490,497,500,507,515,524],geometri:[3,6,7,9,13,24,38,41,58,75,86,166,178,200,225,226,227,229,232,252,322,373,380,448,497,500],georg:[7,9],georgia:13,gerar:524,gerber:439,germani:9,germann:[276,433,492,511],germano:422,gerolf:13,get:[0,1,3,6,8,9,11],get_natom:[11,495],get_rank:11,get_siz:11,getenv:524,gettimeofdai:12,gewald:[6,377],gezelt:[409,431],gflop:12,gflp:12,gfortran:9,ghost:[3,6,7,12,15,60,63,64,77,176,181,182,229,231,255,271,306,317,319,375,377,389,393,413,414,415,418,423,430,490,502,507,518],ghostwhit:207,giacomo:9,gif:[4,206],gifsicl:206,gigabit:17,giko:2,gikot:2,gillan:467,gingold:[470,471,473],gio:2,git:[7,12,519],github:[8,13,16,230,248,253,457],give:[0,1,2,3,4,5,6,7,8,9,10,11,12,14,15,16,17,54,75,100,117,124,158,161,165,178,203,204,207,213,215,219,220,222,223,229,231,248,271,289,294,298,299,304,312,314,317,349,377,378,386,389,390,393,395,399,415,418,425,426,443,446,448,460,480,481,482,492,494,495,497,507,511,518,525],given:[3,4,5,6,7,9,11,12,15,16,21,26,36,44,55,63,65,66,70,75,117,124,135,136,137,139,140,143,144,145,146,147,148,149,150,151,152,153,172,176,180,186,187,198,199,203,204,205,207,210,217,219,221,226,227,229,231,232,236,238,246,247,248,249,251,257,263,265,268,270,271,276,297,298,299,300,307,308,314,316,318,321,330,331,333,335,337,342,347,348,351,352,353,356,362,371,377,378,393,394,395,399,400,402,403,405,406,407,408,409,410,413,414,415,416,418,419,420,422,423,425,431,432,433,435,443,444,445,446,447,448,449,450,451,452,453,456,460,461,463,465,466,467,476,489,492,495,497,499,500,506,507,511,523,528,529],gjf:254,gjwagn:7,gkio:2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1,495,506,511,524],increasingli:418,increment:[3,11,140,213,214,224,225,232,237,243,271,303,323,324,358,376,392,429,466,492,495,509,511,524],incur:[16,219,243,347,494],inde:161,indefatig:7,indefinit:344,indent:[2,3,4,210,223],independ:[4,6,9,11,12,16,41,61,65,86,99,128,131,164,178,202,210,218,219,220,222,223,225,228,229,230,231,232,247,249,254,255,257,260,271,299,304,308,312,317,319,323,334,345,347,380,423,446,492,495,514,525],indetermin:[203,204,207],index:[0,3,6,8,11,12,37,39,40,56,57,68,71,73,84,102,119,128,129,131,176,199,203,207,218,219,220,222,223,241,242,251,253,300,319,347,358,359,360,383,392,448,450,451,458,459,478,479,486,497,512,515,524],indianr:207,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,199,203,206,211,212,218,219,220,222,223,229,271,299,317,347,358,361,370,377,387,389,408,415,419,426,443,446,448,452,458,459,466,480,482,494,496,497,499,515,519,524],indigo:207,indirectli:[6,306,524],indistinguish:254,indium:467,individu:[0,1],induc:[0,3],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,152,166,206,231,271,299,377,390],inelig:217,inerti:441,inertia:[2,3,6,40,42,65,90,91,92,93],inertiai:129,inertiax:129,inertiaz:129,inexpens:[248,506],inf:[2,3,12,350,500],infer:[3,104,106,107,172,213,214,225,226,227,237,251,302,335,343,350,380,406,419,497,509,515],infil:[3,13,317,494],infin:[3,386,502,515],infininti:206,infinit:[3,232,245,252,254,257,299,335,347,353,354,378,380,418,497,501,523],infinitesim:6,inflect:[410,433,476],influenc:[3,9,41,85,160,268,303,377,378,448,480,481,482],inform:[0,1,2,3,6,7,8,9,11,12,13,14,15,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,243,244,245,246,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,270,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,324,331,332,333,335,336,338,339,340,341,342,343,344,346,349,350,351,352,354,355,356,357,359,375,377,378,381,385,386,387,388,389,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,494,495,497,498,499,501,502,504,509,511,512,514,516,524,526,527,528,529],informat:[8,12,498],infrequ:[6,271,413,492,511,516],infti:[410,440,441],ingtegr:399,inher:[377,386,448],inherit:[6,483],inhomogen:[17,347,448],inidividu:386,init:[3,8,315,466],init_fil:347,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,179,180,199,202,203,204,206,207,208,211,212,215,216,220,225,227,228,229,231,239,241,242,246,247,251,252,253,254,255,257,262,267,268,269,270,271,276,285,287,299,300,301,306,307,312,315,316,317,318,320,322,332,334,335,337,342,344,345,346,347,348,349,352,353,354,355,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,203,252,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:260,innermost:[37,56,75,391,478,479,506],innernod:260,innner:437,inordin:348,inorgan:[6,485],inp:[230,360,467,485],input1:[71,124,125,128,129,131,337],input2:[71,124,125,128,129,131,337],input:[0,1],input_doubl:3,inquir:324,insensit:12,insert:[3,5,7,8,9,12,61,178,210,232,246,252,303,377,467,475,495,501,518],insertion:[3,232,246,303],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,232,233,238,243,246,252,257,260,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[257,433,495,511],insight:[6,13],instabl:[257,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[0,8],instanc:[6,9,11,211,230,248,354,421,426,448,456,495,518],instantan:[6,65,228,229,247,248,271,276,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,216,426,494],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,246,254,257,260,261,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,459,476,483,492,500,504,511,513,518,524],institut:[9,251,302],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:271,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,232,237,239,243,244,246,249,254,267,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,232,234,244,246,247,248,251,254,255,256,257,299,302,303,306,307,312,317,318,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[2,3,5],integral:[300,450,451],integrate_ulsph:325,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:[3,6,8,12,13,35,221,247,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,236,243,250,260,269,271,276,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,210,515],intepol:524,inter:[17,42,63,64,158,181,182,203,228,254,256,270,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,245,246,251,252,254,256,260,285,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,203,270,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[0,3],interfer:[12,271,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,206,270,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],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:[3,206,212,303,524],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:253,interpenetr:443,interpentr:[470,471,473],interpol:[6,14,37,56,110,199,206,207,216,241,242,257,298,377,378,388,399,448,450,451,459,472,478,479,480],interpret:[2,6,11,197,206,222,423,468,492,495,511,524],interrupt:307,intersect:[3,6,130,207,356,358,500],intersert:356,interspers:386,interstiti:[176,446],intertia:[3,103],interv:[3,6,99,205,220,254,271,307,312,313,326,466,472,492,511,524],intestieti:130,intial:[6,393,395],intiial:[41,502],intiti:[3,334],intra:317,intra_energi:246,intramolecular:[28,154,246],introduc:[6,9,100,117,206,238,271,307,312,317,370,377,394,409,418,431,435,439,477,511,524],introduct:0,intuit:380,inv:[130,177,319],invalid:[3,12,75,97,181,285,388,440,441,499],invari:[117,145,150,152],invent:321,invers:[3,6,51,130,177,207],inverse:518,invert:[1,6,182,299],invis:356,invoc:[176,228,393,463,465,495],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,243,244,245,246,247,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,268,270,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,3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aul:[0,7,13,254,256],pauli:[418,466],paus:505,paves:300,payn:[152,457,467],pb2:177,pb4:177,pbc:[75,352,396],pchain:[271,272,276,317],pcie:1,pd2:177,pd4:177,pdamp:[271,272,276,304,317],pdb:[6,13,208],pdebuyl:9,pdf:[0,8,9,13,16,40,109,110,111,122,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,230,253,264,265,324,325,326,327,330,455,469,470,471,472,473,474,507],pdim:350,pdlammps:[82,85,455],pdlammps_eps:[9,122,455],pdlammps_overview:9,pdlammps_ves:[9,455],pe_eta:271,pe_etap:271,pe_omega:271,pe_strain:271,peachei:13,peachpuff:207,peak:421,pearlman:95,peculiar:12,pedersen:378,peform:[39,309],penalti:[458,459],pencil:[6,75,166],pend:3,penetr:[42,132,462,464,507],penetret:40,peng:177,penn:13,peopl:[7,8,9,12],peptid:[4,9,230],per:[0,1,3,5],peratom:[3,121,153,176],perceiv:206,percent:[3,12,15,229,393,477],percentag:[1,12,229,271,303,304,317],percol:227,perfect:[6,41,74,77,100,225,298,388],perfectli:[41,225,498],perfom:[6,388],perform:0,performac:1,pergamon:[443,482,489],perhap:380,peri:[2,3,4,6,7],peridyma:82,peridynam:[3,4,6,7,9,40,65,82,85,122,455,476,497,507],perimitt:410,period:[2,3,6,7,8,9,12,21],perioid:352,perl:[6,13],perm0:523,perman:[3,39,54,75,182,226,227,251,316,358,393,425,501,509],permeabl:297,permiss:[227,495],permit:[6,257,446],permitt:[410,482,488,489],permut:[12,417,477,480,482,485],perpendicular:[6,75,156,206,231,252,262,268,270,298,301,327,352,353,385,497],perram:[378,422],persepct:206,persist:[3,8,75,244,317,393,494,495,499,503,524],person:[9,519],persp:[3,206],perspect:206,pertain:[406,476],perturb:[9,13,74,95,267,315,352,355,357,502],peru:207,peskin:257,pessimist:378,petersen:[335,378],pettifor:[399,476],pettifor_1:399,pettifor_2:399,pettifor_3:399,pfactor:206,pforc:495,phantom:251,pharmaceut:7,phase:[3,12,15,271,342,350,399,431,481,494],phd:457,phenol:518,phenomena:418,phi0:[196,316],phi1:185,phi2:[185,417,477],phi3:[185,417,477],phi:[1,3,4,7,9,10,12,15,16,84,100,117,152,197,198,199,206,249,316,364,393,394,399,416,419,443,444,445,510],phi_ij:[399,419,456],philadelphia:9,phillip:[255,413,518],phillpot:[309,408,409,466],philosoph:416,philosophi:[6,7,253],phonon:[0,2],phophor:467,phosphid:467,phy:[6,7,13,19,20,24,39,43,45,46,66,74,77,95,96,100,117,121,123,152,153,160,166,184,185,195,205,217,221,229,230,235,238,247,248,253,254,255,256,257,269,270,271,272,276,287,289,293,294,295,299,300,304,307,309,312,317,321,322,323,335,338,339,342,343,344,345,347,350,352,361,370,372,377,378,385,388,395,399,400,404,405,407,408,409,410,411,412,413,414,416,417,418,421,422,423,424,425,428,431,433,435,436,439,440,441,442,443,445,447,448,450,451,453,455,456,460,466,467,475,477,478,479,480,481,482,483,485,492,506,509,511,518],physic:[3,6,12,15,16,17,40,42,53,61,132,160,172,197,216,231,238,248,254,256,257,259,260,261,269,299,308,310,346,347,378,380,388,393,395,397,403,407,416,425,426,446,457,458,459,462,470,471,473,474,492,494,506,507,512,523],physica:[440,441],physik:[7,9],pic:9,picki:8,picocoulomb:523,picogram:523,picosecond:[207,231,515,523],picosend:418,pictur:7,piec:[3,11,152,207,271,504,529],pierr:9,pieter:13,pimd:[2,6,7,13,253],pin:15,pink:207,pipe:[6,203,206],pipelin:[3,6,15],pisarev:347,pishevar:413,piston:[2,3,9,210,215],pitera:6,pixel:206,pizza:[6,7,11,13,41,203,206,225],pjintv:13,pka:347,place:[3,6,7,11,12,32,41,50,75,95,172,178,182,191,199,203,206,207,209,210,211,212,227,228,231,238,246,247,248,250,253,254,255,256,258,260,261,271,277,278,279,291,292,296,303,306,315,317,338,339,340,347,352,355,357,376,406,425,476,484,494,495,498,505,507,512,515,524],placehold:[32,191,394,395,408,416,419,427,428,443,444,445,452,456,458,459,467,475,477,480,481,482,485],placement:[380,431],plai:[6,206,342],plain:[9,439,495],plan:[3,5,6,15,16,180,497],planar:[6,40,42,252,298,353,370,372],planck:[246,300],plane:[3,6,9,41,42,59,61,70,75,100,206,210,216,225,249,252,262,298,301,311,331,334,347,353,361,363,364,365,366,367,372,380,382,441,484,500,507],plane_wiggl:382,planeforc:[2,210,262],plasma:[96,272,347,418],plastic:[2,3,9,65,82,85],plastic_strain:133,platform:[1,3,7,9,12,13,14,15,16,203,206,208,499,504,529],plath:[6,99,210,343,350],player:206,pleas:[0,3,7,11,12,13,15,216,248,257,261,299,302,306,313,342,358,417,419,455,463,465,466],plen:396,plimpton:[0,5,7,15,74,123,153,228,298,308,335,423,455],plog:[3,12,506],ploop:[271,272,276],plos:28,plot:[7,11,13,15,57,307,437,439,478,479,486],plu:[3,11,12,39,61,71,106,176,181,207,224,229,231,232,276,317,390,418,429],plug:9,plugin:[9,13,208,498],plum:207,pm3:177,pmb:[2,9],pme:378,pmf:[230,323,331],png:[3,12,203,206],pni:206,poariz:6,poem:[2,3,6,9,12,210],poems:[3,6,7],point1:497,point2:497,point3:497,point:[1,2,3,4,6,7,8,9,11,12,15,17,28,37,40,41,42,56,61,74,75,90,92,93,124,125,130,152,156,157,171,176,177,178,189,199,201,202,203,204,206,207,210,215,219,221,223,225,229,231,232,233,237,241,242,245,246,248,251,252,257,260,268,270,271,273,274,275,277,278,279,281,282,283,286,289,290,291,292,294,296,299,300,306,307],point_data:319,pointer:[3,7,8,9,11,244,495],pois:5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principl:[6,9,11,251,272,308,418,427,446,477,494,519],prinicp:[42,317,387],print:[0,1,2,3,6,7,8,11,12,15,16,17,18,41,99,106,107,128,152,203,204,206,207,208,210,219,220,221,222,223,228,229,232,251,254,257,266,269,271,273,274,275,276,277,278,279,287,288,291,292,293,294,296,298,302,303,304],printabl:2,printf:[207,514],printflag:427,printfluid:257,prior:[176,201,322,379,528],priori:506,prism:[3,6,166,180,500],priveleg:3,privileg:[11,12,251],prob:[226,227],probab:468,probabl:[3,8,12,40,75,168,181,182,197,217,225,226,227,228,232,246,255,271,303,352,358,386,448,450,451,478,492,511,518],probe:524,problem:[0,1,2],problemat:246,proc:[1,3,8,11,12,14,15,124,203,204,376,494],proce:[41,54,182,225,236,388,446,504,512,515],procedur:[6,12,39,41,207,217,225,246,254,255,256,271,273,274,275,276,277,278,279,291,292,294,295,296,299,338,339,340,341,344,345,386,388,395,401,498,518],proceed:[12,446],procesor:[41,494],process:[1,3,4],processor:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,39,40,41,42,60,61,63,64,65,68,71,73,75,84,102,119,124,126,127,129,166,176,178,180,181,182,202,203,204,206,207,210,216,219,225,226,227,228,229,231,244,247,248,254,255,257,271,300,306,309,312,317,321,322,335,347,358,374,375,376,377,381,388,390,391,392,393,413,415,454,466,491,492],processsor:[41,225,494],procp1:[203,204],procsessor:516,procssor:506,produc:[1,3,4,6,7,12,13,14,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,42,43,45,46,47,48,49,51,53,54,56,65,68,71,73,75,84,102,119,121,123,124,125,126,128,129,131,153,155,165,176,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,210,213,218,219,220,222,223,224,225,228,231,239,244,245,247,248,249,254,255,256,266,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,303,307,308,309,310,312,317,318,319,320,321,336,337,347,348,349,352,355,360,361,363,364,366,367,370,372,378,386,388,391,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,456,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,499,500,502,503,506,511,512,515,524,525],product:[6,15,16,17,152,176,231,294,308,318,348,393,396,418,420,451,459,479,494,524],proessor:393,prof:302,profi:167,profil:[2,3,6,65,156,157,158,161],program:[3,4,6,7,9,11,12,13,15,16,154,203,206,207,208,210,230,244,251,257,311,416,495,496,508,524],programm:[13,16],progress:[1,41,225,251,269,307,385,386,388,515,518],prohibit:507,project:[6,7,13,385,476,519],promis:7,promot:399,prompt:[8,11,12,251,508],proni:[3,247,248],pronounc:250,proofread:8,prop:[6,306],propag:[4,9,215,271,307,324,418,426],propens:6,proper:[228,298,443,495,519],properati:306,properli:[213,237,317,322,330,387,388,414,495,525],properti:[0,2,3],propoerti:335,proport:[6,39,41,95,113,114,174,225,254,255,256,307,318,343,350,351,423],proportion:254,propos:[6,152,217,229,246,271,294,312,431,445,481,483],prospect:7,protect:335,protein:[7,10,15,178,315,317,333,497,505],protocol:251,proton:[482,489,523],prototyp:[42,455],prouduc:[223,349],prove:[88,89,240,257,322],proven:294,provid:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,28,40,42,63,70,74,130,151,154,172,176,177,178,205,206,208,211,218,219,223,228,229,230,231,244,246,251,253,257,261,269,271,299,306,307,308,311,312,317,322,323,342,344,345,348,349,360,375,377,378,384,388,393,395,399,401,406,408,409,413,417,418,423,425,428,430,439,440,443,445,446,456,457,458,459,466,467,475,476,477,480,481,482,485,494,499,505,507,510,511,515,516,519,524],proxim:202,psa:355,pscreen:[3,12,506],pscrozi:[0,7,13],psec:[207,231,250,254,255,271,304,317,338,339,517,523],psend:494,pseudo:[418,492,497,502],pseudodynam:342,pseudopotenti:[9,446],psf:6,psi:[419,488],psi_ij:419,pstart:[3,271,272,276,304,317],pstop:[3,271,272,276,304,317],pstyle:[95,118,211,212],psu:[458,459],psuedo:502,psxevar:15,pt2:177,pt4:177,ptarget:229,pthread:[12,15,16],ptr:[6,11,244,495],ptype1:126,ptype2:126,pu3:177,pu4:177,pu6:177,publicli:5,publish:[7,257,261,287,293,308,382,409,443,446,480,482],pull:[323,331,519],puls:347,pump:[440,441],punctuat:[2,492,511],purchas:206,purdu:[9,13],pure:[11,335,426,444,445,480,482,506],purg:[3,498],purpl:[2,207],purport:11,purpos:[3,6,7,9,12,42,63,75,130,140,146,161,162,177,178,180,182,199,203,223,228,229,254,298,300,303,305,316,335,377,403,429,435,446,448,484,490,497,500,504,507,509,510,524,529],push:[3,8,213,224,231,252,270,298,315,323,386,423,468,519],pushd:252,put:[3,6,8,11,12,13,39,61,166,178,203,232,236,354,355,358,380,458,495,497,501],putenv:[508,524],px1:506,px2:506,pxx:[229,271,304,317,377,378,514,515],pxy:[3,6,515],pxz:[3,6,515],py1:506,py2:506,pydir:11,pyi:[229,271,304,317,377,378,515],pymol:[7,11,13],pymol_aspher:0,pympi:11,pypar:11,python:[0,2,3,4,6,7],pythonpath:11,pyz:[3,6,515],pz1:506,pz2:506,pzz:[229,269,271,304,307,317,377,378,515],q_1:466,q_2:466,q_3:466,q_d:518,q_i:[419,439],q_j:439,qbmsst:[2,9],qcore:308,qdamp:308,qdist:[409,431,435,439],qeq1:308,qeq2:308,qeq:[2,3,4,6,7],qeqall:466,qeqallparallel:466,qfile:[308,409],qin:250,qinitmod:4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0,412,413,414,415,418,421,422,424,425,426,429,431,432,433,434,435,436,437,438,439,440,441,442,447,449,453,455,456,458,459,460,461,466,468,475,476,484,487,488,490,494],read_dump:[2,3,203,388,497],read_restart:[2,3,6,8,9,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,39,40,41,43,44,45,46,47,48,49,51,53,54,55,59,60,61,64,178,184,185,186,187,188,189,190,192,193,195,196,198,210,216,217,229,230,231,232,246,257,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,300,306,317,323,334,337,347,353,361,362,363,364,365,366,367,370,371,372,383,388,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,418,421,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,447,449,453,455,460,461,468,475,476,484,487,488,490,494,497,498],read_restart_set:8,readabl:[204,206,387,504,529],reader:[3,13,498],readi:[11,12,179,181,182,251,507,518,527,528,529],readme:[1,4,6,8,9,10,11,12,13,15,176,203,204,208,311,382,427,446,458,459,495],real:[3,6,7,11,26,29,30,61,75,99,100,117,152,167,178,187,202,207,215,231,232,235,251,252,255,268,300,307,312,315,351,352,354,355,357,366,377,378,380,384,390,409,446,448,458,459,482,497,500,506,514,517,523,525],realist:[3,232,501],realiz:[75,210,495],realli:[1,3,8,12,123,134,153,207,252,389,426,509,519],realloc:3,realtim:251,reamin:[352,356],rearrang:[204,388],reason:[3,6,7,11,12,18,39,159,170,178,197,219,254,304,317,344,345,348,358,387,388,393,406,410,418,419,421,441,448,484,486,501,506,525],reax:[0,2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,210,308,310,313,314,426,458,459,476,509],rebal:[41,225],rebalanc:[41,225],rebo:[2,7,9,314],rebuild:[11,12,14,15,246,389,413,515],rebuilt:[3,12,203,204,205,206,208,389,393],recalcul:[75,95,335],receiv:[3,224,251,253,298,494],recent:[2,3,11,12,15,210,219,222,223,225,226,227,250,267],reciproc:[6,12,130,176,177,299,377,400,402,403,409,412,418,431,435,453,461,511],recog:12,recoginz:3,recogn:[3,12,77,180,226,227,271,318,387,416,443,458,495,497,504,505,518],recomend:6,recommed:318,recommend:[7,12,15,206,207,238,307,345,377,418,426,440,441,446,459,460,463,465,466,506,516,519],recompil:[1,3,9,12,208,321],recomput:[112,140,182,236,323,415,509],reconstruct:[3,230,466],record:[208,230,323],recov:[229,238,271],recreat:359,rectangl:[41,225,380],rectangular:[7,41,64,180,225,246,380,497,499,501],rectilinear:[130,177,204],rector:53,recurs:[41,225,399,484],recust:41,recv:494,red:[2,206,207,228,300],redefin:[3,499,505,524],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:[17,18,128,130,177,269,307,377],redund:419,ree:471,reed:[269,307],rees:[7,9,13],ref:[344,345,385],refactor:6,refer:[2,3,6,7,8,9,11,12,14,15,28,65,71,75,85,91,94,95,112,113,114,124,126,128,131,156,157,158,171,178,202,203,204,205,210,216,218,219,220,222,223,228,229,231,232,238,245,269,271,272,276,298,300,302,303,305,306,307,317,321,323,342,349,354,360,361,372,377,378,385,389,394,401,415,422,429,443,445,446,460,473,474,480,482,492,493,495,499,502,505,506,507,510,511,515],referenc:[3,6,12,65,71,75,125,131,203,204,210,220,246,306,349,378,409,425,452,460,495,515,524],reflect:[2,3,6,75,130,152,177,198,206,210,226,227,232,260,269,297,299,317,352,354],refman:9,reformat:7,refresh:216,reg:500,regard:[6,61,268,321,322,327,455,459],regardless:[14,75,178,181,202,222,231,254,271,273,274,275,277,278,279,304,317,328,335,393,494,500,507],regim:[6,343,350,410,506],region:[0,2,3,6,7],region_spher:8,region_styl:356,regist:[8,127,154,330],regoin:6,regress:524,regspher:178,regstrip:358,regul:6,regular:[1,3,41,64,96,176,180,203,206,217,225,246,306,347,378,410,429,494,497,499,501],reigon:524,reinder:15,reinhardt:[344,345],reject:[178,228,458,512],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,207,210,217,225,231,232,235,238,246,252,255,267,268,294,298,303,312,314,315,318,323,331,335,337,342,343,347,354,358,377,378,386,418,422,423,440,441,443,460,488,498,506,511,515,518,525],relat:[1,6,8,9,10,12],relationship:[6,241,308,360,377,466,488,518,524],relax:[2,3,4,6,7,210],releas:[0,5,7,8,13,226],relect:[3,448],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,207,211,212,215,216,217,218,219,220,221,222,223,225,226,227,231,232,236,238,239,243,245,246,247,250,251,257,258,259,261,262,263,264,265,267,268,270,280,281,282,283,284,285,286,287,288,289,290,293,297,301,302,303,305,306,311,313,314,315,319,321,328,333,335,336,337,342,343,346,347,348,349,350,351,352,353,354,355,357,358,377,382,386,396,397,401,407,409,410,412,413,415,418,421,422,423,424,425,430,432,433,434,436,437,438,440,441,448,449,450,451,455,460,468,475,478,479,487,488,489,494,510,525],reli:[3,12,309,418,459,489,497,507],reloc:12,reltol:318,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,231,254,255,262,271,272,277,278,279,291,292,294,296,301,302,326,335,338,339,340,346,347,358,360,368,371,387,399,418,426,439,446,448,476,492,497,498,502,507,509,511,515,516,518,519,524,525],remaina:399,remaind:[9,178,203,232,303,335,348,482,497],remap:[3,6,12,61,63,75,161,178,202,231,252,268,294,377,497,498,499],remedi:[6,518],rememb:[2,519],remot:519,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,243,254,255,260,263,267,269,271,277,278,279,291,292,294,296,302,308,317,318,319,321,335,338,339,340,342,358,377,388,412,441,446,497,500,508,509,519,524,525],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,359,508,519],render:[12,13,203,206,207],rendon:[271,272],reneighbor:[3,8,12,39,59,75,225,246,335,348,358,413,514,515],renssela:302,renumb:75,reorder:[3,12,39,494],rep:512,repeat:[2,6,206,207,228,229,246,318,327,380,399,480,482,484,492,511],repeatedli:2,repel:252,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,232,254,276,305,306,312,314,353,393,395,409,423,433,450,451,478,498,499,504,505,515,524,525,527,529],replic:[2,3,7,380,494,497],replica:[0,2,3,4],replica_fil:12,report:[0,1],repositori:[7,9,12,427,457,458,459,519],reprens:347,repres:[1,3,6,8,9,12,14,40,41,42,61,70,74,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,235,242,247,249,254,257,271,300,302,304,312,317,318,319,323,331,332,347,349,356,378,388,394,399,422,429,439,440,441,443,444,445,453,456,458,459,483,484,492,494,497,507,509,512,518,524,527],represent:[3,6,8,9,59,61,146,180,203,247,248,300,347,399,418,422,446,460,497,500,518],reprocess:502,reproduc:[3,15,271,353,409,416,423],repul:443,repuls:[6,7,35,40,45,46,119,252,308,352,353,356,395,399,407,409,413,418,420,423,425,439,443,447,466,475,482,485,488,489,507],reqir:[308,310],request:[3,6,8,12,41,113,181,199,203,251,257,315,322,335,337,375,377,448,458,459,492,502,507,511,516,519,524,525,527],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,76,81,100,117,127,152,203,206,448,498],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,210,217,220,222,223,238,246,248,250,254,255,267,271,276,294,302,304,312,317,335,338,339],research:[5,7,88,89,240,257,261,322,446,492,511],resembl:[312,519],resepct:6,reserv:[12,251,518],reservoir:[99,238,246,250,254,347],reset:[2,3,6,8,11,12,63,69,75,78,79,86,87,97,98,103,113,114,116,173,182,210,211,212,229,231],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[2,6,99,498,502],resid:13,residu:251,residue1:389,resist:[6,251],resolut:[221,466,478,479],resolv:[229,300,335,441,519],resort:3,resourc:[7,394,416],respa:[3,15,213,214,224,233,236,237,249,251,252,266,271,298,309,316,320,323,331,332,333,334,351,352,356,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,505,506,516,517,524],respecifi:446,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,231,238,239,245,249,252,254,255,257,271,273,274,275,276,277,278,279,280,281,287,289,291,292,294,296,308,309,310,317,319,321,323,331,334,347,352,355,361,363,364,366,367,370,372,375,377,378,383,386,387,392,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,452,453,455,459,460,461,465,466,467,468,477,478,480,481,482,483,485,487,488,489,494,498,507,510,516,518,524,526,527,529],respon:9,respond:[6,7,161,231,418,455],respons:[6,7,269,343,350],resquar:[2,3,6,7,9,422],rest:[6,8,12,38,58,200,306,310,316,373,399,441,443,490,514,515,518],restart1:300,restart2:300,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,62,63,113,178,211,212,266,306,323,331,332,337,359,514,515],restore_bia:8,restore_bias_al:8,restrain:[2,3,28,210,217,246,269],restraint:[9,230,269,316,334,430],restratin:316,restrict:[1,2,3,6,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,199,202,203,204,206,207,210,213,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,235,238,239,241,245,246,247,249,254,255,257,261,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,295,296,299,300,308,309,310,314,315,317,318,320,321,335,343,344,345,347,348,349,352,353,355,357,360,361,363,364,366,367,370,372,377,378,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,443,444,446,448,449,450,451,452,453,455,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,497,499,500,502,506,507,508,509,511,523,524,525],resum:524,retain:[2,226,227,395,399,446,494],retart:[32,50,191,368],retir:[3,458],retreiv:8,retriev:[6,8,244,444,445,524],reus:[3,509],rev:[6,13,66,74,100,117,121,152,153,166,217,248,254,256,269,271,272,276,294,299,309,312,317,323,335,339,342,344,345,350,385,399,407,408,409,412,416,417,418,422,423,428,433,440,441,442,443,445,450,451,456,460,467,477,480,481,482,485,492],revers:[2,6,8,95,189,228,252,271,289,297,298,308,327,343,344,350,388,439,506,518],revert:[207,514],review:[152,308,323,342,446,457,467,492,511,518,519],rewind:376,rewrap:203,rewrit:[5,12],rewritten:18,rezwanur:455,rfac0:[152,467],rfactor:335,rfile:317,rg0:333,rgb:207,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[450,451,478,479],rho0:[443,463,465,473,474],rho0_meam:443,rho:[2,3,40],rho_0:[473,474],rho_alpha_beta:416,rho_bkgd:443,rho_colloid:352,rho_e:347,rho_fin:346,rho_i:[444,445],rho_initi:346,rho_ref_meam:443,rho_wal:352,rhodo:[9,10],rhodopsin:[1,10,15],rhohi:303,rholo:303,rhosum:[2,110,469,470,471],rhot:238,rhs:318,ribier:385,richard:9,richardson:317,richi:[9,18],rick:[308,309,408,466],rick_and_stuart:309,ridg:[9,18],right:[3,6,11,12,41,74,154,178,196,198,202,204,225,228,252,257,268,297,298,318,360,380,409,497,500,507,519,524],rightmost:[41,225],rigid:[2,3,4],rigidid:129,rigidifi:317,rii:[97,98],rij:[100,117,226,227,298,413,414,450,451,475],rin:[425,436,437],ring:[2,3,6,127,184,300,302],rino:[77,485],rinv:377,rirj:[353,423],risi:[152,467],risk:[8,316,506],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rk4:318,rkf45:318,rlo:[450,451,478,479],rmask:[3,524],rmass:[3,306],rmax:[75,179,226],rmdir:508,rmin0:[152,467],rmin:[75,179,227,433],rms:[318,377,378],rmsd:346,rnemd:6,robert:9,robin:207,robust:[384,385,386,459],rock:443,rockett:456,rod:317,rodata:12,rodnei:312,roi:7,role:[6,342],roll:12,ronchetti:117,room:[59,61],root:[11,95,97,98,205,342,346,416,504],rosati:39,rose:443,ross:443,rosski:300,rosybrown:207,rot:[6,99,300,316,342,525],rotat:[2,3,4,6,7,9,40,65,90,91,92,93,104,142,152,156,157,158],rotate:327,rotation:117,rotaton:500,rough:[6,178,206,357],roughli:[7,10,12,41,161,206,221,246,254,255,263,270,271,285,304,317,335,338,339,342,378,388,393,462,464,499,506],round:[1,3,12,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,42,43,45,46,47,48,49,51,53,54,56,75,123,155,165,184,185,187,188,189,190,192,193,195,196,199,207,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,429,431,432,433,434,435,436,437,438,439,440,444,449,450,451,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,499,500,506,523,524],rous:247,rout:[95,425,439],routin:[5,6,8,11,14,15,37,39,56,96,182,257,446,457,478,479,510],roux:[6,235,255,483,518],row:[6,68,69,71,73,79,84,86,98,102,103,114,116,119,125,126,127,129,131,158,166,173,175,176,177,219,220,222,223,260,317,347,349,357,418],royalblu:207,rozero:443,rperp:[268,327],rpi:302,rpm:12,rrespa:[1,3,5,7,8,15,211,212,268,271,389,394,395,396,397,398,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,447,449,450,451,453,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,506],rspace:3,rsq:[450,451,478,479,486],rsurfac:347,ru3:177,ru4:177,rub:19,rubia:[444,445],rudd:[448,478,479],rudra:[7,9],rudranarayan:[7,302],ruiz:217,rule:0,run1:[6,392,524],run2:[6,374,376,392,524],run3:[6,392,524],run4:[6,392,524],run5:[6,392,524],run6:[6,392,524],run7:[6,392,497,498,502,524],run8:[6,392,524],run:[0,1,2,3,4],run_styl:[2,3,7,8,9,12,15,17,271,272,355,386,389,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,491,492,494,505],rung:318,runloop:376,runtim:[12,16,206,393],russia:9,rutherford:347,rutuparna:[480,482],rxn:[318,479],ryan:9,ryckaert:[321,370],rycroft:176,rydberg:446,s00:455,s0st:6,s2050:1,s2629:416,s319:216,s_fact:324,s_i:[6,418],s_ij:6,sack:7,saddl:[270,388],saddlebrown:207,sadigh:[217,416,444,445],saed:319,saed_vtk:130,safe:[12,206,235,255,393,519],safe_zone:3,safest:[3,335],safeti:324,safezon:459,safran:488,sagui:[378,412],sai:[1,3,12,13,207,458,459,495,519],said:386,sakai:481,sall:[9,466],salmon:207,salt:[410,421,443,497],salter:466,same:[1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,37,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,59,61,64,65,68,73,75,76,81,84,87,90,92,93,95,96,97,98,99,100,102,104,107,113,114,115,117,119,121,123,124,126,127,128,152,153,154,155,156,15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5,483],submit:0,subramaniyan:13,subscript:[11,347,361,419,485,524],subsequ:[3,6,11,12,41,61,113,179,207,221,225,229,246,342,347,348,349,380,392,416,476,495,497,498,504,507,508,516,517,524,529],subset:[6,11,12,15,41,85,152,203,204,207,225,267,271,273,274,275,276,277,278,279,303,304,308,317,388,393,395,399,426,448,491,494,497,499,502,506,524],subspac:9,substanti:[6,477,506],substep:271,substitut:[1,2,3,12,203,253,306,388,392,418,448,495,508,524],substract:409,substrat:[180,229,271,273,274,275,277,278,279,304,317,497],substyl:[439,506],subsystem:347,subtl:[104,106,107,248],subtleti:164,subtract:[3,6,54,65,75,86,99,104,107,112,113,115,123,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,203,204,210,219,238,246,247,250,254,255,256,258,262,263,267,294,301,317,358,389,438,497,507,515,524,525],succe:12,succeed:[220,221],succes:221,succesfulli:3,success:[2,6,11,12,14,127,203,207,217,220,229,232,246,285,303,317,335,342,360,386,388,495,496,504,505,512],successfulli:[3,11,203,232,495,508],successulli:11,successv:502,sucessfulli:3,sudden:35,suddenli:356,sudo:[11,12],sufac:42,suffer:[16,17,293,350,356,393],suffici:[2,3,6,7,16,17,41,63,75,205,225,269,271,299,335,342,349,352,360,430,448,497,518],suffix2:12,suffix:[1,2,3,6,9,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,206,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,318,320,321,346,355,361,363,364,366,367,370,372,377,378,388,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,445,449,452,453,455,456,459,460,461,468,477,478,480,481,482,483,485,487,488,489,495,497,498,500,506],suggest:[0,6,7,12,269,307,495,518],suit:[7,13,212,257,418],suitabl:[4,12,13,16,54,95,203,228,306,339,399,406,423,439,443,458,459,492,511],sukumaran:221,sum:[3,6,8,12,40,74,75,80,85,91,96,97,98,100,104,108,113,115,117,119,120,121,123,126,127,128,135,151,152,153,155,158,159,160,161,164,165,166,167,168,170,172,174,175,176,219,220,222,223,232,244,247,254,255,260,298,299,303,307,312,317,319,323,334,345,347,349,352,356,358,377,378,386,398,409,413,418,419,429,431,434,443,458,459,467,484,495,515,518,523,524,525],summar:[6,12,419,466],summari:1,summat:[6,9,42,74,96,117,377,378,403,409,416,417,431,435,446,466,477,480,481,482,485],summer:[3,13,458,459],sumsq:128,sun:[20,43,185,361,405,448,459],sunderland:16,sup:[307,312,408,466],supercomput:[12,17,495],superpos:[426,476],superposit:7,superspher:382,supinski:446,supplement:[248,458,459],supplementari:[230,422,460],suppli:[9,12,199,246,269,347],support:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,40,41,42,63,95,96,112,118,203,204,205,206,207,208,211,212,213,214,219,224,225,228,229,230,233,237,244,248,249,252,254,255,256,257,266,269,271,273,274,275,276,277,278,279,287,291,292,293,294,295,296,298,299,304,307,309,311,316,317,320,323,324,325,326,327,328,330,331,332,333,334,338,339,340,341,345,350,351,352,356,375,376,377,378,382,385,386,387,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,494,498,499,500,504,506,507,508,510,511,512,517,518,523,524,528,529],suppos:[3,8,419,519,524],suppress:[6,12,176],surc:8,sure:[6,8,11,13,199,211,212,229,303,317,321,357,416,478,479,519],surf:[8,146,179],surfac:[2,3,4,6,8,9,40,42,59,74,130,146,152,176,178,181,206,210,232,243,252,257,260,287,293,298,309,316,327,330,331,335,342,347,352,356,357,377,382,388,399,426,440,441,446,464,466,484,488,494,500],surface_exterior:8,surface_interior:8,surface_mov:347,surfact:[410,421],surpris:418,surround:[37,56,74,178,199,207,229,241,242,271,273,274,275,277,278,279,298,304,317,450,451,478,479,518],suspect:3,suspens:[440,441],sustain:[203,204,229,423],suzuki:[271,317],svg:6,svn:[7,11,12],sw_exampl:457,swamp:317,swap:[2,3,6,7,9,210],swegat:346,swiggl:[3,268,352,355,357,500,524],swiler:[152,467],switch7_section_start:421,switchflag:[152,467],swm4:518,swol:53,swope:6,sxx:207,sy0302:9,symbol:[6,12,130,177,314,399,418,467],symmetr:[6,74,95,103,123,143,144,145,148,149,150,153,211,212,229,271,272,343,350,394,406,412,416,480,482,524],symmetri:[3,5,6,7,8,65,66,74,100,117,180,203,204,269,298,361,378,394,497,518],symplect:[271,289],sync:[3,6,516],synchron:[1,248,388,516],synechococcu:7,syntax:[1,2,3,6,7,8,9,11,12,13,14,17],sysdim:299,sysmt:16,sysstem:399,syst:466,system:[0,1,2,3,4,5],system_:300,systemat:[6,9,221,246,254,446],systemx:3,t10:512,t11:512,t12:512,t13:512,t14:512,t15:512,t3e:12,t_chain:3,t_corr:3,t_correl:492,t_dephas:492,t_e:347,t_e_min:347,t_equil:[344,345],t_event:[3,492,511],t_hi:511,t_infil:347,t_init:[307,347],t_iter:3,t_j:28,t_lb:257,t_lo:511,t_order:3,t_oufil:347,t_out:347,t_outfil:347,t_qm:307,t_switch:[344,345],t_target:401,ta06a:467,ta4:446,ta5:177,ta6:446,tab:[2,497],tabbernor:130,tabinn:448,table:[241,242],tabul:[3,7,13,21,36,37,44,55,56,57,68,75,84,102,199,241,242,318,335,377,394,399,400,402,403,404,405,406,409,416,418,420,431,435,442,450,451,453,456,459,461,476,478,479,480,486,499],tabular:456,tabulate_long_rang:459,tad:[2,3,4,6,9,94,492],tadmor:9,tag:[216,242,318,420,451,479,518],tagint:3,tail:[3,95,96,118,121,172,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,515,524],tailor:[75,348],tait:[9,473,474],taitwat:[2,472],take:[1,2,3,6,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,61,81,95,97,99,123,124,127,128,153,155,165,172,176,182,184,185,186,187,188,189,190,192,193,195,196,199,203,206,207,211,212,213,218,219,220,222,223,224,225,229,231,238,239,245,249,253,254,255,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,304,306,309,310,317,318,320,321,331,333,334,335,337,338,339,340,348,355,358,361,362,363,364,366,367,370,372,377,378,383,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,431,432,433,434,435,436,437,438,439,440,444,446,449,452,453,455,458,459,460,461,466,468,475,477,478,480,481,482,483,485,487,488,489,491,495,498,500,505,506,507,512,514,515,516,524],taken:[6,61,160,178,202,228,232,246,247,248,254,255,256,257,303,307,310,318,347,366,416,418,422,450,451,477,485,492,506,507],talk:[6,7],talli:[2,3,6,8,9,41,118,124],tally:8,tan:[207,524],tandem:317,tang:446,tangent:[42,270],tangenti:[6,119,335,353,357,423],tanh:347,tantalum:[4,446,467],taper:[3,310,382,442],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,16,39,41,207,215,225,229,230,232,238,246,247,248,254,255,256,271,272,273,274,275,276,277,278,279,291,292,294,295,296,300,304,307,312,317,323,333,338,339,340,341,346,347,350,351,354,375,378,401,413,492,503,505,525],target_fil:346,task:[1,6,7,10,12,13,14,15,16,17,54,207,251,300,348,393,495,516],taskset:15,tatb:[4,313],tatom:518,tatoms:518,tau:[3,167,221,254,255,257,271,304,317,338,339,344,345,347,517,523],tau_1:247,tau_k:247,tau_n_k:247,tb3:177,tbead:170,tbp:399,tchain:[271,272,276,287,293,294,295,317],tcl:312,tcom:255,tcsh:[11,12,406],tdamp:[254,271,272,276,293,317,338,339],tdephas:492,tdrude:[163,235,255,518],teal:207,tech:[7,13],technic:[6,7,9,257,310,335,459],techniqu:[6,7,9,95,210,229,269,307,317,351,354,378,448,478,479,518],technolgi:9,technolog:[9,15,18,251],tediou:306,tell:[2,6,11,12,36,55,198,210,299,371,389,458,459,476,495,497,499,518],telsa:16,temeperatur:11,temp:[2,3,6,9,13,42,65,95,99,104,106,107,112,121,123,128,153],temp_drud:518,temp_eff:107,tempcom:[156,157,171],temper:[2,3,6,7,9,388,492,505,511],temperar:300,temperatur:[0,2,3,4,5],temperature_definit:216,tempfix:512,templ:[7,9,17],templat:[3,8,13,16,18,40,178,179,181,232,246,303,317,321,387,497],templeton2010:216,templeton2011:216,templeton:[9,216],tempor:247,temporari:[2,3,504],temporarili:[199,316,510,511],tend:[28,271,298,318],tensil:[7,231],tensor:[3,6,8,65,90,91,97,98,99,103,116,123,129,139,142,143,144,145,148,149,150,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,229,257,260,271,272,276,302,304,317,350,377,378,387,418,440,441,446,463,465,515,524],tenth:[139,211,376],term:[0,1,3,5,6,7,8,9,12,19,20,21,26,37,40,45,46,63,95,96,97,99,121,123,153,154,156,157,166,171,172,185,186,187,197,199,207,211,212,218,220,222,223,231,237,238,247,248,249,254,255,256,257,270,271,272,273,274,275,276,277,278,279,291,292,294,296,300,304,307,316,317,333,338,339,340,347,349,351,353,361,362,372,377,386,389,394,395,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,416,417,418,419,420,422,423,424,431,435,438,439,440,441,443,444,445,446,448,449,453,460,466,475,477,480,481,482,485,488,506,507,509,515,518],termin:[130,271,386,388,463,465,496,505,516],termostat:339,terrel:385,terri:7,tersoff:[2,3,5,7,8,9,15,96,121,153,154,226,227,409,417,426,456,476],tersoff_1:[480,481,482],tersoff_2:[480,481,482],tersoff_mod:481,tertiari:190,tessel:[9,176],test:[0,3,4,6,7,9,10],test_descriptor_str:3,testf:199,testu:199,tether:[6,266,315,323,331,332,334,345,421],tetot:[9,466],tex:8,texa:455,texas_holdem:316,text:[2,3,4,6,7,8,12,13,37,41,56,199,203,204,206,207,210,216,219,220,221,222,223,225,230,241,242,251,305,346,347,359,378,380,388,416,419,430,443,450,451,467,478,479,493,497,498,514,519,524,526,527],textur:16,tfac_insert:246,tfactor:[3,207],tfinal:524,tfix:316,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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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 deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","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":[36,39,40,55,59,60,61,63,64,74,75,95,96,100,112,113,115,117,118,119,126,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,231,232,236,243,246,247,252,254,255,256,257,258,260,266,269,271,272,276,294,295,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[221,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,addition:[12,13],addtorqu:214,adiabat:6,adjust_dt:324,adp:394,airebo:395,alloi:416,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:[6,90,156,273,277,281,282,291],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,306,524],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:224,awpmd:[9,396],balanc:[41,225],barostat:6,basal:70,bcc:298,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,274,278,283,292,398],body:9,bond:[8,13,72,73,226,227,228,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,229],brownian:401,buck:[402,403,411,442],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,change_box:61,charmm:[6,19,184,404,439],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,230],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,custom:[8,203,204],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,431],defgrad:139,deform:[161,162,231],delete_atom:181,delete_bond:182,delta:23,deposit:232,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],diagnost:7,diel:410,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:[6,28,86,412],dipole:9,direct:235,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:202,distanc:365,distribut:[7,12],document:0,dpd:[9,88,89,413,414],drag:233,dreid:425,dreiding:6,drude:[6,9,163,234,235,255,518],dsf:[409,431],dsmc:415,dump:[6,8,203,204,205,206,208],dump_modifi:207,dynam:308,eam:[13,416],echo:209,edip:417,eff:[9,13,106,107,162,164,169,256,272,284,295,341,418],efield:237,ehex:238,eim:419,elastic:6,emac:13,energi:[135,414],enforce2d:239,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:243,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],exp6:420,exp:[26,187],expand:[46,434],extend:[8,11],extern:244,fcc:298,fdt:414,featur:[7,8,524],fene:[45,46],fep:[9,13,95,212],field:[6,7],file:6,finit:6,fire:308,fix:[2,6,8,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,2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