diff --git a/doc/html/_sources/fix_viscosity.txt b/doc/html/_sources/fix_viscosity.txt
index a4e93cf9af..1435dcaa3c 100644
--- a/doc/html/_sources/fix_viscosity.txt
+++ b/doc/html/_sources/fix_viscosity.txt
@@ -65,7 +65,7 @@ which writes the profile to the file tmp.profile:
 
 .. parsed-literal::
 
-   compute layers all chunk/atom z lower 0.05 units reduced
+   compute layers all chunk/atom bin/1d z lower 0.05 units reduced
    fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile
 
 Note that by default, Nswap = 1 and vtarget = INF, though this can be
diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html
index e389623055..03773104e4 100644
--- a/doc/html/fix_viscosity.html
+++ b/doc/html/fix_viscosity.html
@@ -180,7 +180,7 @@ within each pair.  This resets their velocities, typically in opposite
 directions.  Over time, this induces a shear velocity profile in the
 system which can be measured using commands such as the following,
 which writes the profile to the file tmp.profile:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
 <span class="n">fix</span> <span class="n">f1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">vx</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
 </pre></div>
 </div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 71b6923830..6d0e744b23 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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,11,12,13,14,56,62,96,176,229,245,249,252,258,268,295,315,323,342,371,434,470,514,517],active:484,actual:[1,3,6,8,12,57,65,134,161,202,203,206,210,211,223,225,226,234,252,253,292,296,301,302,310,320,331,334,335,336,338,344,353,354,373,385,417,419,424,429,435,436,469,487,488,499,500,508,517],actualli:333,adam:[373,374],adapt:[2,3,6,9,96,172,209],adaptiv:[9,229,391],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,41,43,76,96,100,113,126,129,131,176,178,179,202,203,204,205,209,210,211,212,213,215,217,218,219,221,222,226,229,234,236,237,242,246,247,248,250,252,254,255,259,267,268,269,270,271,272,273,274,275,276,277,289,290,292,293,294,296,304,314,315,317,318,328,330,334,336,337,341,342,343,345,347,348,352,354,374,376,381,383,391,396,398,401,405,414,421,426,438,443,444,447,453,455,488,490,491,496,498,500,502,509,511,512],add_molecul:215,add_speci:215,add_to_nodeset:215,added:[491,512],addforc:[2,3,209],adding:[8,212,236,314],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,18,20,22,29,33,37,38,40,41,42,43,45,51,56,57,66,119,120,125,154,178,179,181,182,186,191,197,198,199,200,205,206,207,209,212,220,223,224,228,229,234,236,237,240,244,246,247,248,252,255,269,270,271,272,273,274,275,276,277,289,290,292,293,294,296,304,315,317,318,319,321,344,347,348,352,358,364,367,369,374,376,384,386,389,390,391,395,396,398,400,402,404,405,408,410,411,412,413,414,415,418,419,421,422,423,425,426,434,436,437,438,439,440,441,443,445,446,447,450,452,453,455,460,461,470,471,472,473,474,475,478,482,485,490,491,492,497,498,499,502,504,511,512,513,515,517,520,521,522],addition:[0,4,6,8,11],additionali:203,addres:9,address:[7,8,11,205,251,512],addtorqu:2,adequ:[261,331,344,373,384,499],adher:29,adhikari:255,adiabat:0,adiam:[205,206],adjac:[40,176,178,237,384,443,472,473,504,505],adjiman:442,adjust:[2,3,6,16,17,42,62,130,140,156,157,158,161,162,165,166,171,172,177,182,202,205,218,224,228,230,249,252,256,260,265,266,269,270,274,292,296,299,301,302,305,306,307,308,313,315,323,331,335,339,344,346,347,348,350,351,353,373,374,382,384,389,391,411,435,436,460,475,500,518],adjust_radiu:323,adjust_radius_factor:323,admiss:274,adof:[158,218],adopt:[314,511],adp:[2,3,7],adri:[9,311,452,453],adust:172,advanc:[3,249,395,485,496],advantag:[1,6,8,11,14,18,40,41,42,224,389,413,499,504],advect:[3,6,331],advertis:8,advis:[384,451],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,225,226,227,228,230,231,237,242,248,250,252,258,266,270,271,272,273,275,276,277,283,289,290,292,294,315,316,329,343,353,366,373,380,381,382,384,385,386,389,414,435,436,443,487,488,490,492,493,495,498,500],affin:[16,17,18,230,389,404],affiniti:389,afile:246,aforement:18,afresh:[303,498,517],afshar:409,after:[2,3,5,6,8,11,12,15,21,22,33,40,41,42,45,51,60,61,62,64,66,76,156,157,158,159,160,161,162,165,166,167,168,170,171,178,179,181,182,185,186,191,201,202,203,204,205,206,207,209,210,211,215,216,218,219,224,225,226,227,228,230,234,244,255,256,257,258,259,265,266,267,269,275,276,277,283,289,290,292,294,297,301,305,313,315,318,327,332,334,335,336,338,339,340,341,342,346,348,350,354,357,358,364,372,379,380,382,383,385,387,388,389,390,391,395,402,404,412,413,414,415,421,422,423,434,435,436,438,439,440,441,445,446,450,452,453,460,461,470,471,473,474,475,478,485,487,489,490,491,492,493,495,496,498,500,502,504,507,508,511],afterrun:498,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,230,237,248,301,357,372,384,435,436,485,487,488,490,492,497,504,506,517,520],against:[11,12,13,67,231,384,452,453],aggreg:[6,12,69,72,74,85,103,120,127,248,265,313,315,329,485,518],aggress:[237,248,504],agilio:[9,13],agre:[3,8,198,382,391,423,453],agreement:[5,7],ahd:420,ahead:350,aidan:[0,5,7,9,13,376],aij:13,aim:6,airebo:[2,3,7,225,226,312],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,249],aktulga:[7,9,308,453],al2o3:460,al2o3_001:[130,316],al3:177,ala:[255,460],alain:9,alat:[296,438],albe:[450,473,475],albeit:314,albert:9,alchem:[96,172],alcohol:346,alcu:[390,395],alcu_eam:450,alderton:408,alejandr:[269,270],alessandro:13,algebra:441,algorithm:[0,1,6,7,8,9,42,64,206,215,224,227,230,237,248,255,257,258,283,298,306,315,318,319,338,339,343,346,351,380,381,382,386,389,410,414,436,441,457,459,485,487,504],alia:[9,16],alias:[1,374],aliceblu:206,align:[6,9,12,29,42,76,180,198,224,250,376,490,493,511],alkali:414,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,2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91,401],capac:[9,41,112,164,239,310,343,464,490,500],capit:[233,490],capolungo:[130,177,316],captur:[6,344,391,399,414,418,430,438,511],carbid:405,carbon:[7,205,366,391,404,423,438],card:[12,14,16,22,45,82,96,128,186,210,211,315,358,379,402,420,484,492,497,520,522],care:[3,6,62,76,178,181,201,218,225,226,231,246,251,255,269,301,315,338,394,488,490,493,494,499,500],carefulli:[11,12,55,312,354,421,423,495],carlo:[4,6,7,9,209,216,227,244,315,338,411,470],caro:[216,412],carpent:[7,13],carri:[16,262,304,343,418,453],cart:[3,487],carter:[9,17],cartesian:[3,6,65,390,487],carv:181,cascad:[235,343],cash:7,cast:[246,517],cat:[15,205],catastroph:306,cate:255,categori:0,cation:[415,460],cauchi:[145,150],caus:[1,2,3,6,8,12,16,17,178,180,181,182,202,206,214,228,235,244,269,283,296,301,313,315,318,348,350,351,352,353,356,372,374,382,384,388,420,426,432,435,436,443,484,488,489,490,491,494,495,497,498,517,522],caution:[1,374],cautiou:[225,226],cautious:391,caveat:[391,499],cbecker:[390,412],cc1:[6,14,70,80,87,99,104,115,117,126,158,173,175,218],cc2:14,ccc:[413,471,473,475,478],ccflags:[9,16,17,18,19,202],ccm6:412,ccsi:[413,471,473,475,478],ccu:395,cd2:177,cdeam:412,cdennist:9,cdll:11,cdof:[6,158,218],cdte:395,cdte_bop:395,cdtese:395,cdzn:395,cdznte:395,ce3:177,ce4:177,ceas:381,ceil:517,cell:[3,6,62,97,128,130,176,177,178,202,214,228,229,244,249,267,269,270,274,297,305,308,319,343,373,374,376,411,414,441,508],cella:[6,508],cellalpha:[6,508],cellb:[6,508],cellbeta:[6,508],cellc:[6,508],cellgamma:[6,508],center:[3,6,25,43,66,70,76,79,80,87,95,98,99,109,114,115,116,126,128,130,158,159,160,163,166,170,173,175,178,205,206,209,210,211,213,218,221,228,230,231,232,234,244,245,250,252,253,258,265,269,275,276,277,289,290,292,294,301,306,312,313,315,316,320,328,329,331,333,334,335,336,338,339,341,348,352,357,376,378,383,394,413,414,417,418,424,435,436,438,439,440,452,453,471,473,474,475,477,478,493,500,511,517],centimet:516,centr:237,central:[3,64,75,81,82,101,118,128,134,152,176,258,296,318,329,361,383,441,446,452,453,478,490],centro:[2,3,5,6,7,8,66,67,71],centroid:[3,298,477,500],cerda:373,ceriotti2:246,ceriotti:[13,246,251],certain:[1,2,3,6,8,12,17,40,76,125,129,131,182,202,203,205,217,218,219,221,222,227,242,243,315,317,332,345,356,364,372,385,421,443,453,476,492,496,511,517],certainli:250,cerutti:374,cfg:[3,6,7,9,13,202,204,205,206,207],cfile:453,cfl:[140,321],cfor:320,cg_type:455,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:318,ch2lmp:[0,6],ch3:318,ch5md:204,chain3:385,chain:[0,3,4,6,9,10],challeng:[6,320],chalopin:310,champaign:[249,373,374,435],chan:441,chandler:[390,412],chandrasekhar:[6,426],chang:[1,2,3,6,8,9,11,12,14,15,16,17,40,41,42,47,56,60,62,65,76,86,96,114,128,138,140,160,161,162,178,179,180,182,198,201,202,203,204,205,206,207,209,210,211,212,213,215,216,223,224,225,226,227,228,229,230,231,235,236,241,243,244,246,248,249,250,252,254,255,256,258,265,266,267,269,270,271,272,273,274,275,276,277,283,285,289,290,292,293,294,296,297,301,302,304,305,306,309,312,313,314,315,317,318,320,331,334,335,336,337,339,340,341,342,343,344,346,349,352,354,374,380,382,384,387,389,409,414,418,421,435,436,438,441,443,452,453,460,469,470,485,486,487,488,490,491,492,493,494,495,496,498,499,500,501,502,505,508],change_box:[2,3,6,60],changeabl:202,channel:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[0,2,3,5],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[0,2,3],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:2,circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:0,cite:[3,7,8,12,252,460],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[2,3],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:349,clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[2,3,6,7,12,64,66,76],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:7,cmoput:145,cn1:219,cn2:219,cna:[2,3,7,66,75],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[0,2,3,4],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[2,3,4,6,7],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,416,420,452,453,491,505,507,517],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,15,43,66,76],comamnd:230,comand:227,comannd:389,comb3:[2,3],comb:[2,3,4,7,9,209,306],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[0,2,3],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[2,3,6,40],comm_modift:64,comm_styl:[2,3,42,64],comm_world:11,command:[0,1],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[0,1],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:0,comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:[3,6],compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[0,1],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,66],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[0,3,4],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[3,5],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[0,2,3,4,5,8,9,12,13,41,43,66],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[2,3,6,7,11,62,66,76,77,81],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[0,1,3,4],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[2,3,6,100,101,152,174,209,218],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,334,336,338,347,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[2,6,7,22],cosineshift:27,cosmo:[246,251],cossq:2,cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[2,3,6,9,36,46,47,77,96,119,128,172,184,210,211,344,374,382],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterpart:[202,315,485],counterproduct:18,coupl:[0,3,4],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,17,38,40,42,43,57,61,62,65,66,76,88,100,114,115,120,121,124,127,130,146,155,161,162,174,176,178,179,180,181,198,202,203,204,205,206,209,214,215,218,221,222,224,225],create_atom:[2,3,6,7,8,41,42,62,100],create_bond:[2,3],create_box:[2,3,6,22,41,42,45,60,61,62,65,76,100,176,178,179],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:0,creation:[3,5],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[2,3,209],cst:412,cstherm:6,cstyle:487,csvr:[2,3,6,209],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[2,3,38,57,118,198,240,255,296,331,374,376,412],cuda:[1,2,3,4,7],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[0,2,3,6],cut0:488,cut1:499,cut2:499,cut:[1,2,3,6,9,12,14,15,16,17,18,19,42],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[2,7,358],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[2,3,9,66],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],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:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,389,422,443,479,488,489,497,500,507,517],deby:[2,3,7,210,211,310],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[2,3,6,7,8,41,43,60,62,64,66,86,123,134,138,139,153],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[2,3,7,178],delete_bond:[2,3,44,46,47,48,49,50,51,52,54,55,56,57,69,74,127,179],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[2,22],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,347,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[2,3,4,113,180,209,216],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481,511],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[2,3,6,8,9,11,12,13,18],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:389,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[2,5],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:2,dielectr:2,diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:[0,4],diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[0,2,3,7],dihedral_coeff:[2,3,184,185],dihedral_cosine_shift_exp:27,dihedral_styl:0,dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[2,3,62,64,66,83],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[1,2,3,6,7,12,42,60,61,62,64,66,76,100,126,153,158,165,166,167,178,180],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[0,2,3,4],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[2,3,6,7,12,13,29,60,76,118,130,152,176,177,178,201,202,205,209,212,213,214,230,231],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[0,1,2,3],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[0,1,2,3],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[0,2,3],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[2,3,6,7,12,43,62,66],displace_atom:[2,3,7,114],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[2,3,6,7,8,9,12,20,21,40,44,46,47,48,49,50,52,54,55,56,57,58,59,61,62,64,66,67,70,74,76,77,78,79,80,81,82,87,88,95,98,99,101,104,114,115,116,117,118,120,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,201,202,203,205,206,214,218,225,226,227,228,230,231,232,235,237,244,250,255,266,267,268,269,274,283,296,297,301,305,306,313,314,315,318,320,324,328,329,330,331,338,339,341,342,343,346,348,349,350,351,352,353,357],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[0,1,2,4,5,6],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,231,244,252,253,264,269,270,275,276,277,281,289,290,292,293,294,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,517,518],enforce2d:[2,3,6,200,209],eng:[11,69,74,120,202,242,354,356,404,440],eng_previ:356,engiliti:9,engilitycorp:9,engin:230,engineer:[215,300,320,340,412],enginer:439,enhanc:[211,215,237,485],enlarg:[62,205],enough:[3,41,64,95,178,179,181,182,224,253,301,305,310,315,344,348,349,352,385,389,405,448,490,494,495],enpub:412,ensembl:6,ensight:6,ensur:[3,6,152,202,203,216,220,228,244,245,269,321,342,374,395,411,434,471,478],enter:[60,168,415,441,478,504],enthalpi:[135,271,272,273,412,507,508,517],entir:[0,2,3,6,11,14,15,42,43,66,89,90,97,121,122,124,128,130,153,158,177,178,206,209,210,211,218,224,227,229,237,241,244,245,248,252,253,265,269,271,272,273,274,275,276,277,296,298,300,313,315,329,343,345,356,389,408,430,443,472,490,498,499],entireti:477,entiti:[6,8,41,43,202,315],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,305,354,383,395,413,438,445,446,453,461,471,472,473,474,475,478,517],entries:206,entropi:504,entry1:[38,57,206,402,445,472],entry2:206,entryn:206,enumer:[179,202,483],enumuer:6,env:389,environ:[1,3,6,11,12,16,17,18,205,246,251,296,389,390,395,402,404,413,414,450,473,487,501,517],eos:[9,240],epair:[119,206,416,420,452,453,508],epen:[452,453],epfl:[246,251],epp:408,epq:408,eps0:481,eps14:434,eps:[449,470],epsilon0:475,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,244,315,331,348,352,380,382,394,400,401,403,405,406,407,408,417,419,420,421,424,425,426,427,428,429,430,431,432,433,434,437,442,447,454,455,465,471,476,477,480,481,499,511,516],epsilon_0:482,epsilon_14:400,epsilon_:454,epsilon_d:406,epsilon_i:[417,443,454],epsilon_i_:454,epsilon_i_a:[417,454],epsilon_i_b:[417,454],epsilon_i_c:[417,454],epsilon_ij:443,epsilon_j:[417,443,454],epsilon_j_:454,epsilon_j_a:[417,454],epsilon_j_b:[417,454],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[2,3,6,9,66],errata:[473,475],erratum:348,erron:3,error:[0,1,2],erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,389,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[2,3,9,60,113,209,216],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[2,3,6,8,66],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:0,exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,334,336,337,343,347,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,389,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,389,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:2,expand:[2,3,45],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,334,336,337,343,347,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[0,3,6,7],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[2,3,9,95,96,176,205,209,223,228,236],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,334,336,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[2,3,6,7,67,75,78,100,118,209],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[2,9,239,240,319],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[0,3,5,6],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[2,3,6,7,10,45],fennel:[405,426],fep:[0,2],ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[0,2,3,5],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[0,1,2,3,4],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[0,3,4],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[2,3,209],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[0,1],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[2,3,6,8,160,163,209],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[4,5],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[2,6,7,9,10,41,70,80,87,97,104,117,128,129,158,173,175,228,230,247],fluid_veloc:259,flush:[3,206,507],flux:[2,3,6,66],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[0,1,2,3,5],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[12,202],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,224,226,240,297,300,304,306,308,311,315,316,327,342,343,354,355,358,379,383,384,390,391,395,402,412,415,425,438,440,445,451,452,453,455,461,472,478,479,487,488,490,491,492,495,506,507,508,517,519,520],former:[6,12,16,40,42,206,224,343,347,395,397,496,502,517],formerli:[7,13],formul:[1,6,9,41,67,153,212,236,252,269,292,306,308,314,318,342,373,391,395,412,414,417,438,449],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,247,248,250,252,253,266,296,297,303,312,317,325,329,331,334,335,336,345,348,351,353,354,356,357,358,360,367,376,383,391,392,394,395,400,401,402,403,408,409,412,413,417,418,419,420,422,425,426,428,429,430,432,433,435,436,438,442,443,444,454,455,462,470,471,472,473,474,475,478,480,481,486,490,493,500,507,508,516,517,518],forth:[1,6,11,12,13,14,15,388,488,493,497],fortran:[3,6,9,11,12,13,242,412,421,438,452,453],fortun:8,forward:[3,8,96,372,384,389],foster:[395,449,450],foul:181,found:[3,6,9,12,78,172,202,227,229,237,244,249,255,261,297,338,344,356,372,385,402,405,408,485,491,492,507],four:[6,11,55,88,114,115,152,174,267,343,366,383,384,441,485],fourier:[2,6,12],fourth:[6,116,314,328,338,400,446,460],fox:[6,130,184,468,502],fphi:[38,57,472],fpic:12,fplo:[38,57,472],fprime:472,fqdn:251,fqq:408,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,225,226,227,228,267,301,305,312,313,331,336,337,376,384,389,395,397,418,435,436,495,500],fragment:[43,249,312],fraig:43,frame:[92,152,206,215,267,305,350,417],framer:[205,206],framework:[5,246,390,461],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,296,331,340,341,342,343,381,384,392,414,434,441,450,481,487],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,244,246,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,315,318,334,335,336,341,382,408,508,511,518],freeli:[0,6,7,12,156,157,171,176,205],freez:[2,3,6,209,214],frenkel:[6,237,244,341],freq:214,frequenc:[3,6,16,40,114,206,220,283,297,298,305,310,371,409,414,453,460,485,499,504,517,521],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,225,226,237,241,339,346,443,476,497],fri:[267,305],friction:[4,5,6,9,10,43,209,246,252,305,310,315,343,347,349,418,500],friedrich:321,from:[0,1,2,3,5],front:[267,305,350],frontend:[205,309],frozen:[6,124,182,243,245,253,385,416],fs2:[6,100],fscale:249,fstr:517,fstring:488,ftol:[382,384,485,504],fuchsia:206,fuction:405,fudg:318,fugac:244,fugacity_coeff:244,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,100,205,219,220,229,237,255,296,373,374,389,395,412,414,415,417,476,490,492,497,498,502,504,509,511,521],full_energi:[3,244],fuller:382,fulli:[3,6,83,246,251,296,382,384,405,450,451,490,512,519,520],fulton:412,fumi:396,func:[488,517],funcfl:412,functionaliri:229,fund:[0,7],fundament:[331,516],funnel_flow:327,funrol:441,further:[3,4,6,8,12,13,64,66,68,73,76,84,95,102,116,119,128,205,206,209,218,221,222,225,231,235,255,259,298,306,316,319,321,331,343,345,354,374,380,382,383,384,385,390,394,404,441,460,485,504,505,517],furthermor:[27,187,237,410,414],furthest:64,futher:3,futur:0,g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:450,g_p:343,ga3:177,gaa:395,gahler:381,gai:[3,417,470],gain:338,gainsboro:206,galindo:442,game:249,gamma0:29,gamma:[3,6,29,252,255,259,297,305,306,308,310,347,409,410,413,417,438,442,464,467,468,471,473,475,478,508],gamma_:[3,343,349],gamma_ijk:473,gamma_n:[349,418],gamma_p:[3,343],gamma_t:[349,418],gammaa:442,gammafactor:255,gammar:442,gan:[450,471,473,475,478],gan_sw:450,gan_tersoff:450,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,184,400,502],gap:[198,435,436,451,461],gap_2014_5_8_60_17_10_38_466:451,gap_exampl:451,gaseou:7,gass:244,gather:[11,498],gather_atom:11,gather_scatter_loop_unrol:9,gathert_atom:11,gauch:190,gaug:12,gauss:[2,3,119,172,210,211,406],gaussian:[6,41,66,100,114,116,245,246,252,298,314,331,335,353,373,409,411,414,416,451,470,485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25,328,330,331,338,339,340,341,346,347,348,351,352,353,382,384,386,484,498],impose:247,imposs:[1,3,304,490],improp:[0,2,3,7],improper:[3,8,358,364,366,367,383,490],improper_coeff:[2,3,357],improper_styl:0,impropercoeff:[3,369],impropertyp:226,imprortant:108,improtant:[210,211],improv:[0,1,9,16,40,42,206,224,237,248,269,297,389,420,426,441,443,453,471,474],imrop:365,in3:177,inaccur:[1,3,6,181,267,373],inaccuraci:352,inact:420,inappropri:178,incid:[130,177,231],includ:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,40,41,42,44,45,46,47,48,49,50,52,54,55,56,57,58,62,64,66,69,70,72,74,75,77,79,80,82,85,87,88,92,96,97,98,99,100,101,103,104,105,108,109,114,115,116,117,118,119,120,121,122,123,124,126,127,128,130,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,172,173,175,176,177,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,207,209,210,211,212,213,215,216,218,219,220,221,222,223,227,228,230,231,232,234,236,238,242,243,244,245,247,248,249,250,252,253,255,256,258,259,264,265,269,270,271,272,273,274,275,276,277,278,279,287,289,290,292,293,294,296,297,298,300,301,304,305,307,310,311,312,314,315,316,317,318,320,325,328,330,331,332,334,335,336,338,341,342,343,344,345,347,348,349,351,352,353,354,356,357,358,359,360,362,363,366,367,368],include:[12,370],includelink:9,includig:[356,372],inclus:[0,3],inclusion:12,incom:249,incompat:[3,11,261,285,291,422],incomplet:[3,11,490],incompress:[270,414],inconsist:[3,182,227,491],inconveni:376,incorpor:[305,395,406,512],incorrect:[3,161,252,438],incorrectli:[3,376,418,517],increas:[1,3,6,18,38,57,60,62,121,130,153,198,202,203,205,206,220,225,226,227,230,237,240,244,252,302,313,314,315,339,342,346,373,374,384,389,391,414,417,445,453,472,474,488,499,504,517],increasingli:414,increment:[3,11,140,212,213,223,224,231,236,241,269,301,320,321,354,372,388,424,460,485,488,502,504,517],incur:[14,17,218,241,343,487],inde:161,indefatig:7,indefinit:340,indent:[2,3,4,209,222],independ:[4,6,9,11,12,16,17,42,62,66,87,100,129,131,164,178,201,209,217,218,219,221,222,224,227,228,229,230,231,245,247,252,253,255,258,269,297,302,306,310,315,316,320,330,341,343,376,418,441,485,488,507,518],indetermin:[202,203,206],index:[0,3,6,8,11,12,38,40,41,57,58,72,74,129,131,176,198,202,206,217,219,240,249,251,298,316,343,354,355,356,379,388,443,445,452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[0,1],induc:[0,3],industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[2,3,6,41,43,66,91,92,93,94],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[0,1],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,389,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:[0,8],instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,121,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,334,336,347,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,231,236,238,241,242,244,247,252,265,303,304,313,315,331,343,348,352,353,354,356,372,383,385,389,403,417,421,448,454,472,483,487,488,490,491,495,498,499,507,508,517,518],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,331,333,335,338,342,343,362,373,376,397,409,410,411,424,438,452,453,457,459,461,485,487,488,489,490,498,499,500,504,507,517,518],integer:[3,490],integr:[2,3,5],integral:[298,445],integrate_ulsph:322,intel:[1,2,3,7],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,245,451,490],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,241,248,258,267,269,274,312,315,316,331,339,343,345,346,507,508,516],intensiv:[66,209,508],intepol:517,inter:[14,18,43,64,65,158,181,182,202,227,252,254,268,307,315,373,384,395,500,511,517,520,522],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,322,323,331,332,338,343,347,348,349,352,353,358,359,360,361,363,365,367,373,374,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,453,454,455,457,459,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,485,488,490,492,494,495,499,500,502,507,508,511,520],interatom:[3,4,7,9,10,178,202,268,340,341,390,395,412,414,422,438,441,460,474,517],intercept:130,interchang:6,interconnect:18,interconvert:414,intereract:40,interesect:352,interest:[1,5,7,8,9,11,13,76,177,298,338,341,374,413,436,452,453,488,517],interf:[389,512],interfac:[0,3],interfer:[12,269,391],interg:[6,511],intergr:[499,503],interi:436,interior:[3,6,42,352,493],interlac:438,interleav:[6,178,498],intermedi:[6,12,62,205,268,296,366,384,488,489,498,502],intermix:485,intermolecular:[154,391],intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,40,41,43,66,89,90,96,110,112],internal:[3,205,211,301,517],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:251,interpenetr:438,interpentr:[464,465,467],interpol:[6,15,38,57,111,198,205,206,215,240,255,296,373,374,384,395,443,445,453,466,472,473],interpret:[2,6,11,205,221,418,462,485,488,504,517],interrupt:305,intersect:[3,6,130,206,352,354,493],intersert:352,interspers:382,interstiti:[176,441],intertia:[3,104],interv:[3,6,100,204,219,252,269,305,310,311,323,460,466,485,504,517],intestieti:130,intial:[6,389,391],intiial:[42,495],intiti:[3,330],intra:315,intra_energi:244,intramolecular:[29,154,244],introduc:[6,9,101,118,205,237,269,305,310,315,366,373,390,405,414,426,430,434,471,504,517],introduct:0,intuit:376,inv:[130,177,316],invalid:[3,12,76,98,181,283,384,435,436,492],invari:[118,145,150,152],invent:318,invers:[3,6,52,130,177,206],inverse:511,invert:[1,6,182,297],invis:352,invoc:[176,227,389,457,459,488],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,121,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,241,242,243,244,245,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,318,320,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,357,359,360,362,363,366,368,372,373,374,375,376,382,384,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,422,426,427,428,429,430,431,432,433,434,435,436,439,443,444,446,447,449,454,455,457,459,461,462,471,472,473,474,475,476,478,479,480,481,482,484,487,488,489,491,493,495,498,499,501,502,504,507,508,511,517,518],invokd:3,invoke:[3,12,17],involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,225,244,255,300,303,308,331,373,381,382,384,394,411,417,424,471,473,475,486,487,493,495,499,504,505],ioff:[383,490],ion:[6,7,9,160,295,328,343,374,395,406,415,416,438,441,460,470,475,482,490,511],ionic:[6,9,396,398,406,414,415,447,460,511],ioniz:[404,414],ionocoval:9,iparam:[3,226],ipi:[2,13],ipp:0,ir3:177,ir4:177,irregular:[6,42,61,224,228,230,269,315],irrelev:446,irrespect:[435,436],irrevers:234,is_act:[3,517],is_avail:[3,517],is_defin:[3,517],isbn:481,isele:[373,374],isenthalp:[9,269,270,271,272,273],ismail:[373,374,399,430],isn:[3,8,11,12,237,248],iso:[3,228,234,253,269,270,271,272,273,274,275,276,277,302,310,315,511],isobar:[9,269,270,275,276,277,319,410],isodem:414,isoenerget:[9,319,410],isoenthalp:[319,410],isol:[3,181,354],isomorph:298,isotherm:[9,244,269,270,275,276,277,302,319,410],isotop:304,isotrop:[6,101,252,302,373,374,397,417,435,436],isovolum:316,isralewitz:320,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,62,76,78,88,114,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,205,212,223,227,228,230,231,236,237,238,243,244,247,252,267,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,298,302,304,307,315,317,318,330,334,335,336,341,347,351,353,356,357,359,360,362,363,366,368,374,383,384,387,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,469,471,472,473,474,475,476,478,480,481,482,490,492,493,499,502,507,508,517,518],issue:215,ital:[452,453],itali:13,item:[6,7,8,42,202,206,224],iter:[3,6,12,40,42,66,204,212,213,223,224,228,234,236,242,250,285,291,297,306,307,315,318,338,354,356,372,380,381,382,384,388,460,485,495,499,504,508,517],iterat:[12,382],ith:[76,129,131,217,218,219,220,221,222,333,345,508,517],itself:[2,3,6,7,8,9,11,12,13,18,43,62,100,119,169,202,204,205,206,207,219,220,229,234,253,264,268,309,315,343,354,356,383,384,405,415,417,421,422,445,472,488,494,497,498,502,517,522],itset:500,ityp:[3,58,127,128,178,214,226,308,479],itype1:128,itype2:128,itypen:128,ivector:8,ivori:206,ixcm:315,ixi:[43,315,383],ixx:[43,104,315,383,517],ixy:[104,383,517],ixz:[43,104,315,383,517],iycm:315,iyi:[43,104,315,383,517],iyz:[43,104,315,383,517],izcm:315,izrailev:320,izumi:474,izz:[43,104,315,383,517],j0jt:100,j20:219,j_m:152,jackson:442,jacobi:3,jacobsen:381,jacs:[6,184,502],jagreat:13,jame:[9,19],janssen:296,januari:438,jaramillo:[7,9,13,414],jarzynski:320,jatempl:9,jcc:9,jcp:348,jec:13,jeff:13,jello:269,jensen:[252,373],jeremi:[9,440],jerom:9,jewett:13,jiang:[253,511],jiao:[9,13],jiht:[7,9],jik:395,jim:7,jku:[7,9],jmake:12,jmm:152,joannopoulo:267,job:[12,63,318,498],jochim:[269,270],john:[7,9,13,204],johnson:[9,13],join:[6,493],joint:[3,300,420],jon:[9,75],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,4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ta:177,rad:354,radhi:493,radial:[66,76,107,108,125,128,152,162,164,169,218,254,270,282,293,328,337,382,414,420,443,445,490,493],radian:[20,21,24,28,32,35,36,38,177,185,196,198,314,357,359,363,366,490,493,500],radians:198,radiat:[130,177,343],radic:[180,490],radii:[76,81,152,227,231,403,412,417,418,435,436,441,456,458,481,493],radit:414,radiu:[2,3,6,41,43,66,76,81,93,94,98,99,125,130],radlo:493,rafferti:346,rahman:[6,7,228,267,269,270,305,449],rai:[9,17,177],ram:475,ramirez:220,ramp:[2,3,6,9,66,161,162,166],ran:[3,6,11],random:[3,6,40,178,181,201,205,214,216,225,226,227,229,231,241,244,245,246,252,253,254,255,265,269,298,301,305,310,313,315,319,331,335,338,343,347,350,397,409,410,411,485,500,505,511,517,518],random_se:485,randomli:[178,181,216,231,244,252,301,331,353,504,505],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,40,57,64,76,77,82,97,118,120,121,122,124,128,129,133,152,153,164,172,177,179,182,183,190,198,202,203,205,206,215,216,226,230,231,244,246,301,316,331,332,338,339,344,346,373,374,382,385,386,389,391,393,395,396,397,398,399,400,401,403,405,406,407,408,409,411,412,414,417,419,420,421,423,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,447,450,453,454,455,460,469,470,472,475,476,480,481,482,484,488,499,500,508,521],rank:[6,11,12,249,344,371,487],rankin:274,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,76,227,252,267,269,315,334,335,347,405,409],rapp:[306,307,308],rappe_and_goddard:307,rare:6,rasmol:[6,7],rasmussen:417,raster3d:[6,7],rate:[2,6,12,136],rather:[1,2,6,9,12,41,42,65,124,161,205,224,230,245,246,315,335,343,347,349,350,351,354,414,445,452,472,491,495,500,502,507,517],ratio:[6,62,96,112,152,216,224,230,252,254,331,339,346,347,373,387,417,418,454,464,477,487,490,500,504],rational:[344,502],rattl:[2,3,9,209,237,261],rattle:[3,9,209,237,246,285,291,318],rattle_debug:318,ravelo:[274,428],rayleigh:[267,305],rb1:177,rbb:460,rbg:206,rcb:[3,42,224],rcm:[98,99],rcmx:[98,99],rcmy:[98,99],rcold:237,rcut:64,rcutfac:[152,461],rd1:384,rdc:17,rdf:[2,3,66],rdn:384,rdt:384,rdx:4,reach:[6,12,42,131,220,224,226,228,253,274,324,331,338,356,372,388,406,511,517],reacquaint:512,react:6,reactant:414,reaction:[320,329,342,353,384,414],reactiv:[9,312,391],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,62,127,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,201,202,203,205,206,207,208,209,215,216,227,228,230,231,240,244,246,249,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,297,298,300,301,303,304,308,315,318,320,324,327,330,333,341,342,343,349,355,357,358,359,360,361,362,363,365,366,367,368,369,370,372,379,383,384,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,485,487,490,491,492,494,495,496,497,498,500,501,502,504,517,518,519,520,522],read_data:[2,3,6,7,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,59,60,61,62,65,70,76,79,80,87,88,91,98,99,104,114,115,117,127,173,176,178,179,180,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,202,205,226,227,230,266,298,304,314,342,357,358,359,360,361,362,363,365,366,367,368,369,379,383,384,387,388,389,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,414,416,417,419,420,421,424,426,427,428,429,430,431,432,433,434,435,436,437,442,444,447,449,450,452,453,454,455,460,462,469,470,477,480,481,483,487],read_dump:[2,3,202,384,490],read_restart:[2,3,6,8,9,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,40,41,42,44,45,46,47,48,49,50,52,54,55,56,60,61,62,65,178,184,185,186,187,188,189,190,192,193,195,196,197,209,215,216,228,229,230,231,244,255,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,298,304,315,320,330,333,343,349,357,358,359,360,361,362,363,366,367,368,379,384,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,414,416,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,442,444,447,449,454,455,462,469,470,477,480,481,483,487,490,491],read_restart_set:8,readabl:[203,205,383,497,522],reader:[3,13,491],readi:[11,12,179,181,182,249,500,511,520,521,522],readme:[1,4,6,8,9,10,11,12,13,176,202,203,207,309,422,441,452,453,488],real:[3,6,7,11,27,30,31,62,76,100,101,118,152,167,178,187,201,206,214,230,231,234,249,250,253,266,298,305,310,313,347,348,350,351,353,362,373,374,376,380,386,405,441,443,452,453,475,490,493,499,507,510,516,518],realist:[3,231,494],realiz:[76,209,488],realli:[1,3,8,12,124,134,153,206,250,385,421,502,512],realloc:3,realtim:249,reamin:[348,352],rearrang:[203,384],reason:[3,6,7,11,12,19,40,159,170,178,218,252,302,315,340,341,344,354,383,384,389,402,406,414,415,416,436,443,477,479,494,499,518],reax:[0,2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,209,306,308,311,312,421,452,453,470,502],rebal:[42,224],rebalanc:[42,224],rebo:[2,7,9,312],rebuild:[11,12,14,15,16,244,385,409,508],rebuilt:[3,12,202,203,204,205,207,385,389],recalcul:[76,96,331],receiv:[3,223,249,251,296,487],recent:[2,3,11,12,209,218,221,222,224,225,226,248,265],reciproc:[6,12,130,176,177,297,373,396,398,399,405,408,414,426,430,447,455,504],recog:12,recoginz:3,recogn:[3,12,16,78,180,225,226,269,383,412,438,452,488,490,497,498,511],recomend:6,recommend:[7,12,14,16,205,206,237,305,341,373,414,421,435,436,441,453,454,457,459,460,499,509,512],recompil:[1,3,9,12,207,318],recomput:[113,140,182,235,320,411,502],reconstruct:[3,229,460],record:[207,229,320],recov:[228,237,269],recreat:355,rectangl:[42,224,376],rectangular:[7,42,65,180,224,244,376,490,492,494],rectilinear:[130,177,203],rector:54,recurs:[42,224,395,477],recust:42,recv:487,red:[2,205,206,227,298],redefin:[3,492,498,517],redirect:12,redo:12,reduc:[1,2,3,6,12,17,18,19,27,42,66,76,97,121,122,124,125,126,127],reduct:[18,19,129,130,177,267,305,373],redund:415,ree:465,reed:[267,305],rees:[7,9,13],ref:[340,341,381],refactor:6,refer:[2,3,6,7,8,9,11,12,15,29,66,72,76,86,92,95,96,113,114,115,125,127,129,131,156,157,158,171,178,201,202,203,204,209,215,217,218,219,221,222,227,228,230,231,237,243,267,269,270,274,296,298,300,301,303,304,305,318,320,338,345,350,356,357,368,373,374,381,385,390,397,411,417,424,438,440,441,454,467,468,473,475,485,486,488,492,495,498,499,500,503,504,508],referenc:[3,6,12,66,72,76,126,131,202,203,209,219,244,304,345,374,405,420,446,454,488,508,517],reflect:[2,3,6,76,130,152,177,197,205,209,225,226,231,258,267,295,297,315,348,350],refman:9,reformat:7,refresh:215,reg:493,regard:[6,62,266,318,319,324,449,453],regardless:[15,76,178,181,201,221,230,252,269,271,272,273,275,276,277,302,315,325,331,389,487,493,500],regim:[6,339,346,406,499],region:[0,2,3,6,7],region_spher:8,region_styl:352,regist:[8,128,154,327],regoin:6,regress:517,regspher:178,regstrip:354,regul:6,regular:[1,3,42,65,97,176,180,202,205,216,224,244,304,343,374,406,424,487,490,492,494],reigon:517,reinhardt:[340,341],reject:[178,227,452,505],rel:[1,6,14,27,36,42,62,76,101,114,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,244,250,253,265,266,292,296,301,310,312,313,320,328,331,333,338,339,343,350,354,373,374,382,414,417,418,435,436,438,454,481,491,499,504,508,511,518],relat:[1,6,8,9,10,12],relationship:[6,240,306,356,373,460,481,511,517],relax:[2,3,4,6,7,209],releas:[0,5,7,8,13,225],relect:[3,443],reles:43,relev:[2,6,12,42,83,86,123,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,238,241,243,244,245,248,249,255,256,257,259,260,261,262,263,265,266,268,278,279,280,281,282,283,284,285,286,287,288,291,295,299,300,301,303,304,307,309,311,312,313,316,317,318,320,325,329,331,332,333,338,339,342,343,344,345,346,347,348,349,350,351,353,354,373,378,382,392,393,397,403,405,406,408,409,411,414,416,417,418,419,420,425,427,428,429,431,432,433,435,436,443,444,445,449,454,462,469,472,480,481,482,487,503,518],reli:[3,12,307,414,453,482,490,500],reloc:12,remain:[7,12,33,37,42,51,56,62,76,96,115,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,252,253,260,269,270,275,276,277,289,290,292,294,299,300,323,331,334,335,336,342,343,354,356,364,367,383,395,414,421,434,441,443,470,485,490,491,495,500,502,504,508,511,512,517,518],remaina:395,remaind:[9,178,202,231,301,331,344,475,490],remap:[3,6,12,62,64,76,161,178,201,230,250,266,292,373,490,491,492],remedi:[6,511],rememb:[2,512],remot:512,remov:[2,3,6,8,13,55,76,77,82,101,118,126,128,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,241,252,253,258,261,265,267,269,275,276,277,289,290,292,294,300,306,315,316,318,331,334,335,336,338,354,373,384,408,436,441,490,493,501,502,512,517,518],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,355,501,512],render:[12,13,202,205,206],rendon:[269,270],reneighbor:[3,8,12,40,60,76,224,244,331,344,354,409,507,508],renssela:300,renumb:76,reorder:[3,12,40,487],rep:505,repeat:[2,6,205,206,227,228,244,324,376,395,473,475,477,485,504],repeatedli:2,repel:250,repes:202,replac:[2,3,6,11,12,42,66,98,99,129,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,252,274,303,304,310,312,391,405,428,445,472,491,492,497,498,508,517,518,520,522],replic:[2,3,7,376,487,490],replica:[0,2,3,4],replica_fil:12,report:[0,1],repositori:[7,9,12,422,451,452,453],reprens:343,repres:[1,3,6,8,9,12,15,41,42,43,62,71,76,99,125,128,190,198,202,203,205,218,219,220,221,222,228,234,245,247,252,255,269,298,300,302,310,315,316,320,328,343,345,352,374,384,390,395,417,424,434,435,436,438,439,440,447,450,452,453,476,477,485,487,490,500,502,505,511,517,520],represent:[3,6,8,9,60,62,146,180,202,245,246,298,343,395,414,417,441,454,490,493,511],reprocess:495,reproduc:[3,269,349,405,412,418],repul:438,repuls:[6,7,36,41,46,47,120,250,306,348,349,352,391,395,403,405,409,414,418,420,434,438,442,460,469,475,478,481,482,500],reqir:[306,308],request:[3,6,8,12,42,114,181,198,202,249,255,313,319,331,333,371,373,443,452,453,485,495,500,504,512,517,518,520],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,77,82,101,118,128,152,202,205,443,491],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,209,216,219,221,222,237,244,246,248,252,253,265,269,274,292,300,302,310,315,331,334,335],research:[5,7,89,90,239,255,259,319,441,485,504],resembl:[310,512],resepct:6,reserv:[12,249,511],reservoir:[100,237,244,248,252,343],reset:[2,3,6,8,11,12,64,70,76,79,80,87,88,98,99,104,114,115,117,173,182,209,210,211,228,230],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[2,6,100,491,495],resid:13,residu:249,residue1:385,resist:[6,249],resolut:[220,460,472],resolv:[228,298,331,436,512],resort:3,resourc:[7,390,412],respa:[3,16,235,249,269,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,498,499,510,517],respecifi:441,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,62,75,76,96,98,107,108,121,124,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,247,250,252,253,255,269,271,272,273,274,275,276,277,278,279,285,287,289,290,292,294,306,307,315,316,320,328,330,343,348,351,357,359,360,362,363,366,368,371,373,374,379,382,383,388,389,390,391,393,395,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,454,455,459,460,461,462,471,472,473,474,475,476,478,480,481,482,487,491,500,503,511,517,519,520,522],respon:9,respond:[6,7,161,230,414,449],respons:[6,7,267,339,346],resquar:[2,3,6,7,9,417],rest:[6,8,12,39,59,199,304,308,314,369,395,436,438,483,507,508,511],restart1:298,restart2:298,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,63,64,114,178,210,211,304,320,328,333,355,507,508],restore_bia:8,restore_bias_al:8,restrain:[2,3,29,209,216,244,267],restraint:[9,229,267,314,330,425],restratin:314,restrict:[1,2,3,6,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,66,67,70,71,76,80,87,96,99,100,104,114,115,117,121,122,124,126,127,128,129,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,198,201,202,203,205,206,209,212,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,234,237,238,240,243,244,245,247,252,253,255,259,267,269,271,272,273,274,275,276,277,278,279,287,289,290,292,293,294,297,298,306,307,312,313,315,317,318,331,334,336,339,340,341,343,344,345,347,348,349,351,353,356,357,359,360,362,363,366,368,373,374,384,387,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,438,439,441,443,444,445,446,447,449,453,454,455,462,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,494,495,499,500,501,502,504,516,517,518],resum:517,retain:[2,225,226,391,395,441,487],retart:[33,51,191,364],retir:[3,452],retreiv:8,retriev:[6,8,242,439,440,517],reus:[3,502],rev:[6,13,67,75,101,118,122,152,153,166,216,246,252,254,267,269,270,274,292,297,307,310,315,320,331,335,338,340,341,346,381,395,403,404,405,408,412,413,414,417,418,423,428,435,436,437,438,440,445,450,454,461,471,473,474,475,478,485],revers:[2,6,8,96,189,227,250,269,295,296,306,324,339,340,346,384,434,499,511],review:[152,306,320,338,441,451,461,485,504,511,512],rewind:372,rewrap:202,rewrit:[5,12],rewritten:19,rezwanur:449,rfac0:[152,461],rfactor:331,rfile:315,rg0:329,rgb:206,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[445,472],rho0:[438,457,459,467,468],rho0_meam:438,rho:[2,3,41],rho_0:[467,468],rho_alpha_beta:412,rho_bkgd:438,rho_colloid:348,rho_e:343,rho_fin:342,rho_i:[439,440],rho_initi:342,rho_ref_meam:438,rho_wal:348,rhodo:[9,10],rhodopsin:[1,10],rhohi:301,rholo:301,rhosum:[2,111,463,464,465],rhot:237,ribier:381,richard:9,richardson:315,richi:[9,19],rick:[306,307,404,460],rick_and_stuart:307,ridg:[9,19],right:[3,6,11,12,42,154,178,196,197,201,203,224,227,250,255,266,295,356,376,405,490,493,500,512,517],rightmost:[42,224],rigid:[2,3,4],rigidifi:315,rii:[98,99],rij:[101,118,225,226,296,409,410,445,469],rin:[420,431,432],ring:[2,3,6,128,298,300],rino:[78,478],rinv:373,rirj:[349,418],risi:[152,461],risk:[8,314,499],rix:[98,99],rjk:[225,226],rjone:[7,9,13],rlo:[445,472],rmask:[3,517],rmass:[3,304],rmax:[76,179,225],rmdir:501,rmin0:[152,461],rmin:[76,179,226,428],rms:[373,374],rmsd:342,rnemd:6,robert:9,robin:206,robust:[380,381,382],rock:438,rockett:450,rod:315,rodata:12,rodnei:310,roi:7,role:[6,338],roll:12,ronchetti:118,room:[60,62],root:[11,96,98,99,204,338,342,389,412,497],rosati:40,rose:438,ross:438,rosski:298,rosybrown:206,rot:[6,100,298,314,338,518],rotat:[2,3,4,6,7,9,41,66,91,92,93,94,105,142,152,156,157,158],rotate:324,rotation:118,rotaton:493,rough:[6,178,205,353],roughli:[7,10,12,42,161,205,220,244,252,253,261,268,269,283,302,315,331,334,335,338,374,384,389,456,458,492,499],round:[1,3,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,206,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,334,336,347,351,357,359,360,362,363,366,368,374,387,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,424,426,427,428,429,430,431,432,433,434,435,439,444,445,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,492,493,499,516,517],rous:245,rout:[96,420,434],routin:[5,6,8,11,15,16,38,40,57,97,182,184,255,441,451,472,503],roux:[6,234,253,476,511],row:[6,69,70,72,74,80,85,87,99,103,104,115,117,120,126,127,128,131,158,166,173,175,176,177,218,219,221,222,258,315,343,345,353,414],royalblu:206,rozero:438,rperp:[266,324],rpi:300,rpm:12,rrespa:[1,3,5,7,8,16,210,211,266,269,385,390,391,392,393,394,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,442,444,445,447,449,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,499],rspace:3,rsq:[445,472,479],rsurfac:343,ru3:177,ru4:177,rub:20,rubia:[439,440],rudd:[443,472],rudra:[7,9],rudranarayan:[7,300],ruiz:216,rule:0,run1:[6,388,517],run2:[6,370,372,388,517],run3:[6,388,517],run4:[6,388,517],run5:[6,388,517],run6:[6,388,517],run7:[6,388,490,491,495,517],run8:[6,388,517],run:[0,1,2,3,4],run_styl:[2,3,7,8,9,12,16,18,269,270,351,382,385,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,484,485,487,498],runloop:372,runtim:[12,17,205,389],russia:9,rutherford:343,rutuparna:[473,475],ryan:9,ryckaert:[318,366],rycroft:176,rydberg:441,s00:449,s0st:6,s2050:1,s2629:412,s319:215,s_fact:321,s_i:[6,414],s_ij:6,sack:7,saddl:[268,384],saddlebrown:206,sadigh:[216,412,439,440],saed:316,saed_vtk:130,safe:[12,205,234,253,389,512],safe_zone:3,safest:[3,331],safeti:321,safezon:453,safran:481,sagui:[374,408],sai:[1,3,12,13,206,452,453,488,512],said:382,sakai:474,sall:[9,460],salmon:206,salt:[406,416,438,490],salter:460,same:[1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,44,45,46,47,48,49,50,51,52,54,55,57,60,62,65,66,69,74,76,77,82,85,88,91,93,94,96,97,98,99,100,101,103,105,108,114,115,116,118,120,121,122,124,125,127,128,129,152,153,154,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,174,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,198,200,201,202,203,204,205,206,209,210,211,212,215,216,218,221,222,223,224,225,226,227,228,230,231,235,236,237,238,243,244,245,246,247,248,249,250,251,252,253,254,255,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,293,294,296,297,298,300,301,302,304,305,306,307,308,310,311,312,313,314,315,317,318,320,325,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,345,346,347,349,350,351,352,354,355,356,357,358,359,360,362,363,366,368,373,374,376,377,378,379,383,384,385,386,387,388,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,438,439,442,443,444,446,447,449,450,454,455,460,462,469,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,492,493,495,498,499,500,501,502,503,504,508,511,512,516,517,518,521],sampl:[1,2,4,6,9,11,12,14,100,114,156,157,171,176,201,205,209,218,219,229,231,242,244,246,248,269,270,291,298,301,310,312,316,328,329,331,335,338,341,353,385,395,411,490,504],sample_frequ:215,san:449,sandia:[0,5,7,9,13,14,17,75,123,415,438,449],sandybrown:206,saniti:[314,385],satellit:[6,160],satifsi:517,satisfi:[3,12,78,130,152,177,228,237,255,261,274,285,291,318,351,382,385,418,504],satur:406,save:[6,8,12,19,41,62,198,203,205,220,227,245,246,252,253,254,301,310,343,355,374,385,387,395,492,495,502],sb3:177,sb5:177,sc3:177,scalabl:[0,1,7,9],scalar:3,scalars:316,scale:[0,1,3,5,6,9,10,13,18,41,62,66,76,77,100,113,125,128,129,152,164,172,198,201,202,203,205,206,209,210,211,215,216,219,228,230,244,248,249,250,252,254,255,267,269,271,272,273,274,275,276,277,298,302,305,306,315,322,323,331,333,335,338,340,341,343,347,354,373,374,3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478],summer:[3,13,452,453],sumsq:129,sun:[21,44,185,357,401,443,453],sunderland:17,sup:[305,310,404,460,511],supercomput:[12,18,488],superpos:[421,470],superposit:7,superspher:378,supinski:441,supplement:[246,452,453],supplementari:[229,417,454],suppli:[9,12,198,244,267,343],support:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,41,42,43,64,96,97,113,119,202,203,204,205,206,207,210,211,212,213,218,224,227,228,229,236,242,246,247,250,252,253,254,255,264,267,269,271,272,273,274,275,276,277,285,289,290,291,292,293,294,296,297,302,305,307,309,314,315,317,321,322,323,324,325,327,328,330,334,335,336,337,341,346,348,352,371,372,373,374,378,381,382,383,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,487,491,492,493,497,499,500,501,503,504,505,510,511,516,517,521,522],suppos:[3,8,415,512,517],suppress:[6,12,176],surc:8,sure:[6,8,11,13,14,198,210,211,228,301,315,318,353,412,472,512],surf:[8,146,179],surfac:[2,3,4,6,8,9,41,43,60,75,130,146,152,176,178,181,205,209,231,241,250,255,258,285,291,296,307,314,324,327,328,331,338,343,348,352,353,384,395,421,435,436,441,458,460,477,481,487,493],surface_exterior:8,surface_interior:8,surface_mov:343,surfact:[406,416],surpris:414,surround:[38,57,75,178,198,206,228,240,269,271,272,273,275,276,277,296,302,315,445,472,511],suspect:3,suspens:[435,436],sustain:[202,203,228,418],suzuki:[269,315],svg:6,svn:[7,11,12],sw_exampl:451,swamp:315,swap:[2,3,6,7,9,209],swegat:342,swiggl:[3,266,348,351,353,493,517],swiler:[152,461],switch7_section_start:416,switchflag:[152,461],swm4:511,swol:54,swope:6,sxx:206,sy0302:9,symbol:[6,12,130,177,312,395,414,461],symmetr:[6,75,96,104,124,143,144,145,148,149,150,153,210,211,228,269,270,339,346,390,402,408,412,473,475,517],symmetri:[3,5,6,7,8,66,67,75,101,118,180,202,203,267,296,357,374,390,490,511],sync:[3,6,509],synchron:[1,246,384,509],synechococcu:7,syntax:[1,2,3,6,7,8,9,11,12,13,14,15,18],sysdim:297,sysmt:17,sysstem:395,syst:460,system:[0,1,2,3,4,5],system_:298,systemat:[6,9,220,244,252,441],systemx:3,t10:505,t11:505,t12:505,t13:505,t14:505,t15:505,t3e:12,t_chain:3,t_corr:3,t_correl:485,t_dephas:485,t_e:343,t_e_min:343,t_equil:[340,341],t_event:[3,485,504],t_hi:504,t_infil:343,t_init:[305,343],t_iter:3,t_j:29,t_lb:255,t_lo:504,t_order:3,t_oufil:343,t_out:343,t_outfil:343,t_qm:305,t_switch:[340,341],t_target:397,ta06a:461,ta4:441,ta5:177,ta6:441,tab:[2,490],tabbernor:130,tabinn:443,table:240,tabul:[3,7,13,22,37,38,45,56,57,58,69,76,85,103,198,240,331,373,390,395,396,398,399,400,401,402,405,412,414,426,430,437,445,447,450,453,455,470,472,473,479,492],tabular:450,tabulate_long_rang:453,tad:[2,3,4,6,9,95,485],tadmor:9,tag:[215,511],tagint:3,tail:[3,96,97,119,122,172,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,508,517],tailor:[76,344],tait:[9,467,468],taitwat:[2,466],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,50,52,54,55,57,62,82,96,98,100,121,124,125,128,129,153,155,165,172,176,182,184,185,186,187,188,189,190,192,193,195,196,198,202,205,206,210,211,212,223,224,228,230,237,238,243,247,251,252,253,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,304,307,315,317,318,328,329,330,331,333,334,335,336,344,347,351,354,357,358,359,360,362,363,366,368,373,374,379,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,426,427,428,429,430,431,432,433,434,435,439,441,444,446,447,449,452,453,454,455,460,462,469,471,472,473,474,475,476,478,480,481,482,484,488,491,493,498,499,500,505,507,508,509,517],taken:[6,62,160,178,201,227,231,244,245,246,252,253,254,255,301,305,308,343,362,412,414,417,445,471,478,485,499,500],talk:[6,7],talli:[2,3,6,8,9,42,119,125],tally:8,tan:[206,517],tandem:[16,315],tang:441,tangent:[43,268],tangenti:[6,120,331,349,353,418],tanh:343,tantalum:[4,441,461],taper:[3,308,378,437],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,17,40,42,206,214,224,228,229,231,237,244,245,246,252,253,254,269,270,271,272,273,274,275,276,277,289,290,292,293,294,298,302,305,310,315,320,329,334,335,336,337,342,343,346,347,350,371,374,397,409,485,496,498,518],target_fil:342,task:[1,6,7,10,12,13,14,15,16,17,18,55,206,249,298,344,389,488,509],taskset:16,tatb:[4,311],tatom:511,tatoms:511,tau:[3,167,220,252,253,255,269,302,315,334,335,340,341,343,510,516],tau_1:245,tau_k:245,tau_n_k:245,tb3:177,tbead:170,tbp:395,tchain:[269,270,274,285,291,292,293,315],tcl:310,tcom:253,tcsh:[11,12,402],tdamp:[252,269,270,274,291,315,334,335],tdephas:485,tdrude:[163,234,253,511],teal:206,tech:[7,9,13],technic:[6,7,9,255,308,331,453],techniqu:[6,7,9,96,209,228,267,305,315,347,350,374,443,472,511],technolgi:9,technolog:[9,14,19,249],tediou:304,tell:[2,6,11,12,37,56,197,209,297,367,385,452,453,470,488,490,492,511],telsa:17,temeperatur:11,temp:[2,3,6,9,13,43,66,96,100,105,107,108,113,122,124,129,153],temp_drud:511,temp_eff:108,tempcom:[156,157,171],temper:[2,3,6,7,9,384,485,498,504],temperar:298,temperatur:[0,2,3,4,5],temperature_definit:215,tempfix:505,templ:[7,9,18],templat:[3,8,13,17,19,41,178,179,181,231,244,301,315,318,383,490],templeton2010:215,templeton2011:215,templeton:[9,215],tempor:245,temporari:[2,3,497],temporarili:[198,314,503,504],ten:14,tend:[29,269,296],tensil:[7,230],tensor:[3,6,8,66,91,92,98,99,100,104,117,124,139,142,143,144,145,148,149,150,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,228,255,258,269,270,274,300,302,315,346,373,374,383,414,435,436,441,457,459,508,517],tenth:[139,210,372],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,64,96,97,98,100,122,124,153,154,156,157,166,171,172,185,186,187,198,206,210,211,217,219,221,222,230,236,237,245,246,247,252,253,254,255,268,269,270,271,272,273,274,275,276,277,289,290,292,294,298,302,305,314,315,329,334,335,336,343,345,347,349,357,358,368,373,382,385,390,391,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,412,413,414,415,417,418,419,426,430,433,434,435,436,438,439,440,441,443,444,447,454,460,469,471,473,474,475,478,481,499,500,502,508,511],termin:[130,269,382,384,457,459,489,498],termostat:335,terrel:381,terri:7,tersoff:[2,3,5,7,8,9,97,122,153,154,225,226,405,413,421,450,470],tersoff_1:[473,474,475],tersoff_2:[473,474,475],tersoff_mod:474,tertiari:190,tessel:[9,176],test:[0,3,4,6,7,9,10],test_descriptor_str:3,testf:198,testu:198,tether:[6,313,320,328,330,341,416],tetot:[9,460],tex:8,texa:449,texas_holdem:314,text:[2,3,4,6,7,8,12,13,38,42,57,198,202,203,205,206,209,215,218,219,220,221,222,224,229,240,249,303,342,343,355,374,376,384,412,415,425,438,445,461,472,486,490,491,507,512,517,519,520],textur:17,tfac_insert:244,tfactor:[3,206],tfinal:517,tfix:314,tflag:205,tfmc:[2,3,7,209],th4:177,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,60,61,62,64,66,72,76,81,95,97,101,116,118,120,124,127,128,131,153,176,179,180,181,187,198,201,202,204,206,209,214,216,218,221,222,224,225,226,227,228,230,231,232,235,240,241,244,245,246,247,250,251,252,255,267,296,297,301,302,303,305,306,308,310,313,314,315,316,319,320,321,327,328,329,331,335,336,338,339,343,346,347,348,349,350,351,352,353,354,356,373,374,380,381,382,383,384,385,386,389,391,394,395,396,398,399,400,412,414,417,418,424,435,436,438,443,445,452,453,454,460,462,469,470,471,472,475,477,479,481,482,485,486,487,488,490,491,492,493,494,495,498,499,502,504,505,507,517,518,520],thank:[249,473,475],thb:453,thb_cutoff:453,thb_cutoff_sq:[452,453],thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,60,62,64,66,67,70,72,75,76,79,80,87,88,91,93,96,97,98,99,100,104,114,115,117,119,120,121,124,126,127,128,129,131,152,155,156,158,160,161,164,165,171,173,175,176,178,180,181,182,184,185,187,188,189,190,192,193,195,196,197,198,202,203,205,206,209,210,211,212,214,217,218,219,221,222,223,224,225,226,227,228,230,231,236,238,243,244,245,247,248,249,252,253,255,258,266,269,271,272,273,274,275,276,277,278,279,280,281,287,289,290,292,294,300,301,302,303,304,306,307,314,315,316,317,318,331,332,334,335,336,338,342,343,345,346,347,349,351,352,354,355,356,357,359,360,361,362,363,366,367,368,371,373,374,376,378,379,381,382,383,384,385,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,444,446,447,449,450,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,486,488,490,491,492,493,494,495,499,500,502,503,508,511,512,517,520,521],them:[1,2,3,6,7,8,9,11,12,13,14,17,40,41,42,55,62,76,100,114,119,126,129,131,154,180,185,202,205,206,207,217,218,219,221,222,224,227,228,230,241,249,252,253,261,265,269,271,272,273,274,275,276,277,289,290,294,296,302,304,312,313,314,315,318,331,334,335,336,338,342,343,345,349,350,351,353,354,357,374,376,378,383,384,385,389,390,395,402,412,415,417,421,424,443,454,462,476,477,485,488,490,497,502,505,511,512,517,518],themselv:[6,9,11,181,210,211,224,253,373,374,384,386,390,395,405,412,434,438,439,440,461,517],theor:338,theorem:[245,252,319,395,410],theoret:[116,249,305,471],theori:[3,6,9,12,41,152,215,229,246,269,297,373,374,395,441,481,504],thereaft:[76,260,299,315,339,346,488],therebi:[344,435,436],therefor:[3,6,12,67,96,163,234,237,244,253,255,318,338,374,407,451,453,471,476,499,511],therein:[6,438],thereof:96,thermal:[0,2,3,4],thermo:[0,1,2,3],thermo_modifi:[2,3,6,60,66,107,108,129,155,159,161,162,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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 &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","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":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:[9,14,121,124,155,165,212,223,238,243,247,269,278,317,318,334,336,347,396,398,400,401,412,418,419,426,427,429,432,444,471,473],custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235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04,314,315,317,318,328,330,334,336,337,341,342,343,345,347,348,352,354,374,376,381,383,391,396,398,401,405,414,421,426,438,443,444,447,453,455,488,490,491,496,498,500,502,509,511,512],add_molecul:215,add_speci:215,add_to_nodeset:215,added:[491,512],addforc:[2,3,209],adding:[8,212,236],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,18,20,22,29,33,37,38,40,41,42,43,45,51,56,57,66,119,120,125,154,178,179,181,182,186,191,197,198,199,200,205,206,207,209,212,220,223,224,228,229,234,236,237,240,244,246,247,248,252,255,269,270,271,272,273,274,275,276,277,289,290,292,293,294,296,304,315,317,318,319,321,344,347,348,352,358,364,367,369,374,376,384,386,389,390,391,395,396,398,400,402,404,405,408,410,411,412,413,414,415,418,419,421,422,423,425,426,434,436,437,438,439,440,441,443,445,446,447,450,452,453,455,460,461,470,471,472,473,474,475,478,482,485,490,491,492,497,498,499,502,504,511,512,513,515,517,520,521,522],addition:[4,8],additionali:203,addres:9,address:[7,8,11,205,251,512],addtorqu:2,adequ:[261,331,344,373,384,499],adher:29,adhikari:255,adiabat:[],adiam:[205,206],adjac:[40,176,178,237,384,443,472,473,504,505],adjiman:442,adjust:[2,3,6,16,17,42,62,130,140,156,157,158,161,162,165,166,171,172,177,182,202,205,218,224,228,230,249,252,256,260,265,266,269,270,274,292,296,299,301,302,305,306,307,308,313,315,323,331,335,339,344,346,347,348,350,351,353,373,374,382,384,389,391,411,435,436,460,475,500,518],adjust_radiu:323,adjust_radius_factor:323,admiss:274,adof:[158,218],adopt:[314,511],adp:[2,3,7],adri:[9,311,452,453],adust:172,advanc:[3,249,395,485,496],advantag:[1,6,8,11,14,18,40,41,42,224,389,413,499,504],advect:[3,6,331],advertis:8,advis:[384,451],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,225,226,227,228,230,231,237,242,248,250,252,258,266,270,271,272,273,275,276,277,283,289,290,292,294,315,316,329,343,353,366,373,380,381,382,384,385,386,389,414,435,436,443,487,488,490,492,493,495,498,500],affin:[16,17,18,230,389,404],affiniti:389,afile:246,aforement:18,afresh:[303,498,517],afshar:409,after:[2,3,5,8,12,15,22,33,40,41,45,51,60,61,62,64,66,76,156,157,158,159,160,161,162,165,166,167,168,170,171,179,181,182,186,191,201,202,203,204,206,207,209,210,211,216,218,219,225,226,230,234,244,256,257,258,259,265,266,267,275,276,277,283,289,290,292,294,297,301,313,315,327,332,334,335,336,338,339,342,350,354,358,364,372,379,380,383,385,387,388,389,402,421,422,423,452,453,470,485,487,489,490,491,492,493,495,496,498,500,502,504,507,508,511],afterrun:498,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,230,237,248,301,357,372,384,435,436,485,487,488,490,492,497,504,506,517,520],against:[11,12,13,67,231,384,452,453],aggreg:[6,12,69,72,74,85,103,120,127,248,265,313,315,329,485,518],aggress:[237,248,504],agilio:[9,13],agre:[3,8,198,382,391,423,453],agreement:[5,7],ahd:420,ahead:350,aidan:[0,5,7,9,13,376],aij:13,aim:6,airebo:[2,3,7,225,226,312],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,249],aktulga:[7,9,308,453],al2o3:460,al2o3_001:[130,316],al3:177,ala:[255,460],alain:9,alat:[296,438],albe:[450,473,475],albeit:314,albert:9,alchem:[96,172],alcohol:346,alcu:[390,395],alcu_eam:450,alderton:408,alejandr:[269,270],alessandro:13,algebra:441,algorithm:[0,1,6,7,8,9,42,64,206,215,224,227,230,237,248,255,257,258,283,298,306,315,318,319,338,339,343,346,351,380,381,382,386,389,410,414,436,441,457,459,485,487,504],alia:[9,16],alias:[1,374],aliceblu:206,align:[6,9,12,29,42,76,180,198,224,250,376,490,493,511],alkali:414,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,261,262,264,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,327,328,330,331,332,333,334,335,338,339,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,356,357,358,362,367,369,371,372,373,374,375,376,379,382,383,384,385,386,388,389,390,391,392,394,395,396,398,399,400,401,402,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,481,48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14,70,80,87,99,104,115,117,126,158,173,175,218],cc2:14,ccc:[413,471,473,475,478],ccflags:[9,16,17,18,19,202],ccm6:412,ccsi:[413,471,473,475,478],ccu:395,cd2:177,cdeam:412,cdennist:9,cdll:11,cdof:[6,158,218],cdte:395,cdte_bop:395,cdtese:395,cdzn:395,cdznte:395,ce3:177,ce4:177,ceas:381,ceil:517,cell:[3,6,62,97,128,130,176,177,178,202,214,228,229,244,249,267,269,270,274,297,305,308,319,343,373,374,376,411,414,441,508],cella:[6,508],cellalpha:[6,508],cellb:[6,508],cellbeta:[6,508],cellc:[6,508],cellgamma:[6,508],center:[3,6,25,43,66,70,76,79,80,87,95,98,99,109,114,115,116,126,128,130,158,159,160,163,166,170,173,175,178,205,206,209,210,211,213,218,221,228,230,231,232,234,244,245,250,252,253,258,265,269,275,276,277,289,290,292,294,301,306,312,313,315,316,320,328,329,331,333,334,335,336,338,339,341,348,352,357,376,378,383,394,413,414,417,418,424,435,436,438,439,440,452,453,471,473,474,475,477,478,493,500,511,517],centimet:516,centr:237,central:[3,64,75,81,82,101,118,128,134,152,176,258,296,318,329,361,383,441,446,452,453,478,490],centro:[2,3,5,7,8,66,67,71],centroid:[3,298,477,500],cerda:373,ceriotti2:246,ceriotti:[13,246,251],certain:[1,2,3,6,8,12,17,40,76,125,129,131,182,202,203,205,217,218,219,221,222,227,242,243,315,317,332,345,356,364,372,385,421,443,453,476,492,496,511,517],certainli:250,cerutti:374,cfg:[3,6,7,9,13,202,204,205,206,207],cfile:453,cfl:[140,321],cfor:320,cg_type:455,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:318,ch2lmp:[],ch3:318,ch5md:204,chain3:385,chain:[3,4,9,10],challeng:[6,320],chalopin:310,champaign:[249,373,374,435],chan:441,chandler:[390,412],chandrasekhar:[6,426],chang:[2,3,8,9,12,14,15,16,17,40,41,56,60,62,65,76,86,114,128,138,140,160,161,162,179,180,182,198,201,202,203,204,206,207,209,210,211,212,213,216,223,225,226,229,230,231,235,236,241,243,244,246,248,249,250,252,254,256,258,265,266,267,270,271,272,273,275,276,277,283,285,289,290,292,293,294,297,301,302,304,306,309,312,313,315,317,320,331,334,335,336,337,339,342,344,349,354,374,380,387,389,421,443,452,453,470,485,486,487,488,490,491,492,493,494,495,496,498,499,500,501,502,505,508],change_box:[2,3,60],changeabl:202,channel:[4,212],chapter:[298,374],charact:[2,3,6,12,38,42,57,66,198,202,203,205,206,207,209,224,240,304,312,356,383,388,414,425,445,450,452,453,460,472,487,488,492,497,498,517,520,521,522],character:[6,71,75,118,128,152,461,485,504],characterist:[253,331,340],charg:[1,3,4,5,6,7,9,11,15,41,87,96,97,125,130,177,178,202,203,207,209,210,211,216,231,236,244,304,306,307,308,312,333,346,373,374,383,396,398,404,405,407,408,412,414,415,421,426,430,434,447,452,453,460,470,475,476,478,479,481,482,490,491,495,500,502,511,516,517],charmm2lammp:13,charmm:[2,3,5],chartreus:206,cheap:331,cheaper:[235,417,454],check:[3,6,8,9,11,12,15,17,39,40,42,59,76,100,198,199,216,224,225,226,231,241,244,250,251,301,314,318,331,339,341,346,354,356,369,372,382,383,384,385,386,389,411,422,425,443,453,483,485,487,488,490,498,504,507,508,517],checkf:198,checkout:512,checkqeq:453,checku:198,chem:[6,13,20,21,25,40,41,44,46,47,96,97,118,124,153,184,185,195,220,229,234,237,245,246,253,255,268,269,270,292,293,298,302,305,307,315,319,320,331,334,335,338,339,340,341,348,357,366,368,373,374,381,384,391,396,400,401,404,405,406,408,409,410,414,416,417,419,420,426,430,431,434,438,442,443,445,447,460,469,476,499,502,504,511],chemic:[9,130,172,177,202,203,215,216,244,306,311,312,338,374,452,453,465],chemistri:[305,306,308,391,395,414,452,453],chen:343,cheng:404,chenoweth:[452,453],chenoweth_2008:[452,453],chi:[103,167,201,296,306,308,369,415,417,518],chiefli:451,child:8,chip:[7,9,17,18,389,503],chipot:229,chiral:366,chmod:[11,12],cho:438,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,224,227,230,231,246,252,255,267,269,298,302,306,315,338,367,374,380,381,384,386,389,421,434,443,448,490,499,500,503,504,510,511,516],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,225,226,227,228,231,241,252,255,267,269,271,272,273,274,275,276,277,301,302,319,331,335,349,373,374,381,479,485,487,499,505],chose:[473,475],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,228,231,241,244,245,253,255,267,269,274,298,301,312,331,335,338,339,344,346,347,353,374,375,381,389,410,414,418,425,428,455,473,485,499,504,505,511],chri:176,christian:[7,9,14,17],christoph:7,chunk:[2,3],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,247],ciccotti:318,cieplak:[6,184,502],cii:219,cij:219,ciko:2,circl:[43,76,327],circular:[3,6,156,200],circumst:18,circumv:[101,118,310],citat:[],cite:[3,7,8,12,252,460],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,408],clarifi:[7,473,475],clariti:356,clark:447,class2:[2,3],classic:[0,3,5,6,7,8,9,242,298,305,310,343,368,414],classifi:[470,478],claus:488,clean:[6,12,14,15,17,498],cleanli:[489,521],clear:[2,3,8],clearli:7,clebsch:152,clermont:[9,13],clever:494,click:[2,11,22,37,45,56,178,186,197,205,249,358,367,384,402,470,512],client:[249,251],climb:[268,384,504],clinic:[7,13],clo:[167,201,518],clock:[12,485,504],clockwis:349,clone:512,close:[3,6,11,12,13,40,42,71,76,153,181,202,226,227,228,246,253,255,269,285,292,315,318,349,352,372,374,377,380,381,384,389,391,395,405,406,424,438,443,445,452,456,458,472,475,494,500,511,512,514],closer:[3,10,42,128,176,201,202,224,228,232,340,384],closest:[226,296,315,346,417,454,469,479],cloud:[460,511],clovertown:18,clsuter:77,clump1:[300,315],clump2:[300,315],clump3:[300,315],clump:315,cluster:[2,3,7,12,64,66,76],clutter:3,cmap:490,cmatrix:246,cmax:438,cmd:[11,12,298,501],cmdarg:11,cmin:438,cmm:7,cmoput:145,cn1:219,cn2:219,cna:[2,3,7,66],cnn:219,cnr:13,cnrs:9,cnt:[421,494],co2:[41,177,318,383],coars:[7,9,10,29,36,41,55,190,300,315,331,419,455,499,502],coarser:[374,517],coarsest:152,code:[3,5],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,357,358,364,402,421,425,443,457,459,462,490,519],coeffcient:490,coeffici:[2,3,4],coefficienct:409,coefficient0:412,coefficient1:412,coeffieci:[6,393,424],coeffincientn:412,coexist:[244,414],cohes:[6,415,438],coincid:[134,352,400,435,436,485],colberg:204,cold:[6,163,244,248,385,511],coldest:339,coleman8:9,coleman:[9,130,177,316],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,229,258,265,300,310,313,315,354,373,383,385,403,490,497,503,509,522],collid:[235,331,353],colliex:177,collinear:[3,300],collis:[3,255,331,349,353,411,418,482],colllis:331,colloid:[2,3,4,7],colombo:40,colon:[207,354,491],color1:206,color2:206,color:[3,9,42,202,205,206,224,245,305,310],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,258,266,267,305,315,332,333,343,353,416,420,452,453,491,505,507,517],columnar:176,colvar:[2,9,12],colvarmodul:12,com:[2,3,7,9,13,15,43,66,76],comamnd:230,comand:227,comannd:389,comb3:[2,3],comb:[2,3,4,7,9,209,306],comb_1:307,comb_2:307,combiant:406,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,237,249,258,261,269,285,291,298,304,319,335,344,352,355,357,373,374,376,381,389,403,405,406,410,414,415,421,433,434,461,471,473,475,476,478,481,493,498,503,511,517,519],come:[2,3],comfort:[12,13],comit:512,comm:[0,3,11,12,64,78,204,249,251,252,374,384,389,409,443,449,472,492],comm_modifi:[2,3,40],comm_modift:64,comm_styl:[2,3,64],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,240,253,315,343,383,384,390,412,413,415,425,438,445,446,453,460,461,471,472,473,474,475,478,487,488,490,511,512,517],commerci:7,commit:[9,512],commmand:[3,6,12,62,119,293,424,484,485,487,504,521],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,368,419,428,461,473,475,490,493,502],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,224,225,226,228,229,230,249,251,255,257,258,259,269,297,304,306,307,308,315,319,331,343,354,371,373,385,386,387,389,410,411,448,483,487,488,499,500,517,520,522],communc:373,comp:[7,204,251,252,285,291,318,374,384,414,443,449,454,468,472,474],compact:[66,209,402,470],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,234,306,354,356,373,374,382,384,438,460,485,504,505,511,516],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compart:378,compass:[7,9,21,22,37,44,45,56,185,186,197,357,358,367,401,470],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,224,237,297,309,335,338,345,348,351,373,389,422,441,443,472,487,488,517],compens:[6,225,226,313,385,414],compet:342,competit:374,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,249,342,374,389,441,490,491,495,517],compl:17,complain:[11,12,17],complement:438,complementari:[7,405,426],complet:[3,6,9,11,12,15,42,62,76,206,224,229,258,298,301,304,331,342,344,355,356,372,384,389,415,457,459,477,485,490,495,498,502,504,507,511,517],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,255,285,327,352,371,384,414,441,472,488,490,493,517],compli:[338,342],complic:[6,7,9,12,13,216,244,488],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,242,247,251,252,255,258,260,261,265,266,268,269,270,274,275,276,277,289,290,292,294,295,297,298,299,302,313,315,317,318,320,324,325,328,331,334,335,336,338,345,346,351,352,353,373,376,381,382,383,384,389,409,414,418,435,436,457,459,460,461,490,491,500,508,517,518],componenet:6,composit:[6,216,255,412],compound:[404,414,415,478],compres:[76,126,218],compress:3,compris:[41,352,454,477],compton:[130,177],comptu:3,compuat:374,comput:[],computation:[3,6,225,226,343,395],computational:511,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,66],compute_peratom:8,compute_sa:[130,316],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,521],concav:352,concentr:[76,412],concept:[6,158,168,218,499],conceptu:[3,6,76,166,228,230,384,405,421,438,495],concern:[6,78,96,204,245],concetr:76,concis:[11,342],conclud:12,concret:8,concurr:[16,374,517],conden:[343,473,475],condens:[6,160,343,391,407,412,426,478],condit:[2,3,5],conducit:6,conduct:[2,3,4],cone:493,confer:441,confid:[3,504],config:[12,202,487],configfil:229,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,228,229,230,231,235,244,251,252,283,298,306,342,371,382,384,391,395,413,438,441,471,473,475,478,485,490,492,493,504,512],confin:[490,504],conflict:[3,12,41,203,443,488,512],conform:[3,6,13,62,227,228,268,314,320,342,366,384,414,502],confus:[3,478],conjuct:[9,409],conjug:[7,8,252,381,414,452,453],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,252,255,259,283,301,302,306,307,308,310,315,319,331,339,346,351,373,374,384,396,398,402,405,409,414,420,426,443,447,455,476,490,493,497,511,522],connect:[3,6,9,96,163,181,227,249,300,315,318,328,378,384,406,418,452,453,469,475,487,488,490,494,511],conner:391,connor:391,conput:3,consecut:[3,11,12,40,76,178,206,210,211,231,249,250,405,426,430,485,491,493],consequ:[1,6,216,343,425,504],conserv:[3,9,29,209,216,227,234,235,245,248,252,254,255,259,265,267,269,283,285,315,318,319,334,335,339,346,347,351,384,408,409,410,418,432,460,499,504],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,256,270,297,315,338,339,342,343,346,374,402,414,421,453,454,460,469,485,486,488,491,492,493,495,498,500,508,511,517],consider:[6,8,252,253,334,335,336,389,499],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,230,231,234,236,242,245,252,253,254,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,287,288,289,290,292,293,294,302,305,310,312,314,315,334,335,336,337,347,373,374,376,378,383,384,389,391,395,397,403,405,414,417,421,424,435,436,438,441,443,445,454,457,459,460,472,479,488,490,491,492,493,494,495,502,511,517],consistent_fe_initi:215,consit:315,constant:[3,4],constantli:237,constitu:[3,6,258,315,348,352,403,454],constitut:[457,459],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,244,245,250,258,261,263,285,291,300,301,313,315,318,329,339,346,382,383,414,495,502,511],constraint:[3,5],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,228,269,297,314,352,385,389,408,441,443,469,471,472,493,494,509,517],constructor:[8,11],consult:453,consum:[1,310,448,517],consumpt:371,contact:[2,3,4,5,8,9,12,13,41,43,66],contact_stiff:[456,458],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,246,250,251,252,255,267,283,296,297,300,301,303,304,305,308,312,315,316,321,331,338,342,343,352,353,356,372,374,383,384,387,388,390,391,392,395,404,405,408,412,413,414,421,422,438,441,445,446,450,451,452,453,461,471,472,473,474,475,476,478,485,486,487,488,490,491,492,493,495,497,499,502,504,505,507,508,511,512,517,520,522],content:[4,8,9,12,18,453,506,508],context:[3,6,8,12,17,128,129,206,225,226,231,300,312,347,381,481,490,497,506,516,517,518],contibut:75,contigu:487,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,244,245,246,248,249,250,252,253,254,260,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,299,301,304,305,315,316,320,330,331,333,340,341,343,349,352,356,372,388,389,395,409,411,428,431,452,453,454,457,459,474,485,488,490,492,493,498,504,505,507,508,517,520],continuum:[6,7,9,215,343,457,459],contour_integr:215,contract:[62,228,230,269,302,315],contradictori:3,contrain:318,contraint:283,contrari:[246,253],contrast:[1,6,43,56,67,160,163,203,230,354,457,459,481,521],contrib:343,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,244,252,255,258,259,264,270,292,293,300,301,309,312,315,316,318,345,373,382,384,392,409,411,412,414,421,435,436,441,443,452,453,460,502,508,511,512],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,224,228,229,230,248,249,252,253,269,271,272,273,274,275,276,277,302,307,315,322,323,334,335,336,343,347,371,373,386,414,417,441,452,453,456,458,471,475,485,487,499,505,506],control_typ:215,controlfil:453,convect:100,conveni:[6,12,29,202,207,222,316,376,461,476,512,517],convent:[3,8,29,189,196,197,203,206,314,328,355,412,414,517],converg:[3,6,42,97,202,203,205,207,212,224,227,228,236,242,274,285,291,305,307,310,314,318,380,381,382,384,404,405,426,460,485,497,504],convers:[3,8,152,205,206,216,219,302,373,405,406,407,414,426,430,434,447,488,504,516],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,222,267,301,304,354,357,359,363,366,376,384,390,412,441,473,475,482,488,490,491,492,497,507,511,516,517,520,522],convex:[43,352],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,248,313],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218],coord2:[3,126,218],coord3:[3,126,218],coord:[2,3,7,62,66,76,77,81],coordb:460,coordbb:460,coordiat:382,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,242,244,247,248,249,250,251,252,253,266,268,269,271,272,273,275,276,277,292,295,296,297,300,301,302,312,313,315,317,318,320,325,328,329,330,331,333,341,342,343,350,351,353,354,376,382,383,384,389,390,391,394,413,460,485,490,491,492,493,495,498,500,504,511,517,518],coordn:[126,218],coords:460,copi:[0,3,4,8,9,11,12,15,17,41,131,205,343,384,402,452,488,512],copper:482,coproccesor:16,coprocessor:[1,7,9,16,17,389,503],coproprocessor:17,copy_arrai:8,copyright:[7,8,300],coral:206,core:[3,4],core_shel:160,cores:511,coreshel:[4,6,9],coreshell:4,cornel:[6,184,502],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,352,353,376,477,490,512],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:404,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,230,237,244,246,252,269,270,292,300,302,305,342,348,352,373,384,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,490,505,508,511,512],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,242,253,263,269,270,308,315,318,328,330,349,352,384,385,389,407,436,441,487,488,490,500,512,516,518],correl:[2,3,174,209,218],correpond:240,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,242,243,247,252,255,256,265,266,267,269,271,272,273,274,275,276,277,278,279,283,287,289,290,292,294,297,298,302,307,315,317,318,334,336,338,347,348,349,351,352,353,355,357,358,359,360,362,363,366,368,374,379,381,383,384,390,391,393,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,424,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,450,452,453,454,455,460,461,462,471,472,473,474,475,476,478,480,481,482,485,487,488,490,491,493,503,504,505,507,508,511,517],correspondingli:[435,436,499],corrupt:3,cosin:[2,7,22],cosineshift:27,cosmo:[246,251],cossq:2,cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,224,225,226,241,269,307,343,373,374,387,405,426,430,441,443,471,487,499],costheta0:[471,473,475,478],costheta:450,costli:[11,97,246,385],couett:4,coul:[2,3,9,77,119,128,172,210,211,344,374],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,242,251,304,305,306,310,313,315,317,331,332,338,342,343,344,348,352,354,356,364,370,372,380,382,385,389,392,416,420,421,424,452,453,486,487,488,490,492,494,497,498,505,506,511,517,518],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,306,308,344,373,374,382,389,396,398,399,400,401,404,405,406,407,408,414,418,419,421,426,430,434,437,443,447,452,453,455,460,470,475,476,478,481,495,502,508,511,516],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,223,224,231,236,241,244,250,269,283,301,318,334,335,352,374,382,383,384,386,389,416,420,443,508,517],counter:[3,349,485,496,498,504],counteract:244,counterbal:[237,248],counterbalanc:29,counterpart:[202,315,485],counterproduct:18,coupl:[3,4],couple:[4,6,11,12],courant:321,cours:[3,8,138,140,172,202,210,211,245,314,328,342,348,350,351,353,354,374,435,462,487,490,503,511,517,520],courtesi:376,cov:460,coval:[6,9,29,414,438,460,511],covari:246,cover:[6,12,76,198,206,215,255,414,477],coverag:76,cpc:251,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,242,318],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,234,253,344,371,374,389,402,470,485,503,504,507,508,509,517],cpuremain:508,cpus:12,cr2:177,cr3:177,crack:[4,385],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,385,511],craympi:389,creat:[2,3,4,7,8,9,12,13,14,15,17,38,40,43,57,61,62,65,66,76,88,114,115,120,121,127,146,155,161,162,174,176,179,180,181,198,202,203,204,206,209,214,218,221,222,225],create_atom:[2,3,7,8,41,62],create_bond:[2,3],create_box:[2,3,22,41,45,60,61,62,65,76,176,179],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[3,5],crimson:206,critchlei:300,criteria:[3,128,179,205,206,225,226,227,264,382,449,477,492,495,517],criterion:[12,42,133,178,181,216,224,227,244,283,307,321,349,354,382,384,404,414,418,460,495,504,505],criterioni:504,critic:[6,49,50,267,338,343,382],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,226,230,266,268,292,315,324,328,330,339,346,358,376,384,400,409,411,412,419,420,421,426,428,430,450,455,457,459,473,475,482,490,494,500,520],crossov:1,crossterm:490,crozier:[0,7,13],crucial:305,crystal:[3,4,6,13,78,118,296,297,341,376,385,490,494,508,511],crystallin:[6,114,297,376,474,511],crystallis:338,crystallogr:[130,177],crystallograph:[376,508],crystallographi:[130,177,376],cs1:177,cs_chunk:6,cs_im:[41,490],cs_re:[41,490],csanyi:[152,451,461],cscl:438,csequ:6,csh:[11,12,402],cshrc:[11,12],csic:[413,471,473,475,478],csinfo:6,csisi:[413,471,473,475,478],csld:[2,3,209],cst:412,cstherm:6,cstyle:487,csvr:[2,3,209],ctcm:[390,412],ctemp_core:234,cterm:320,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:438,cube:[6,176,181,234,352,376,511],cubes:[42,224],cubic:[2,3,38,57,198,240,331,374,376],cuda:[2,3,4,7],cuda_arch:[9,15],cuda_get:15,cuda_home:[9,15],cuda_prec:[9,15],cufft:14,cuh:395,cummul:[3,6,222,225,226,227,229,241,246,252,254,331,334,335,336,337,339,346,420,508],cumul:[6,216,218,221,235,244,252,267,269,274,283,315,316,384],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,242,244,246,249,250,252,258,266,269,270,275,276,277,283,285,289,290,291,292,294,300,301,306,307,309,312,313,314,315,318,319,320,321,322,323,324,325,327,329,330,331,334,335,336,342,343,346,347,348,349,350,351,353,354,356,371,372,373,374,377,378,379,381,382,383,384,389,395,402,404,408,412,414,415,418,421,422,425,435,436,438,439,440,443,450,452,453,456,457,458,459,462,473,475,476,479,485,486,487,488,490,491,492,493,494,496,497,498,500,502,504,505,507,508,512,517,518,519,520,521,522],curv:[6,178,244,285,291,297],curvatur:[417,454,482],custom:[2,3],cut0:488,cut1:499,cut2:499,cut:[2,3,9,12,14,15,16,17,18,19],cuthi:[296,308],cutinn:[397,435,436],cutlo:[296,308],cutmax:450,cutoff1:[401,408,426,430,434,437,447,455],cutoff2:[396,398,399,401,407,408,426,430,434,437,447,455,476],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,226,227,232,240,296,305,306,308,310,312,315,319,331,344,348,352,354,371,373,374,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,454,455,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,488,492,495,499,511,517],cutoffa:413,cutoffc:413,cuu3:412,cval:177,cvd:338,cvel:320,cvff:[2,7,358],cwiggl:[3,266,348,351,353,517],cyan:[2,205,206],cycl:[3,244,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,250,291,301,349,352,378,493],cylinder_d:378,cylindr:[6,250,328,349],cypress:389,cyrot:395,cyrstal:297,d3q15:255,d3q19:255,d_double_double:15,d_e:343,d_flag2:304,d_flag:304,d_name:[125,202,304,333,500],d_single_double:15,d_single_single:15,d_sx:304,d_sy:304,d_sz:304,daan:341,dai:12,daili:12,daivi:292,damag:[2,3,9,66],dammak:310,damp:[3,6,209,214,252,253,254,259,269,270,274,291,302,305,306,310,315,334,335,347,349,350,381,382,384,396,398,400,405,408,414,418,426,434,447,455,470,476,504,511],damp_com:253,damp_drud:253,dampen:[315,511],dampflag:[349,418],dan:17,danger:[3,12,244,354,409,508],dangl:181,daniel:9,darden:[374,408],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:306,dash:[418,507],dat:[6,100,198,215,486],data2xmovi:[],data:[2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,316],dataset:316,datatyp:3,date:[0,4,6,12,13,201,452,453,517],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:437,davi:348,david:[9,19,373,374,473,475],daw:[412,450],dbg:14,dcd:[3,6,7,202,204,205,206,207,298,491,495],dcs:9,ddim:201,deactiv:434,dealt:251,debug:[6,7,11,12,13,14,17,58,130,134,177,178,298,303,371,373,389,422,443,479,488,489,497,500,507,517],deby:[2,3,7,210,211,310],decai:[101,405,482],decid:[3,6,12,16,76,266,304,315,344,505,512],decipher:376,deck:304,declar:204,declin:331,decod:205,decompos:[96,461],decomposit:[3,5,7,18,65,215,298,319],decoupl:[6,511],decreas:[3,202,203,212,213,220,227,230,236,237,242,244,252,342,373],decrement:320,deepli:370,deeppink:206,deepskyblu:206,def:[12,13,488],defaul:64,defect:[6,75,176,441],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,242,243,244,247,250,251,252,253,254,255,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,287,288,289,290,292,293,294,296,297,298,300,301,302,304,306,308,313,315,316,317,318,321,325,329,331,333,334,335,336,337,339,340,341,343,345,346,348,349,350,351,352,353,354,356,357,358,359,360,361,362,363,366,367,368,369,371,373,374,376,379,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,405,406,408,409,410,411,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,436,437,441,442,443,444,445,446,447,449,450,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,490,491,493,494,495,496,499,500,501,502,504,505,507,508,511,513,514,515,516,517,518,519],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,230,239,250,274,316,333,345,348,351,353,355,367,371,383,392,395,403,410,414,424,450,457,459,461,477,488,490,492,499,501,516,517],defint:508,deform:[2,3,7,8,41,43,60,62,64,66,86,123,134,138,139],deg2theta:177,deg:511,degener:[3,300],degrad:[8,18,297,374,499],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,244,246,247,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,314,315,318,334,335,336,341,357,359,363,366,368,382,408,412,420,500,508,511,518],degrees:198,degress:[158,218],del:504,delai:[3,6,12,385,411,508],deleg:421,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,225,227,241,244,269,316,334,335,354,356,372,383,385,388,443,469,490,491,492,493,501,502,507,512,513,515,517,518],delete_atom:[2,3,7],delete_bond:[2,3,51,56,57,69,74,127,179],delete_el:215,deli:201,delimit:[488,517],dellago:[6,237],deloc:[270,414,460],delr:438,delt_lo:504,delta:[2,22],delta_1:395,delta_3:395,delta_7:395,delta_conf:3,delta_ij:[438,450],delta_pi:395,delta_r:450,delta_sigma:395,delx:201,delz:201,demand:310,demo:11,demon:295,demonstr:[305,438],den:301,dendrim:420,dendtrit:378,denniston:[9,255,257,258,259,297],denomin:[7,183],denot:[130,234,237,253,297,308,310,405,419,421,453,457,459],dens:[76,227,414],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,224,230,242,255,258,262,263,297,301,302,304,306,343,348,376,379,383,390,391,395,412,438,439,440,445,450,454,460,464,466,467,468,490,499,500,508,516],density_continuity:459,density_summation:459,dent:378,depart:[0,7],departur:[267,305],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,243,246,247,248,250,252,253,255,257,258,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,296,307,310,312,315,317,318,319,325,331,334,335,336,338,340,342,343,345,347,348,351,352,353,354,356,357,358,359,360,362,363,366,368,374,376,382,383,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,442,444,445,446,447,449,450,452,453,454,455,460,461,462,470,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,496,500,502,504,507,508,510,517,518],dependend:6,depflags:12,dephas:[485,504],depos:231,deposit:[2,3,4,113,180,209,216],deprec:[3,306,452],deprect:218,depth:[52,156,205,343,417,454],dequidt:9,der:[96,119,403,404,434,452,453,481,511],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,228,230,237,244,252,266,269,271,272,273,274,275,276,277,296,302,306,310,340,341,343,348,349,352,381,383,391,395,403,408,414,415,419,428,432,433,438,441,452,453,470,472,481,511],derjagin:481,derlet:296,descend:206,descent:[7,381],descib:[41,205,306],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,245,246,249,250,251,252,253,254,255,257,258,259,264,268,269,270,274,282,293,296,298,303,304,305,306,307,308,315,320,328,331,332,333,334,335,336,337,338,339,340,341,346,348,349,351,356,373,374,376,380,381,382,383,384,388,391,392,394,396,397,398,400,401,402,403,404,405,408,412,414,415,417,418,419,421,424,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,445,449,450,451,452,453,454,455,460,461,462,469,470,471,472,473,474,475,476,478,480,481,482,483,485,487,488,490,491,492,493,494,500,503,504,507,512,517,518,520],descript:[2,3,8,9,12,13,18],descriptor:[152,202,422],deserno:374,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,227,233,234,269,270,296,297,316,338,343,392,393,394,397,400,405,407,414,434,435,436,439,440,450,453,472],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,222,228,230,242,244,245,252,253,254,258,269,292,300,301,302,303,306,310,315,318,331,334,335,336,337,342,349,364,370,373,374,376,380,382,383,384,409,412,420,435,436,471,473,475,486,487,488,490,494,499,504,505,507,508,517,518,520],desk:7,desktop:[4,6,7,10,12,205],despit:511,destabil:395,destre:366,destroi:[9,11,40,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,242,244,245,246,247,249,250,252,254,255,259,266,267,268,269,270,271,272,273,274,275,276,277,281,283,289,290,292,293,294,297,300,301,302,304,305,307,308,309,315,318,319,331,334,335,336,337,338,339,341,342,343,344,345,346,347,354,356,358,367,373,374,377,382,383,385,386,389,390,391,392,394,395,397,399,400,401,402,403,404,405,408,409,414,415,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,437,438,442,443,445,449,452,453,454,460,461,462,470,477,480,481,483,488,490,491,492,493,495,496,499,500,502,505,508,509,512,517,518,522],detect:[2,3,12,43,64,66,95,101,243,301,342,384,404,420,425,485,487,490,501,504,517],determ:389,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,244,247,248,250,252,253,258,264,266,267,269,275,276,277,289,290,292,294,296,298,301,302,305,312,313,314,315,316,317,321,323,325,331,334,335,336,338,344,345,348,349,350,351,352,353,354,367,373,374,376,383,385,386,389,391,392,399,404,408,411,412,416,418,421,422,430,438,441,443,453,454,460,469,472,476,481,487,490,491,493,495,497,500,504,506,507,509,516,517,518],determinist:319,detil:120,devan:[9,455],devanathan:475,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,249,274,300,305,306,309,391,395,414,440,441,460,478,492],devemi:9,deviat:[267,274,296,416],deviator:9,devic:[1,3,12,15,17,249,389],device_typ:389,devin:[307,404],devis:440,dfactor:205,dff:511,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,374],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,309,441],dhi:[62,201,230,301],dhug:[267,305],dhugoniot:[267,305],dia:438,diagnost:[2,5],diagon:[3,6,92,152,153,154,228,269,302,315,346,457,459],diagonalstyl:461,diagram:[42,130,177,197,224,298],diallo:420,diam:[205,206,301,383],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,252,301,304,315,331,333,347,349,383,403,417,418,428,454,477,481,490,491,500],diamond:[376,414,438],diamter:[41,301],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,382,409,411,412,418,443,473,475,498],didn:3,die:18,diel:2,dielectr:2,diff:[3,6,12,174,345,373],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,243,244,245,246,247,248,249,252,253,255,266,269,270,271,272,273,275,276,277,279,281,284,287,288,289,290,294,296,298,300,302,305,306,307,310,313,315,318,320,328,329,331,334,335,336,339,340,341,343,346,347,348,349,352,356,357,367,370,372,373,374,376,377,380,381,383,384,386,387,388,389,390,391,395,399,400,402,403,404,409,410,412,414,417,418,419,421,424,426,427,429,430,437,438,439,440,442,443,445,446,450,452,453,454,455,456,457,459,460,461,462,470,471,472,473,475,477,478,481,484,485,487,488,490,492,493,494,495,498,499,500,502,504,505,507,508,509,511,516,517,518,520],differenti:[1,3,6,29,198,373,405,450,474],difficult:[228,298,389,420,499],difficulti:[101,118,318,452],diffract:[7,9,130,177,316],diffus:4,diffuse:[4,6],digit:[2,3,206,356,441,517],dih_table1:198,dih_table2:198,dihedr:[2,3,7],dihedral_coeff:[2,3],dihedral_cosine_shift_exp:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:414,dij:318,dilat:[2,3,62,64,66,83],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,230,250,349,376,438,493,516,517,518],dimdim:517,dimems:297,dimens:[2,3,7,12,60,61,62,64,66,76,126,158,165,166,167,180],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,268,297,343,376,380,384,450,490,500],dimensionless:[116,133,134,136,139,141,143,148,152,343,374,461,481],dimensions:316,diment:3,dimentionless:147,dimer:[6,315,438],dimgrai:206,dimstr:[42,224],dinola:[302,334],dintel_offload_noaffinity:16,dipol:[2,3,4],dipolar:[4,29,41,202,203,333,511],dir1:501,dir2:501,dir:[1,3,4,8,10,11,12,267,296,305,330,450,452,453,488,501,517],dirac:152,direc:450,direct:[2,3,7,12,13,60,76,176,201,202,209,212,213,214,230,231],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,236,246,250,255,297,316,335,347,349,350,351,352,376,381,389,390,391,396,398,399,405,408,412,414,426,430,443,447,455,469,488,500,501,502,508,517],directoi:14,directori:[2,3],disabl:[3,12,16,343,425,488,503,517],disadvantag:[6,224],disallow:[202,230,269],disappear:492,discard:[2,3,42,76,220,224,344,352,487,492,493],discontinu:[198,382,432],discourag:438,discov:[13,344],discret:[6,8,41,43,205,206,252,255,291],discuss:[2,3],disk:[6,93,94,101,171,200,231,244,301,488],disloc:[75,441],disord:[40,75,441],disp:[2,3],dispar:454,disperion:[408,430],dispers:[3,6,7,9,176,297,373,374,399,408,430,435,443,453,472,478],displac:[2,3,7,12,43,62,66],displace_atom:[2,3,7,114],displace_box:62,displacemet:493,displai:[11,13,22,37,45,56,186,197,202,205,358,367,402,470],dispters:3,disregard:441,dissip:[6,9,41,89,90,239,245,252,297,319,340,341,397,409,410,418,435,436,470],dissolut:225,dist:[6,74,100,120,129,202,298,314,411,469,485,518],distanc:[2,3,7,8,9,12,40,56,57,58,59,61,62,64,66,67,70,74,76,77,79,80,81,82,87,88,95,104,114,115,117,120,126,127,128,129,132,146,167,173,176,179,180,181,201,202,203,206,214,218,225,226,230,231,232,235,244,250,266,267,268,283,297,301,306,313,315,320,324,328,330,331,338,339,342,349,350,351,353],distinct:[6,234,312,373,454],distinguish:[6,95,152,258,414,489,517],distort:[176,390],distrbut:390,distribut:[2,4,5],distro:[123,402,449,450],ditto:[8,12,14,15,16,17,18,43,127,226,482,488],div:8,divd:129,diverg:[3,12,40,315,341,391,492,511,520],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,224,230,296,339,346,351,373,382,384,415,453,460,478,499,507,517],divis:[6,255,395,424,434,487,508,517],dl_poly:[6,7],dlambda:172,dlammps_async_imd:249,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,342,490,491,495],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:500,dlmp_intel_offload:[9,16],dlo:[62,201,230,301],dlopen:6,dlvo:[7,403,481],dm_lb:255,dmax:[331,380],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,231,244,252,253,264,269,270,275,276,277,281,289,290,292,293,294,301,304,315,328,331,334,335,336,345,349,352,354,356,358,367,372,382,383,384,389,390,391,394,402,404,405,412,413,415,420,421,423,424,438,439,440,443,446,449,450,451,461,470,471,473,475,477,478,488,490,491,492,493,495,498,499,500,507,508,512,517,518,520,521],docuement:454,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,223,224,226,227,228,230,234,236,237,240,241,244,245,248,250,252,253,255,258,265,269,270,271,272,273,275,276,277,289,290,291,292,293,294,302,303,304,308,310,313,315,331,334,336,338,339,343,346,347,348,351,352,353,354,359,360,361,363,364,366,372,373,374,375,376,383,384,385,390,391,392,393,394,395,397,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,421,422,423,424,425,428,429,431,432,433,435,436,438,439,440,441,443,445,450,451,452,453,454,456,457,458,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,486,487,488,490,491,492,493,494,497,498,500,501,502,503,504,507,508,511,512,517,522],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,328,383,385,389,391,404,413,423,452,453,471,473,474,475,478,490,492],dof:[3,8,124,156,157,158,171,218,315,518],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[383,490],doi:[6,229],domain:[3,6,7,12,13,18,40,42,43,61,64,65,76,130,167,177,180,201,204,205,206,209,216,224,228,230,231,248,251,255,269,270,298,310,315,319,343,348,349,373,374,384,389,411,443,485,487,490,494,507],domin:[1,414,504],don:[0,8,9,12,13,128,181,212,236,253,352,438,460,488,490,512],donadio:335,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,62,65,76,172,175,178,181,198,202,205,206,215,216,218,220,221,222,224,225,226,227,228,230,231,240,242,244,249,250,252,253,260,269,275,276,277,289,290,292,294,295,297,298,299,301,304,312,315,316,318,331,334,335,336,338,340,341,354,356,372,373,374,382,384,385,388,389,391,399,412,421,422,423,430,436,437,438,443,445,452,469,472,477,485,486,487,488,491,494,495,498,508,509,511,512,517,518],donor:420,dot:[153,174,212,236,247,268],doti:[395,450],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,96,230,242,303,352,356,372,374,388,389,395,415,419,441,452,453,486,490,494,498,503,517,518],dover:215,down:[3,6,7,8,11,40,76,228,244,252,331,347,389,414,443,460,489,509],downhil:[380,381],download:[5,7,8,9,11,12,13,17,249,422,451],downsid:6,downward:312,dozen:[8,9,12,119,209,452,453],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[2,3,7],dpde:262,dpdtheta:[41,89,90,410],dpdtheta_i:[239,240],dproduct:392,dr_ewald:[130,316],drag:[2,209],dragforc:255,drai:[267,305],drain:[248,347,382],dramat:[9,62,201,225,226,227,228,230,269,331,334,335,374,389,443,460,487],drautz:395,draw:205,drawback:304,drawn:[43,202,205,206,245,485],drayleigh:[267,305],dreid:[2,3,4,9],dreiding:[],drfourth:116,drho:[125,390,412,445],drift:[6,114,116,237,245,246,248,252,253,265,313,331,499,507,511],drive:[11,12,213,228,230,247,269,296,302,315,350,384],driven:[6,190],driver:[6,12,14,15,209,242,249],drop:[3,206,409],droplet:421,drsquar:116,drude:2,drudes:[253,511],dry:241,dsecriptor:422,dsf:[2,3],dsmc:[2,3,9],dstyle:301,dt_collis:255,dt_lb:255,dt_md:255,dt_srd:331,dtilt:[62,230],dtneb:504,dtqm:305,dtype:[127,226],dual:[16,17,331,389],dudarev:177,due:[1,3,6,9,12,16,17,19,41,55,58,60,61,64,70,75,76,79,80,87,88,95,97,98,99,104,113,114,115,116,117,122,128,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,223,225,226,227,228,229,230,231,236,238,241,242,245,246,249,250,252,253,254,255,258,259,260,265,266,267,268,269,274,283,296,299,301,313,314,315,317,328,330,331,332,334,335,336,337,338,340,341,343,347,348,350,351,352,354,374,380,382,384,385,386,406,409,410,412,416,417,421,435,436,443,450,452,454,455,469,472,473,475,479,481,482,485,487,490,491,492,499,504,507,508,509,511,517,518],duffi:343,duin:[9,306,311,452,453],duke:374,dumbbel:378,dummi:[12,29,474],dump0:203,dump10000:203,dump1:495,dump20000:203,dump2:495,dump2vtk_tri:146,dump:[2,3,4],dump_0:203,dump_1:203,dump_atom:8,dump_custom:8,dump_h5md:204,dump_modifi:[2,3,202,203,204],dump_p:203,dumpcustom:8,dumptimestep:495,dunbrack:[6,20,184,400,502],dunweg:[252,254],duplic:[2,3,14,15,17,42,43,179,203,224,246,296,490,516],dupont:[5,7,13],durat:[37,56,155,156,157,159,160,161,163,164,165,166,167,170,171,197,206,218,244,310,343,367,418,470],dure:[2,3,6,8,9,12,16,17,38,40,42,57,76,96,138,140,154,160,179,182,198,202,203,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,235,236,237,238,240,241,242,243,244,245,246,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,324,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,374,382,384,388,389,409,434,441,443,445,453,472,485,486,488,490,493,495,497,498,500,502,504,505,508,509,517,521,522],dvector:8,dvlo:481,dvx:6,dx_lb:255,dy3:177,dyamic:12,dyanam:6,dyanmic:504,dynam:[2,3,4,5,7,9,12,13,15,16,40,41,62,64,76,90,113,128,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,155,156,157,158,159,161,163,164,165,166,167,168,170,171,176,182,202,206,209,212,229,230,231,236,241,244,246,251,252,253,254,259,267,270,280,283,285,297,301,304],dynamo:[5,390,412,438],dyne:516,dyre:431,dysam:493,e28637:29,e_1:395,e_2:395,e_b:415,e_data:203,e_ee:414,e_hbond:420,e_i:[6,395,415],e_j:[6,395],e_k:395,e_ke:414,e_kl:6,e_lj:[391,408],e_n:395,e_ne:414,e_nn:414,e_pr:414,e_rebo:391,e_torsion:391,e_tot:441,e_vol:441,eaa:357,eaat:185,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,58,60,62,64,65,66,67,68,70,71,72,73,75,76,77,78,79,80,81,82,83,84,86,87,88,90,92,94,96,98,99,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,146,152,153,154,156,157,158,159,160,161,162,165,166,167,168,170,171,172,173,174,175,176,177,178,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,238,240,241,242,244,245,246,247,248,249,250,251,252,253,254,255,256,258,259,260,261,262,263,265,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4],epsilon_j_c:[417,454],epsilon_lj:454,epton:449,eqch:173,eqeq:[452,453],eqp:408,eqq:408,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,244,245,247,248,250,252,253,255,258,259,266,267,274,285,286,296,298,301,303,305,306,307,310,312,314,315,317,320,325,327,334,335,336,339,340,341,343,345,346,348,351,353,354,356,372,376,382,384,385,386,388,389,404,409,410,416,417,420,424,435,441,442,450,452,453,454,456,457,458,460,461,462,472,477,478,482,486,487,488,490,492,493,497,498,501,504,506,508,517,518],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,228,234,235,237,239,240,246,252,253,255,258,267,268,269,270,274,292,296,298,305,306,310,318,319,331,339,343,346,348,349,351,353,373,374,378,403,408,409,410,414,415,418,423,435,436,438,443,454,457,459,464,465,467,468,482,511],equation:[246,296,366],equi:270,equidist:268,equil:[3,306,377,497,522],equilater:500,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,227,228,244,267,269,270,292,293,302,305,306,307,308,339,340,341,346,404,405,452,453,486,500],equilibria:346,equilibribum:[225,226],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,228,230,244,245,246,253,255,269,274,292,305,306,310,314,318,320,328,331,338,339,341,346,357,359,363,366,404,438,446,460,511],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,222,228,230,244,252,269,292,302,314,315,351,391,409,414,460,473,475,476,490,493,498,499,508,511],equlibrium:6,equliibr:[306,308],er3:177,eradiu:[41,125,203,414,490],eras:[317,340],erat:[230,436],erc:405,erfc:[405,426,443],erforc:[125,203],erg:516,erhart:[216,412,473,475],ermscal:392,ernst:9,eror:3,eros:438,erose_form:438,erot:[2,3,9,66],errata:[473,475],erratum:348,erron:3,error:2,erta:418,ervel:[125,203,490],escap:[231,511],especi:[8,16,166,178,209,216,224,244,305,310,313,314,389,487],espresso:[9,309],essenti:[11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,297,347,374,391,405,426,475,495,508],essential:[8,274],essex:29,establish:[96,248],estim:[1,3,6,10,12,38,42,57,100,153,215,224,235,267,331,338,373,374,380,443,453,472,504,508],estimat:3,esu:516,esub:438,eta:[6,255,269,305,306,308,347,413,415,417,450,474,478,516],eta_dot:269,eta_ij:450,eta_ji:415,etag:[41,490],etail:508,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,242,244,245,252,269,301,312,316,343,344,352,356,372,373,382,383,384,385,387,412,413,421,434,436,441,448,452,453,471,473,475,478,485,488,490,491,492,497,499,500,504,505,506,507,508,509,511,516,517,520,522],ethernet:18,etol:[382,384,485,504],etot0:305,etot:[6,105,107,108,122,153,164,206,234,253,267,305,507,508],eu2:177,eu3:177,euler:[382,384],eulerian:215,euqat:463,europhi:255,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,245,247,248,250,251,252,253,297,303,306,317,321,325,334,335,336,345,348,351,353,354,356,380,382,389,441,443,445,450,456,458,460,472,485,486,488,492,493,495,497,498,499,500,504,506,508,517,518],evaluat:[373,374,517],evalut:[356,488],evan:[166,292],evanseck:[6,20,184,400,502],evapor:[2,3,9,60,113,209,216],evaul:[8,382],evdwl:[119,154,452,453,508],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,250,253,267,269,270,297,301,310,312,315,316,327,331,339,343,346,348,352,354,365,373,380,382,384,389,394,414,415,418,421,424,443,454,478,479,483,490,491,493,495,496,497,499,500,502,505,507,508,509,511,522],evenli:[3,42,58,153,198,224,255,424,479],event:[2,3,8,66],eventu:[3,6,12,15,180,504],eventual:306,ever:[9,55,57,251,331],everaer:[403,417,454,470],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,241,242,244,246,248,249,250,255,256,265,269,270,274,285,291,295,296,297,301,302,303,304,305,306,307,308,310,312,313,315,316,318,320,331,333,334,335,336,337,338,339,342,343,344,345,346,354,356,372,374,384,385,386,389,409,411,421,434,452,453,460,466,484,485,486,490,492,494,495,497,498,499,504,505,506,508,512,517,522],everyth:[8,119,512],everywher:[128,428],eviri:414,evolut:[237,246,255,298,485],evolv:[255,298,344],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,344,373,374,382,396,398,399,405,408,414,426,430,447,455,470,472,476],ewald_disp:408,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,224,227,245,246,252,253,254,301,310,311,331,343,358,373,402,492,497,504,517,520,522],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,224,230,235,240,245,252,253,254,270,282,283,293,297,304,305,331,336,337,350,389,402,409,412,418,421,435,443,445,472,492,493,500,504,517],exager:511,examin:[6,8,17,227,297],examp:[488,517],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,224,228,230,235,241,269,297,312,316,322,323,331,382,389,490,517],exceed:[3,42,62,224,230,269,331,498],excel:414,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,243,244,247,250,252,254,269,270,271,272,273,274,275,276,277,278,279,282,283,287,289,290,292,293,294,298,307,308,315,317,318,328,331,334,336,337,343,347,351,354,355,356,357,358,359,360,362,363,366,367,368,373,374,376,379,383,384,385,387,388,389,390,391,393,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,439,444,446,447,449,452,453,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,487,488,490,492,493,495,498,499,500,501,502,504,508,511,516,517,518,521],exception:488,excess:[220,414],exchang:[2,3,6,8,64,65,209,215,216,237,244,248,252,307,315,339,343,346,373,389,414,505],exchange:373,excit:414,excite:414,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,225,226,256,265,300,313,315,338,349,354,382,383,385,397,418,421,424,435,436,443,469,502],exclude:385,exclus:[1,3,12,16,96,389,404,441,443,499,509],excurs:[269,485],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,249,309,356,372,375,388,486,488,498,501,504,517],exempl:460,exemplari:245,exemplifi:414,exert:[6,250,253,285,310,350,351,352,374],exhaust:[215,388,517],exhibit:[101,237,248,269,381,414,499],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,223,226,228,231,244,300,301,303,304,354,355,357,359,360,361,363,367,377,383,389,410,421,452,469,479,486,488,490,491,492,501,502,503,512,517,518,520],exit:[2,3,11,12,42,60,202,224,240,372,388,488,489,498,507,517],exlanatori:3,exp:2,expand:[2,3,45],expans:[12,152,202,501,517],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,224,236,244,246,266,296,302,304,305,310,315,354,374,385,402,438,441,443,485,488,490,492,495,499,504,517],expens:[6,76,206,296,300,315,343,354,373,374,385,389,488],experi:[6,13,15,223,231,249,258,268,302,314,315,380,384,409,443,499,504],experienc:[6,12,257,258],experiment:[17,244,373,389,504],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,269,285,296,304,315,328,354,356,372,373,376,383,384,388,394,412,424,460,462,477,488,491,492,495,497,500,511,512,517,522],explan:[3,6,62,125,152,202,203,218,268,296,421,484,487,488,490,499],explanatori:[3,8,129,202,203,217,218,221,315,383,487,517],explantori:[3,311],explic:442,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,230,322,323,358,379,391,392,395,400,402,412,414,425,435,476,484,487,491,494,512],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,243,245,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,304,305,307,315,317,318,334,336,337,343,347,351,357,359,360,362,363,366,368,383,389,390,391,393,396,397,398,399,400,401,402,403,404,405,406,408,409,411,412,413,415,416,417,418,419,420,421,425,426,427,428,429,430,431,432,433,434,435,439,441,443,444,445,446,447,449,454,455,462,463,464,465,466,467,468,470,471,472,473,474,475,476,478,480,481,482,490,492,493,499,500,502,503,509,511,512],explictli:[16,503],exploit:[15,17,298],explor:[130,177],expon:[3,306,308,412,417,420,434,442,455],exponenti:[96,450,471,478,482,504,517],expos:11,exposit:[215,409,411],express:[6,152,164,178,210,211,228,266,296,306,343,349,356,395,412,414,428,438,460,461,470,517],expression:356,expressiont:395,extend:[3,7],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,242,243,244,246,247,248,250,252,254,267,269,274,283,296,297,313,314,315,317,320,325,328,330,334,335,336,337,338,340,341,343,345,348,352,353,417,438,441,453,454,461,507,508,516],extensiv:[66,209,508],extent:[1,3,42,43,46,60,76,176,180,202,214,224,250,350,353,373,376,391,456,458,472,487,490,493],exterior:[3,6,176,352],extern:[2,3,9,95,176,209,223,236],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,224,226,269,303,304,305,315,331,382,383,386,387,408,418,421,424,438,443,487,488,490,493,502,511,517],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,308,384,405,415,438,461,488,495,507],extract_atom:11,extract_comput:[11,488],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,228,230,269,341,414,474,511],extrema:434,extreme:414,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,345],f_a:[473,474,475],f_ave:129,f_c:474,f_f:475,f_fix_id:305,f_foo:517,f_harm:341,f_i:[29,450],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,264,333,345,508,517],f_ij:450,f_indent:222,f_int:340,f_j:29,f_jj:100,f_k:450,f_langevin:343,f_max:[305,310],f_msst:267,f_r:[253,473,474,475],f_sigma:395,f_solid:341,f_ss:6,face:[3,6,60,62,76,166,176,180,214,348,350,351,352,353,376,417,438,454,490,493],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,246,301,331,341,418,452,460,502],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,244,249,252,254,255,267,269,270,274,298,302,306,314,318,321,323,331,335,339,346,347,348,352,363,374,376,383,389,391,392,395,396,398,400,405,406,407,409,410,414,418,421,425,426,438,441,443,445,446,447,453,455,462,471,476,487,490,493,494,499,502,504,505,508,511,516,517],factori:[3,488],factoriz:373,fail:[3,9,11,12,62,182,228,231,373,382,384,407,453,488],failur:[133,457,489,517],fairli:[11,443,499,504,512],faken:78,falcon:249,fall:[3,6,206,221,301,488,517],fals:[95,354,460,517],fame:8,famili:[478,487],familiar:[0,11,512],fan:450,far:[3,6,12,17,60,62,64,95,202,203,206,207,224,225,226,228,231,269,296,314,315,331,348,359,363,380,384,385,477,488,490,495,508],farago:252,farrel:[473,475],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,224,226,231,244,246,250,266,267,269,271,272,273,274,275,276,277,286,289,290,292,293,294,304,305,307,315,320,324,330,333,341,343,347,348,349,351,353,384,421,435,493,502,517,521],fasolino:423,fast:[6,7,9,12,13,17,40,202,203,280,305,344,373,374,397,435,436,441,470,472,492,497,499,508,518,522],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,243,247,251,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,302,306,307,315,317,318,331,334,336,338,340,343,347,351,357,359,360,362,363,366,368,373,374,386,387,389,390,391,393,395,396,397,398,399,400,401,402,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,470,471,472,473,474,475,476,478,480,481,482,485,493,499,503,511],fastest:[1,6,14,17,166,343,344,389,487],fatal:[3,507],fault:[75,453],faulti:12,fava:417,favor:227,favorit:7,fbmc:338,fcc:[2,3,7,67,209],fcm:[286,517],fcold:237,fdirect:234,fdotr:422,fdt:[2,9,240,319],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[3,5],fecr:412,feedback:[7,249],feel:[7,249,250,258,296,352,354,384,443],felling:440,felt:352,femtosecond:516,fene:[2,3,7,10,45],fennel:[405,426],fep:2,ferguson:[6,184,502],fermi:[1,9,10,12,15,164,389,475],fermion:414,fernando:437,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,237,253,269,301,304,306,318,345,373,382,383,384,391,460,487,490,495,499,501,509,520],fewer:[1,3,11,15,16,64,258,499],fewest:3,fextern:242,feynman:298,fff:488,ffield:[404,415,452,453,460],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,297,373,374,499],fft_inc:[12,374],fft_lib:12,fft_path:12,fftbench:[373,509],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:469,fictiti:[6,212,213,236,242,246,298,314,405,426,430,469],field1:[491,495],field2:491,field:[2,3,5],fifth:[6,328,446],figur:[1,3,8,12,305,487,488,512],fij:408,file0:296,file1:[11,13,296,342,356,383,495,497,501],file2:[11,13,342,356,383,495,497,501],file:[2,3,4],file_from:204,filen:383,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,296,300,303,306,307,308,311,312,315,316,342,343,370,371,372,383,384,390,391,395,405,412,413,415,423,438,439,440,445,446,450,451,452,453,460,461,471,472,473,474,475,478,486,487,488,491,492,497,501,508,517,520,521,522],filennam:497,filep:[3,202,203,206,492,497,522],filepo:312,fill:[7,9,178,205,301,343,376,385,395,441,453,493,512],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,407],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,227,228,240,241,244,268,296,301,302,310,314,380,382,384,385,405,421,426,430,438,445,460,470,472,511,512,517],find_custom:8,fine:[16,17,182,212,236,341,385,389,512,517],finer:[152,178,517],finest:373,finger:[178,201,266,493],finish:[6,11,42,224,356,370,372,373,386,388,389,477,495,517,518],finit:[3,4],finni:[7,412,470],finverse:234,fiorin:[9,229],fire:[2,3,209],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,244,245,250,255,266,267,268,269,296,298,303,304,305,307,312,315,318,320,328,329,331,332,333,340,341,342,343,345,349,354,356,357,364,376,382,383,384,385,388,389,390,391,394,395,396,398,400,402,404,405,412,414,415,418,419,421,422,423,424,425,426,430,435,436,438,440,441,443,445,446,450,452,453,460,461,469,471,472,473,474,475,478,482,485,486,487,488,490,491,492,495,497,499,502,503,504,507,508,511,512,517,518,519,520,522],fischer:[6,9,19,20,184,400,502],fit:[3,6,9,12,38,57,198,240,314,331,391,395,423,438,443,445,465,472,474,498,512,517],five:[78,164,305,383,395,439,490,504],fix:[],fix_deposit:3,fix_ehex07:237,fix_flux:215,fix_heat:237,fix_id:[3,228,267,269,271,272,273,274,275,276,277,302,305],fix_manifoldforc:512,fix_modifi:[2,3,8,160,163,209],fix_nh:8,fix_nv:512,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:318,fix_reax_bond:452,fix_saed_vtk:316,fix_setforc:8,fix_shak:318,fix_srd:3,fixedpoint:[228,269],fixextern:242,fixid:215,fji:408,flag1:[233,387],flag2:[233,387],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,222,227,229,233,249,252,256,258,265,266,297,304,315,328,330,331,338,342,351,354,369,371,374,383,387,388,389,391,420,425,438,441,469,483,485,487,488,490,491,492,494,495,496,500,512,517],flag_buck:399,flag_coul:[399,408,430],flag_lj:[408,430],flagfld:[397,435,436],flaghi:[3,397,435,436],flaglog:[397,435,436],flagn:233,flagvf:[397,435,436],flat:[6,343,348,349,353],flavor:[2,7,12],fld:[348,435,436],flen:392,flex_press:392,flexibl:[3,6,8,179,205,218,229,246,270,339,346,414,474,508],flip:[3,6,230,269,350,351],floor:517,flop:12,floralwhit:206,flow:[4,5],fluctuat:[6,67,96,228,244,245,252,255,269,274,296,297,302,319,341,343,366,410],fluid:[2,7,9,10,41,70,80,87,97,104,117,128,129,158,173,175,230,247],fluid_veloc:259,flush:[3,206,507],flux:[2,3,66],flv:205,fly:[7,9,12,42,205,209,215,220,231,234,315,318,344,395,441,508,511],fmackai:9,fmag:232,fmass:298,fmax:[382,508],fmomentum:234,fmsec:[2,206,252,253,266,269,302,315,334,335,499,510,516,518],fname:372,fno:[9,16],fnorm:[382,508],fnpt:234,fnve:237,fnvt:234,foce:421,fock:392,focu:318,fogarti:[9,308,453],foil:[152,296,461],fold:[329,499],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,242,244,245,246,249,251,252,253,255,258,267,269,274,275,276,277,289,290,292,294,297,298,300,303,304,305,306,308,310,312,314,315,316,318,333,334,335,336,339,340,341,342,343,345,346,354,355,359,360,361,362,363,366,368,371,376,379,382,383,384,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,442,443,444,445,446,447,449,450,451,452,453,454,455,457,459,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,476,477,478,480,481,482,483,485,487,488,490,491,493,495,497,498,499,502,504,505,506,511,512,517,518,521],foo:[4,8,11,12,202,205,242,488,501,517],foot:6,footprint:[12,389],fopenmp:[9,16,18],forc:[2,3,5],force_uvm:17,forceatom:258,forcefield:[314,420],forcegroup:255,forcezero:380,ford:408,forestgreen:206,forev:76,forget:[253,511],forgiv:269,fork:[12,202],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,226,245,246,252,254,258,266,292,297,308,310,314,315,343,348,352,357,358,361,366,379,381,383,384,391,392,395,402,410,412,414,416,420,421,425,437,438,440,441,445,446,447,450,452,453,454,460,461,462,470,472,473,474,475,481,484,487,488,490,495,500,507,511,517],formal:[6,83,86,100,245,246,252,269,298,331,339,460],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,224,226,240,297,300,304,306,308,311,315,316,327,342,343,354,355,358,379,383,384,390,391,395,402,412,415,425,438,440,445,451,452,453,455,461,472,478,479,487,488,490,491,492,495,506,507,508,517,519,520],former:[6,12,16,40,42,206,224,343,347,395,397,496,502,517],formerli:[7,13],formul:[1,6,9,41,67,153,212,236,252,269,292,306,308,314,318,342,373,391,395,412,414,417,438,449],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,247,248,250,252,253,266,296,297,303,312,317,325,329,331,334,335,336,345,348,351,353,354,356,357,358,360,367,376,383,391,392,394,395,400,401,402,403,408,409,412,413,417,418,419,420,422,425,426,428,429,430,432,433,435,436,438,442,443,444,454,455,462,470,471,472,473,474,475,478,480,481,486,490,493,500,507,508,516,517,518],forth:[1,6,11,12,13,14,15,388,488,493,497],fortran:[3,6,9,11,12,13,242,412,421,438,452,453],fortun:8,forward:[3,8,96,372,384,389],foster:[395,449,450],foul:181,found:[3,6,9,12,78,172,202,227,229,237,244,249,255,261,297,338,344,356,372,385,402,405,408,485,491,492,507],four:[6,11,55,88,114,115,152,174,267,343,366,383,384,441,485],fourier:[2,12],fourth:[6,116,314,328,338,400,446,460],fox:[6,130,184,468,502],fphi:[38,57,472],fpic:12,fplo:[38,57,472],fprime:472,fqdn:251,fqq:408,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,225,226,227,228,267,301,305,312,313,331,336,337,376,384,389,395,397,418,435,436,495,500],fragment:[43,249,312],fraig:43,frame:[92,152,206,215,267,305,350,417],framer:[205,206],framework:[5,246,390,461],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,296,331,340,341,342,343,381,384,392,414,434,441,450,481,487],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,244,246,252,253,258,269,270,274,275,276,277,289,290,292,294,298,300,315,318,334,335,336,341,382,408,508,511,518],freeli:[0,6,7,12,156,157,171,176,205],freez:[2,3,209,214],frenkel:[6,237,244,341],freq:214,frequenc:[3,6,16,40,114,206,220,283,297,298,305,310,371,409,414,453,460,485,499,504,517,521],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,225,226,237,241,339,346,443,476,497],fri:[267,305],friction:[4,5,6,9,10,43,209,246,252,305,310,315,343,347,349,418,500],friedrich:321,from:[2,3,5],front:[267,305,350],frontend:[205,309],frozen:[6,124,182,243,245,253,385,416],fs2:[6,100],fscale:249,fstr:517,fstring:488,ftol:[382,384,485,504],fuchsia:206,fuction:405,fudg:318,fugac:244,fugacity_coeff:244,fulfil:6,full:[1,2,3,6,9,12,17,38,40,41,100,205,219,220,229,237,255,296,373,374,389,395,412,414,415,417,476,490,492,497,498,502,504,509,511,521],full_energi:[3,244],fuller:382,fulli:[3,6,83,246,251,296,382,384,405,450,451,490,512,519,520],fulton:412,fumi:396,func:[488,517],funcfl:412,functionaliri:229,fund:[0,7],fundament:[331,516],funnel_flow:327,funrol:441,further:[3,4,6,8,12,13,64,66,68,73,76,84,95,102,116,119,128,205,206,209,218,221,222,225,231,235,255,259,298,306,316,319,321,331,343,345,354,374,380,382,383,384,385,390,394,404,441,460,485,504,505,517],furthermor:[27,187,237,410,414],furthest:64,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:450,g_p:343,ga3:177,gaa:395,gahler:381,gai:[3,417,470],gain:338,gainsboro:206,galindo:442,game:249,gamma0:29,gamma:[3,6,29,252,255,259,297,305,306,308,310,347,409,410,413,417,438,442,464,467,468,471,473,475,478,508],gamma_:[3,343,349],gamma_ijk:473,gamma_n:[349,418],gamma_p:[3,343],gamma_t:[349,418],gammaa:442,gammafactor:255,gammar:442,gan:[450,471,473,475,478],gan_sw:450,gan_tersoff:450,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,184,400,502],gap:[198,435,436,451,461],gap_2014_5_8_60_17_10_38_466:451,gap_exampl:451,gaseou:7,gass:244,gather:[11,498],gather_atom:11,gather_scatter_loop_unrol:9,gathert_atom:11,gauch:190,gaug:12,gauss:[2,3,119,172,210,211],gaussian:[6,41,66,100,114,116,245,246,252,298,314,331,335,353,373,409,411,414,416,451,470,485,517,518],gave:[3,443],gaybern:[2,3,7,9,156],gcc:17,gcmc:[2,3,7,9,209,216],gcores:234,gd3:177,gdot:436,gdrudes:234,ge4:177,gec:[473,475],gen:[269,270],gener:[],genom:7,gentler:[348,351,353],gentli:413,geom:[6,373,411,485,518],geometr:[3,6,7,8,43,60,62,76,87,168,169,178,180,202,206,212,223,224,231,236,248,269,275,276,277,289,290,292,294,315,317,325,334,335,336,352,354,373,376,384,394,397,401,403,405,408,414,417,419,426,427,428,429,430,431,432,433,434,435,436,437,442,443,454,462,476,477,480,481,483,490,493,500,508,517],geometri:[3,6,7,9,13,25,39,42,59,76,87,166,178,199,224,225,226,228,231,250,319,369,376,443,490,493],georg:[7,9],georgia:13,gerar:517,gerber:434,germani:[9,14],germann:[274,428,485,504],germano:417,gerolf:13,get:[3,8,9],get_natom:[11,488],get_rank:11,get_siz:11,getenv:517,gettimeofdai:12,gewald:[6,373],gezelt:[405,426],gf100:14,gf104:14,gf200:14,gflop:12,gflp:12,gfortran:9,ghost:[3,6,7,12,16,61,64,65,78,176,181,182,228,230,253,269,304,315,316,371,373,385,389,409,410,411,414,418,425,483,495,500,511],ghostwhit:206,giacomo:9,gif:[4,205],gifsicl:205,gigabit:18,gillan:461,gingold:[464,465,467],gio:2,git:[7,12,512],github:[8,13,17,229,246,251,451],give:[0,1,2,3,4,5,6,7,8,9,10,11,12,14,15,16,17,18,55,76,101,118,125,158,161,165,178,202,203,206,212,214,218,219,221,222,228,230,246,269,292,296,297,302,310,312,315,345,373,374,382,385,386,389,391,395,411,414,420,421,438,441,443,454,473,474,475,485,487,488,490,500,504,511,518],given:[3,4,5,6,7,9,11,12,16,17,22,27,37,45,56,64,66,67,71,76,118,125,135,136,137,139,140,143,144,145,146,147,148,149,150,151,152,153,172,176,180,186,187,197,198,202,203,204,206,209,216,218,220,225,226,228,230,231,235,237,244,245,246,247,249,255,261,263,266,268,269,274,295,296,297,298,305,306,312,314,318,327,328,329,331,333,338,343,344,347,348,349,352,358,367,373,374,389,390,391,395,396,398,399,401,402,403,404,405,406,409,410,411,412,414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:[0,3,6,8,11,12,38,40,41,57,58,72,74,129,131,176,198,202,206,217,219,240,249,251,298,316,343,354,355,356,379,388,443,445,452,453,472,479,490,505,517],indianr:206,indic:[2,3,6,8,11,12,16,21,41,43,55,68,71,73,79,84,88,89,90,97,98,100,102,114,116,124,127,129,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,269,297,315,343,354,357,366,373,383,385,404,411,415,421,438,441,443,446,452,453,460,473,475,487,489,490,492,508,512,517],indigo:206,indirectli:[6,304,517],indistinguish:252,indium:461,individu:[],induc:3,industri:7,ineffici:[3,6,41,67,71,75,77,78,82,101,118,152,166,205,230,269,297,373,386],inelig:216,inerti:436,inertia:[2,3,41,43,66,91,92,93,94],inexpens:[246,499],inf:[2,3,12,346,493],infer:[3,105,107,108,172,212,213,224,225,226,236,249,300,331,339,346,376,402,415,490,502,508],infil:[3,13,315,487],infin:[3,382,495,508],infininti:205,infinit:[3,231,243,250,252,255,297,331,343,349,350,374,376,414,490,494,516],infinitesim:6,inflect:[406,428,470],influenc:[3,9,42,86,160,266,301,373,374,443,473,474,475],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,40,42,43,62,64,65,66,72,97,127,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,241,242,243,244,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,268,278,279,280,281,282,283,284,285,286,287,288,291,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,321,328,329,331,332,334,335,336,337,338,339,340,342,345,346,347,348,350,351,352,353,355,371,373,374,377,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,480,481,482,483,487,488,490,491,492,494,495,497,502,504,505,507,509,517,519,520,521,522],informat:[8,12,491],infrequ:[6,269,409,485,504],infti:[406,435,436],ingtegr:395,inher:[373,382,443],inherit:[6,476],inhomogen:[18,343,443],inidividu:382,init:[3,8,313,460],init_fil:343,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,60,62,65,76,86,88,95,96,114,115,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,244,245,249,250,251,252,253,255,260,265,266,267,268,269,274,283,285,297,298,299,304,305,310,313,314,315,317,319,330,331,333,338,340,341,342,343,344,345,348,349,350,351,353,354,356,373,377,381,382,384,391,392,408,409,411,441,445,451,452,453,460,472,485,487,488,490,492,493,495,497,498,500,504,505,508,511,517,518,520,522],initial:[2,3,6,88,114,180,517],initial_integr:8,initial_integrate_respa:8,initialis:451,initialt:343,inlclud:11,inlin:488,inner2:[400,419],inner:[3,8,16,58,202,250,356,372,380,381,382,384,388,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,479,480,481,482,483,499,504,517],inner_distance_cutoff:420,innergroup:258,innermost:[38,57,76,387,472,499],innernod:258,innner:432,inordin:344,inorgan:[6,478],inp:[229,356,461,478],input1:[69,72,74,85,103,120,125,126,127,129,131,333],input2:[69,72,74,85,103,120,125,126,127,129,131,333],input:[],input_doubl:3,inquir:321,insensit:12,insert:[3,5,7,8,9,12,62,178,209,231,244,250,301,373,461,469,488,494,511],insertion:[3,231,244,301],insid:[2,3,6,8,11,76,141,147,178,202,203,206,217,231,232,237,241,244,250,255,258,301,315,331,348,350,351,352,353,354,371,376,488,489,490,492,493,500,517],inside:[255,428,488,504],insight:[6,13],instabl:[255,408,459],instal:[1,3,6,8,9,11,12,14,15,16,17,176,202,204,205,207,374,384,389,399,400,422,426,430,434,441,485,491,492,497,505,512,522],install:8,instanc:[6,9,11,210,229,246,350,416,421,443,450,488,511],instantan:[6,66,227,228,245,246,269,274,297,302,305,310,312,315,338,496,508],instanti:[6,11,12,215,421,487],instead:[1,3,6,8,11,12,13,17,18,41,42,62,64,66,75,76,99,114,129,156,160,182,198,202,203,211,218,221,222,224,228,229,244,252,255,258,259,297,303,304,313,315,333,351,371,373,374,377,385,389,398,399,412,425,427,434,438,441,470,476,485,493,497,504,506,511,517],institut:[9,249,300],instruct:[3,4,6,8,9,10,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,121,124,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,243,247,252,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,307,315,317,318,334,336,347,351,357,359,360,362,363,366,368,374,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,471,472,473,474,475,476,478,480,481,482,493,499,511],instruction:11,insuffici:[3,6,12],insult:269,insur:[3,6,11,12,17,40,41,64,78,113,115,178,179,198,202,203,205,206,212,225,226,231,236,238,241,242,244,247,252,265,303,304,313,315,331,343,348,352,353,354,356,372,383,385,389,403,417,421,448,454,472,483,487,488,490,491,495,498,499,507,508,517,518],insure:17,int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,67,72,75,76,118,125,127,129,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,242,244,245,246,249,252,253,254,255,297,300,301,304,305,310,315,331,333,335,338,342,343,362,373,376,397,409,410,411,424,438,452,453,457,459,461,485,487,488,489,490,498,499,500,504,507,517,518],integer:[3,490],integr:[2,3,5],integral:[298,445],integrate_ulsph:322,intel:[2,3,7],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,220,245,451,490],intens:[1,3,6,9,66,70,79,80,87,95,98,99,100,104,114,115,116,117,124,126,128,129,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,241,248,258,267,269,274,312,315,316,331,339,343,345,346,507,508,516],intensiv:[66,209,508],intepol:517,inter:[14,18,43,64,65,158,181,182,202,227,252,254,268,307,315,373,384,395,500,511,517,520,522],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,58,60,64,66,69,74,77,82,85,96,97,101,103,118,119,120,122,124,127,128,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,243,244,249,250,252,254,258,283,296,298,300,301,306,308,314,315,322,323,331,332,338,343,347,348,349,352,353,358,359,360,361,363,365,367,373,374,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,447,448,449,450,453,454,455,457,459,460,461,462,469,470,471,472,473,474,475,476,477,478,479,480,481,482,485,488,490,492,494,495,499,500,502,507,508,511,520],interatom:[3,4,7,9,10,178,202,268,340,341,390,395,412,414,422,438,441,460,474,517],intercept:130,interchang:6,interconnect:18,interconvert:414,intereract:40,interesect:352,interest:[1,5,7,8,9,11,13,76,177,298,338,341,374,413,436,452,453,488,517],interf:[389,512],interfac:3,interfer:[12,269,391],interg:[6,511],intergr:[499,503],interi:436,interior:[3,6,42,352,493],interlac:438,interleav:[6,178,498],intermedi:[6,12,62,205,268,296,366,384,488,489,498,502],intermix:485,intermolecular:[154,391],intern:[2,3,5,9,16,40,41,43,66,90,110,112],internal:[3,205,211,301,517],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:251,interpenetr:438,interpentr:[464,465,467],interpol:[6,15,38,57,111,198,205,206,215,240,255,296,373,374,384,395,443,445,453,466,472,473],interpret:[2,6,11,205,221,418,462,485,488,504,517],interrupt:305,intersect:[3,6,130,206,352,354,493],intersert:352,interspers:382,interstiti:[176,441],intertia:[3,104],interv:[3,6,100,204,219,252,269,305,310,311,323,460,466,485,504,517],intestieti:130,intial:[6,389,391],intiial:[42,495],intiti:[3,330],intra:315,intra_energi:244,intramolecular:[29,154,244],introduc:[6,9,101,118,205,237,269,305,310,315,366,373,390,405,414,426,430,434,471,504,517],introduct:[],intuit:376,inv:[130,177,316],invalid:[3,12,76,98,181,283,384,435,436,492],invari:[118,145,150,152],invent:318,invers:[3,206],inverse:511,invert:[1,6,182,297],invis:352,invoc:[176,227,389,457,459,488],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,121,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,241,242,243,244,245,247,248,249,250,252,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,318,320,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,357,359,360,362,363,366,368,372,373,374,375,376,382,384,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,422,426,427,428,429,430,431,432,433,434,435,436,439,443,444,446,447,449,454,455,457,459,461,462,471,472,473,474,475,476,478,479,480,481,482,484,487,488,489,491,493,495,498,499,501,502,504,507,508,511,517,518],invokd:3,invoke:[3,12,17],involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,225,244,255,300,303,308,331,373,381,382,384,394,411,417,424,471,473,475,486,487,493,495,499,504,505],ioff:[383,490],ion:[6,7,9,160,295,328,343,374,395,406,415,416,438,441,460,470,475,482,490,511],ionic:[6,9,396,398,406,414,415,447,460,511],ioniz:[404,414],ionocoval:9,iparam:[3,226],ipi:[2,13],ipp:[],ir3:177,ir4:177,irregular:[6,42,61,224,228,230,269,315],irrelev:446,irrespect:[435,436],irrevers:234,is_act:[3,517],is_avail:[3,517],is_defin:[3,517],isbn:481,isele:[373,374],isenthalp:[9,269,270,271,272,273],ismail:[373,374,399,430],isn:[3,8,11,12,237,248],iso:[3,228,234,253,269,270,271,272,273,274,275,276,277,302,310,315,511],isobar:[9,269,270,275,276,277,319,410],isodem:414,isoenerget:[9,319,410],isoenthalp:[319,410],isol:[3,181,354],isomorph:298,isotherm:[9,244,269,270,275,276,277,302,319,410],isotop:304,isotrop:[6,101,252,302,373,374,397,417,435,436],isovolum:316,isralewitz:320,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,62,76,78,88,114,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,205,212,223,227,228,230,231,236,237,238,243,244,247,252,267,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,298,302,304,307,315,317,318,330,334,335,336,341,347,351,353,356,357,359,360,362,363,366,368,374,383,384,387,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,454,455,462,469,471,472,473,474,475,476,478,480,481,482,490,492,493,499,502,507,508,517,518],issue:215,ital:[452,453],itali:13,item:[6,7,8,42,202,206,224],iter:[3,6,12,40,42,66,204,212,213,223,224,228,234,236,242,250,285,291,297,306,307,315,318,338,354,356,372,380,381,382,384,388,460,485,495,499,504,508,517],iterat:[12,382],ith:[76,129,131,217,218,219,220,221,222,333,345,508,517],itself:[2,3,6,7,8,9,11,12,13,18,43,62,100,119,169,202,204,205,206,207,219,220,229,234,253,264,268,309,315,343,354,356,383,384,405,415,417,421,422,445,472,488,494,497,498,502,517,522],itset:500,ityp:[3,58,127,128,178,214,226,308,479],itype1:128,itype2:128,itypen:128,ivector:8,ivori:206,ixcm:315,ixi:[43,315,383],ixx:[43,104,315,383,517],ixy:[104,383,517],ixz:[43,104,315,383,517],iycm:315,iyi:[43,104,315,383,517],iyz:[43,104,315,383,517],izcm:315,izrailev:320,izumi:474,izz:[43,104,315,383,517],j0jt:100,j20:219,j_m:152,jackson:442,jacobi:3,jacobsen:381,jacs:[6,184,502],jagreat:13,jame:[9,19],janssen:296,januari:438,jaramillo:[7,9,13,414],jarzynski:320,jatempl:9,jcc:9,jcp:348,jec:13,jeff:13,jello:269,jensen:[252,373],jeremi:[9,440],jerom:9,jewett:13,jiang:[253,511],jiao:[9,13],jiht:[7,9],jik:395,jim:7,jku:[7,9],jmake:12,jmm:152,joannopoulo:267,job:[12,63,318,498],jochim:[269,270],john:[7,9,13,204],johnson:[9,13],join:[6,493],joint:[3,300,420],jon:[9,75],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,47,67,96,119,122,209,215,237,302,331,348,352,374,376,382,391,394,398,399,400,401,403,408,417,419,420,421,424,425,426,427,428,430,431,433,434,437,442,443,450,454,455,465,470,477,502,511],jonsson:[78,268,381,384,460],jorgensen:[6,195,405,426,430],joul:516,journal:[172,190,215,308,374,412,441,452,453,464,465,467],jparam:[3,226],jpeg:[3,12,205],jpeglib:12,jpg:[4,8,12,202,205,206,237,521],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:517,jtype1:128,jtype2:128,jtype:[3,58,128,226,479],jtypen:128,judg:504,judici:6,julien:9,jump:[2,356,370],june:207,just:[3,6,8,11,12,13,17,19,22,29,43,45,62,64,100,119,122,128,153,156,157,171,182,186,202,205,218,230,234,241,258,266,302,304,315,338,343,354,356,358,383,384,389,391,394,402,421,450,477,488,492,494,495,497,498,509,511,512,517,521,522],justo:413,jusufi:[406,416],jut:352,jzimmer:9,k11:100,k22:100,k33:100,k_2:361,k_4:361,k_d:511,k_sigma:395,k_ub:20,kadiri:71,kalia:478,kamberaj:315,kapfer:118,kappa:[4,6,100,319,339,405,410,426,480,481],kappa_:343,karplu:96,karttunen:255,kate:[],kayser:406,kbit:206,kboltz:331,kbp:206,kbt:310,kcal2j:100,kcal:[249,499,511,516],kde:13,ke_eta_dot:269,ke_etap_dot:269,ke_omega_dot:269,keblinski:[405,460],kecom:158,keef:130,keep:[3,7,12,62,76,196,226,230,250,261,297,313,341,346,373,382,405,434,461,485,490,496,498,504,508,512,517],keflag:3,kei:[6,17,62,331,478,504],keir:13,kelchner:75,kelkar:346,kelvin:516,kemper:[307,404],kepler30:17,kepler32:17,kepler35:17,kepler37:17,kepler:[1,9,10,12,14,15,17,389],kept:[6,209,274,340,341,511],kernel:[7,13,17,41,111,141,147,215,245,246,323,441,463,464,465,466,467,468,490,500],keword:205,keyboard:12,keyword:[3,8,12,16,17,38,40,43,57,58,61,62,64,69,72,74,76,82,85,97,103,105,107,108,113,114,119,120,121,122,126,129,131,156,157,158,166,167,171,172,176,180,181,182,198,201,202,203,204,206,207,210,211,212,213,214,216,217,218,219,220,221,222,223,225,226,229,230,231,232,234,235,236,238,240,241,242,243,244,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,297,299,300,301,302,303,304,306,307,308,309,310,311,312,313,315,316,317,320,322,323,324,325,328,330,331,332,333,334,335,336,337,338,339,342,344,345,347,349,350,351,353,354,356,371,373,374,376,377,379,380,383,385,389,392,397,411,421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priveleg:3,privileg:[11,12,249],prob:[225,226],probab:462,probabl:[3,8,12,41,76,168,181,182,184,216,224,225,226,227,231,244,253,269,301,348,354,382,443,445,472,485,504,511],probe:517,problem:2,problemat:244,proc:[1,3,8,11,12,15,125,202,203,372,487],proce:[42,55,182,224,235,384,441,497,505,508],procedur:[6,12,40,42,206,216,224,244,252,253,254,269,271,272,273,274,275,276,277,289,290,292,293,294,297,334,335,336,337,340,341,382,384,391,397,491,511],proceed:[12,441],procesor:[42,487],process:[3,4],processor:[2,3,4,7,8,9,12,13,14,15,17,18,40,41,43,61,62,64,65,66,69,72,74,76,85,103,120,125,127,128,166,176,180,181,182,201,202,203,206,209,218,225,226,230,242,246,252,253,304,307,310,315,319,331,354,370,371,372,373,377,386,387,388,389,411,448,484,485],processsor:[42,224,487],procp1:[202,203],procsessor:509,procssor:499,produc:[1,3,4,6,7,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,46,47,48,49,50,52,54,55,57,66,69,72,74,76,85,103,120,121,122,124,125,126,127,129,131,153,155,165,176,184,185,187,188,189,190,192,193,195,196,198,202,203,206,209,212,217,218,219,221,222,223,224,227,230,238,242,243,245,246,247,252,253,254,264,266,269,271,272,273,274,275,276,277,278,279,287,289,290,292,294,301,305,306,307,310,315,316,317,318,332,333,334,336,343,344,345,347,348,351,356,357,359,360,362,363,366,368,374,382,384,387,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,439,444,446,447,449,450,453,454,455,462,471,472,473,474,475,476,478,480,481,482,485,487,492,493,495,496,499,504,505,508,517,518],product:[6,16,17,18,152,176,230,292,306,344,389,392,414,453,487,517],proessor:389,prof:300,profi:167,profil:[2,3,66,156,157,158,161],program:[3,4,6,7,9,11,12,13,17,154,202,205,206,207,209,229,242,249,255,309,412,488,489,501,517],programm:[13,17],progress:[1,42,224,249,267,305,381,382,384,508,511],prohibit:500,project:[6,7,13,14,381,470,512],promis:7,promot:395,prompt:[8,11,12,249,501],proni:[3,245,246],pronounc:248,proofread:8,prop:[6,304],propag:[4,9,214,269,305,321,414,421],propens:6,proper:[227,296,438,488,512],properati:304,properli:[212,236,315,319,327,383,384,410,488,518],properti:[2,3],propoerti:331,proport:[6,40,42,96,114,115,174,224,252,253,254,305,339,346,347,418],proportion:252,propos:[6,152,216,228,244,269,292,310,426,440,474,476],prospect:7,protect:331,protein:[7,10,178,313,315,329,490,498],protocol:249,proton:[475,482,516],prototyp:[43,449],prouduc:[222,345],prove:[89,90,239,255,319],proven:292,provid:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,29,41,43,64,71,75,130,151,154,172,176,177,178,204,205,207,210,217,218,222,227,228,229,230,242,244,249,251,255,259,267,269,297,304,305,306,309,310,315,319,320,338,340,341,344,345,356,371,373,374,380,384,389,391,395,397,402,404,405,409,413,414,418,420,423,425,434,435,438,440,441,450,451,452,453,460,461,469,470,471,473,474,475,478,487,492,498,500,503,504,508,509,512,517],proxim:201,psa:351,pscreen:[3,12,499],pscrozi:[0,7,13],psec:[206,230,248,252,253,269,302,315,334,335,510,516],psend:487,pseudo:[414,485,490,495],pseudodynam:338,pseudopotenti:[9,441],psf:6,psi:[415,481],psi_ij:415,pstart:[3,269,270,274,302,315],pstop:[3,269,270,274,302,315],pstyle:[96,119,210,211],psu:[452,453],psuedo:495,pt2:177,pt4:177,ptarget:228,pthread:[12,17],ptr:[6,11,242,488],ptype1:127,ptype2:127,pu3:177,pu4:177,pu6:177,publicli:5,publish:[7,255,259,285,291,306,378,405,438,441,473,475],pull:[320,328,512],puls:343,pump:[435,436],punctuat:[2,485,504],purchas:205,purdu:[9,13],pure:[11,331,421,439,440,473,475,499],purg:[3,491],purpl:[2,206],purport:11,purpos:[3,6,7,9,12,43,64,76,130,140,146,161,162,177,178,180,182,198,202,222,227,228,252,296,298,301,303,314,331,373,389,399,424,430,441,443,477,483,490,493,497,500,502,503,517,522],push:[3,8,212,223,230,250,268,296,313,320,382,418,462,512],pushd:250,put:[3,6,8,11,12,13,40,62,166,178,202,231,235,350,351,354,376,452,488,490,494],putenv:[501,517],px1:499,px2:499,pxx:[228,269,302,315,373,374,507,508],pxy:[3,6,508],pxz:[3,6,508],py1:499,py2:499,pydir:11,pyi:[228,269,302,315,373,374,508],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[2,3,4,7],pythonpath:11,pyz:[3,6,508],pz1:499,pz2:499,pzz:[228,267,269,302,305,315,373,374,508],q_1:460,q_2:460,q_3:460,q_d:511,q_i:[415,434],q_j:434,qbmsst:[2,9],qcore:306,qdamp:306,qdist:[405,426,430,434],qeq1:306,qeq2:306,qeq:[2,3,4,7],qeqall:460,qeqallparallel:460,qfile:[306,405],qin:248,qinitmod:460,qmin:381,qmmm:2,qmol:309,qout:248,qstep:306,qtb:2,quad:[12,18,389,487],quadrat:[2,3],quadratur:[96,215],quadrupl:390,quadruplet:[194,197,199,357,359,360,361,363,365,366,367,369],qualifi:[3,251],qualiti:[7,205,206,391],quantic:460,quantit:[79,88,114,115,116,174,418],quantiti:[3,4],quantum:[6,9,152,242,246,298,305,309,310,391,395,414,441,460,470],quantum_temperatur:305,quartic:[2,3,7],quartic_spher:215,quartz:[305,310],quasi:298,quat:[3,500],quaternion:[3,6,41,91,125,142,156,157,178,271,272,275,276,279,280,281,289,290,417,490,500],quati:[125,490],quatj:[125,490],quatk:[125,490],quatw:[125,490],queen:13,quench:[354,485,504],queri:[3,11,55,286,488,517],quest:[6,242],question:[8,9,12,13,285,296,354,449,512,517],queteschin:9,quick:[0,4,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,40,101,224,230,244,249,331,381,382,384,391],quickmin:[261,285,291,380,381,382,384,504],quicktim:[4,205],quip:2,quit:[2,338,356],quot:[2,3,12,204,258,303,356,438,485,486,488,498,517],quotat:460,r10:395,r12:417,r_1:152,r_2:152,r_c:[406,408,416,475],r_cut:[395,437],r_d:511,r_e:415,r_ewald:316,r_fu:[435,436],r_i:[29,152],r_ii:152,r_ij:[29,395,414,450,482],r_ik:450,r_j:29,r_jik:450,r_m:437,r_me:406,r_mh:416,r_min:407,r_ub:20,r_x86_64_32:12,ra2:177,rad2theta:177,rad:354,radhi:493,radial:[66,76,107,108,125,128,152,162,164,169,218,254,270,282,293,328,337,382,414,420,443,445,490,493],radian:[20,21,24,28,32,35,36,38,177,185,196,198,314,357,359,363,366,490,493,500],radians:198,radiat:[130,177,343],radic:[180,490],radii:[76,81,152,227,231,403,412,417,418,435,436,441,456,458,481,493],radit:414,radiu:[2,3,41,43,66,76,81,93,94,125],radlo:493,rafferti:346,rahman:[6,7,228,267,269,270,305,449],rai:[9,17,177],ram:475,ramirez:220,ramp:[2,3,9,66,161,162,166],ran:[3,6,11],random:[3,6,40,178,181,201,205,214,216,225,226,227,229,231,241,244,245,246,252,253,254,255,265,269,298,301,305,310,313,315,319,331,335,338,343,347,350,397,409,410,411,485,500,505,511,517,518],random_se:485,randomli:[178,181,216,231,244,252,301,331,353,504,505],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,40,57,64,76,77,82,97,118,120,121,122,124,128,129,133,152,153,164,172,177,179,182,183,190,198,202,203,205,206,215,216,226,230,231,244,246,301,316,331,332,338,339,344,346,373,374,382,385,386,389,391,393,395,396,397,398,399,400,401,403,405,406,407,408,409,411,412,414,417,419,420,421,423,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,447,450,453,454,455,460,469,470,472,475,476,480,481,482,484,488,499,500,508,521],rank:[6,11,12,249,344,371,487],rankin:274,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,76,227,252,267,269,315,334,335,347,405,409],rapp:[306,307,308],rappe_and_goddard:307,rare:6,rasmol:[6,7],rasmussen:417,raster3d:[6,7],rate:[2,12,136],rather:[1,2,6,9,12,41,42,65,124,161,205,224,230,245,246,315,335,343,347,349,350,351,354,414,445,452,472,491,495,500,502,507,517],ratio:[6,62,96,112,152,216,224,230,252,254,331,339,346,347,373,387,417,418,454,464,477,487,490,500,504],rational:[344,502],rattl:[2,3,9,209,261],rattle:[3,9,209,237,246,285,291,318],rattle_debug:318,ravelo:[274,428],rayleigh:[267,305],rb1:177,rbb:460,rbg:206,rcb:[3,42,224],rcm:[98,99],rcmx:[98,99],rcmy:[98,99],rcold:237,rcut:64,rcutfac:[152,461],rd1:384,rdc:17,rdf:[2,3,66],rdn:384,rdt:384,rdx:4,reach:[6,12,42,131,220,224,226,228,253,274,324,331,338,356,372,388,406,511,517],reacquaint:512,react:6,reactant:414,reaction:[320,329,342,353,384,414],reactiv:[9,312,391],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,39,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,59,62,127,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,201,202,203,205,206,207,208,209,215,216,227,228,230,231,240,244,246,249,266,267,269,271,272,273,274,275,276,277,289,290,292,293,294,297,298,300,301,303,304,308,315,318,320,324,327,330,333,341,342,343,349,355,357,358,359,360,361,362,363,365,366,367,368,369,370,372,379,383,384,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,447,449,450,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,485,487,490,491,492,494,495,496,497,498,500,501,502,504,517,518,519,520,522],read_data:[2,3,7,8,12,22,33,34,37,39,40,41,43,45,51,53,56,59,60,61,62,65,70,76,79,80,87,88,91,104,114,115,117,127,173,176,179,180,181,186,191,194,199,200,202,226,230,266,304,342,358,365,367,369,379,383,387,388,389,392,397,402,411,421,424,449,452,453,470,477,483,487],read_dump:[2,3,202,490],read_restart:[2,3,8,9,12,13,22,37,40,41,45,56,60,61,62,65,186,209,216,229,230,231,244,266,267,271,272,273,275,276,277,289,290,292,293,294,304,315,320,330,333,349,358,367,379,392,397,402,411,421,424,449,470,477,483,487,490,491],read_restart_set:8,readabl:[203,205,383,497,522],reader:[3,13,491],readi:[11,12,179,181,182,249,500,511,520,521,522],readme:[1,4,6,8,9,10,11,12,13,176,202,203,207,309,422,441,452,453,488],real:[3,6,7,11,27,30,31,62,76,100,101,118,152,167,178,187,201,206,214,230,231,234,249,250,253,266,298,305,310,313,347,348,350,351,353,362,373,374,376,380,386,405,441,443,452,453,475,490,493,499,507,510,516,518],realist:[3,231,494],realiz:[76,209,488],realli:[1,3,8,12,124,134,153,206,250,385,421,502,512],realloc:3,realtim:249,reamin:[348,352],rearrang:[203,384],reason:[3,6,7,11,12,19,40,159,170,178,218,252,302,315,340,341,344,354,383,384,389,402,406,414,415,416,436,443,477,479,494,499,518],reax:[2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,209,306,308,311,312,421,452,453,470,502],rebal:[42,224],rebalanc:[42,224],rebo:[2,7,9,312],rebuild:[11,12,14,15,16,244,385,409,508],rebuilt:[3,12,202,203,204,205,207,385,389],recalcul:[76,96,331],receiv:[3,223,249,251,296,487],recent:[2,3,12,209,218,221,222,225,226,248,265],reciproc:[6,12,130,176,177,297,373,396,398,399,405,408,414,426,430,447,455,504],recog:12,recoginz:3,recogn:[3,12,16,78,180,225,226,269,383,412,438,452,488,490,497,498,511],recomend:6,recommend:[7,12,14,16,205,206,237,305,341,373,414,421,435,436,441,453,454,457,459,460,499,509,512],recompil:[1,3,9,12,207,318],recomput:[113,140,182,235,320,411,502],reconstruct:[3,229,460],record:[207,229,320],recov:[228,237,269],recreat:355,rectangl:[42,224,376],rectangular:[7,42,65,180,224,244,376,490,492,494],rectilinear:[130,177,203],rector:54,recurs:[42,224,395,477],recust:42,recv:487,red:[2,205,206,227,298],redefin:[3,492,498,517],redirect:12,redo:12,reduc:[2,3,12,17,18,19,66,76,97,121,122,125,126,127],reduct:[18,19,129,130,177,267,305,373],redund:415,ree:465,reed:[267,305],rees:[7,9,13],ref:[340,341,381],refactor:6,refer:[2,3,7,8,9,12,15,66,72,76,86,92,95,113,114,115,125,127,129,131,156,157,158,171,201,202,203,204,209,217,218,219,221,222,230,231,243,267,270,300,301,303,304,320,338,345,350,356,373,374,381,385,397,411,424,485,486,488,492,495,498,499,500,503,504,508],referenc:[3,6,12,66,72,76,126,131,202,203,209,219,244,304,345,374,405,420,446,454,488,508,517],reflect:[2,3,76,209,225,226,231,258,267,295,297,315,350],refman:9,reformat:7,refresh:215,reg:493,regard:[6,62,266,318,319,324,449,453],regardless:[15,76,178,181,201,221,230,252,269,271,272,273,275,276,277,302,315,325,331,389,487,493,500],regim:[6,339,346,406,499],region:[2,3,7],region_spher:8,region_styl:352,regist:[8,128,154,327],regoin:6,regress:517,regspher:178,regstrip:354,regul:6,regular:[1,3,42,65,97,176,180,202,205,216,224,244,304,343,374,406,424,487,490,492,494],reigon:517,reinhardt:[340,341],reject:[178,227,452,505],rel:[1,6,14,27,36,42,62,76,101,114,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,244,250,253,265,266,292,296,301,310,312,313,320,328,331,333,338,339,343,350,354,373,374,382,414,417,418,435,436,438,454,481,491,499,504,508,511,518],relat:[8,9,10,12],relationship:[6,240,306,356,373,460,481,511,517],relax:[2,3,4,7,209],releas:[0,5,7,8,13,225],relect:[3,443],reles:43,relev:[2,6,12,42,83,86,123,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,223,224,225,226,230,231,232,235,237,238,241,243,244,245,248,249,255,256,257,259,260,261,262,263,265,266,268,278,279,280,281,282,283,284,285,286,287,288,291,295,299,300,301,303,304,307,309,311,312,313,316,317,318,320,325,329,331,332,333,338,339,342,343,344,345,346,347,348,349,350,351,353,354,373,378,382,392,393,397,403,405,406,408,409,411,414,416,417,418,419,420,425,427,428,429,431,432,433,435,436,443,444,445,449,454,462,469,472,480,481,482,487,503,518],reli:[3,12,307,414,453,482,490,500],reloc:12,remain:[7,12,33,37,42,51,56,62,76,96,115,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,252,253,260,269,270,275,276,277,289,290,292,294,299,300,323,331,334,335,336,342,343,354,356,364,367,383,395,414,421,434,441,443,470,485,490,491,495,500,502,504,508,511,512,517,518],remaina:395,remaind:[9,178,202,231,301,331,344,475,490],remap:[3,6,12,62,64,76,161,178,201,230,250,266,292,373,490,491,492],remedi:[6,511],rememb:[2,512],remot:512,remov:[2,3,6,8,13,55,76,77,82,101,118,126,128,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,241,252,253,258,261,265,267,269,275,276,277,289,290,292,294,300,306,315,316,318,331,334,335,336,338,354,373,384,408,436,441,490,493,501,502,512,517,518],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,355,501,512],render:[12,13,202,205,206],rendon:[269,270],reneighbor:[3,8,12,40,60,76,224,244,331,344,354,409,507,508],renssela:300,renumb:76,reorder:[3,12,40,487],rep:505,repeat:[2,6,205,206,227,228,244,324,376,395,473,475,477,485,504],repeatedli:2,repel:250,repes:202,replac:[2,3,6,11,12,42,66,98,99,129,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,252,274,303,304,310,312,391,405,428,445,472,491,492,497,498,508,517,518,520,522],replic:[2,3,7,376,487,490],replica:[2,3,4],replica_fil:12,report:[],repositori:[7,9,12,422,451,452,453],reprens:343,repres:[1,3,6,8,9,12,15,41,42,43,62,71,76,99,125,128,190,198,202,203,205,218,219,220,221,222,228,234,245,247,252,255,269,298,300,302,310,315,316,320,328,343,345,352,374,384,390,395,417,424,434,435,436,438,439,440,447,450,452,453,476,477,485,487,490,500,502,505,511,517,520],represent:[3,6,8,9,60,62,146,180,202,245,246,298,343,395,414,417,441,454,490,493,511],reprocess:495,reproduc:[3,269,349,405,412,418],repul:438,repuls:[6,7,36,41,46,47,120,250,306,348,349,352,391,395,403,405,409,414,418,420,434,438,442,460,469,475,478,481,482,500],reqir:[306,308],request:[3,6,8,12,42,114,181,198,202,249,255,313,319,331,333,371,373,443,452,453,485,495,500,504,512,517,518,520],requir:[2,3,4,7,8,9],rerun:[2,3,7,77,82,128,202,443,491],rescal:[2,3,155,159,160,161,165,166,167,168,170,209,216,219,221,222,244,246,248,252,253,265,292,300,302,310,315,331,334,335],research:[5,7,89,90,239,255,259,319,441,485,504],resembl:[310,512],resepct:6,reserv:[12,249,511],reservoir:[100,237,244,248,252,343],reset:[2,3,8,12,64,70,76,79,80,87,88,104,114,115,117,173,182,209,210,211,230],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[2,491,495],resid:13,residu:249,residue1:385,resist:[6,249],resolut:[220,460,472],resolv:[228,298,331,436,512],resort:3,resourc:[7,390,412],respa:[3,16,235,249,269,387,390,391,392,393,394,395,396,397,398,399,400,401,403,404,405,406,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,447,449,451,452,453,454,455,460,461,462,463,464,465,466,467,468,469,471,472,473,474,475,477,478,480,481,482,483,498,499,510,517],respecifi:441,respect:[1,6,9,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,46,47,48,49,50,52,54,55,57,62,75,76,96,98,107,108,121,124,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,198,203,205,206,221,226,227,228,230,237,247,250,252,253,255,269,271,272,273,274,275,276,277,278,279,285,287,289,290,292,294,306,307,315,316,320,328,330,343,348,351,357,359,360,362,363,366,368,371,373,374,379,382,383,388,389,390,391,393,395,396,397,398,399,400,401,403,404,405,408,409,412,413,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,438,439,441,443,444,446,447,449,454,455,459,460,461,462,471,472,473,474,475,476,478,480,481,482,487,491,500,503,511,517,519,520,522],respon:9,respond:[6,7,161,230,414,449],respons:[6,7,267,339,346],resquar:[2,3,7,9],rest:[6,8,12,39,59,199,304,308,314,369,395,436,438,483,507,508,511],restart1:298,restart2:298,restart2data:12,restart:[2,3],restartfil:[12,13],restor:[3,8,63,64,114,178,210,211,304,320,328,333,355,507,508],restore_bia:8,restore_bias_al:8,restrain:[2,3,209,216,244,267],restraint:[9,229,267,314,330,425],restratin:314,restrict:[2,3,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,46,47,48,49,50,52,54,55,57,66,67,70,71,76,80,87,96,99,100,104,114,115,117,121,122,124,126,127,128,129,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,198,201,202,203,205,206,209,212,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,234,237,238,240,243,244,245,247,252,253,255,259,267,269,271,272,273,274,275,276,277,278,279,287,289,290,292,293,294,297,298,306,307,312,313,315,317,318,331,334,336,339,340,341,343,344,345,347,348,349,351,353,356,357,359,360,362,363,366,368,373,374,384,387,389,390,391,393,396,397,398,399,400,401,403,404,405,408,409,412,413,414,415,416,417,418,419,420,421,426,427,428,429,430,431,432,433,434,435,436,438,439,441,443,444,445,446,447,449,453,454,455,462,471,472,473,474,475,476,478,480,481,482,485,487,490,492,493,494,495,499,500,501,502,504,516,517,518],resum:517,retain:[2,225,226,391,395,441,487],retart:[33,51,191,364],retir:[3,452],retreiv:8,retriev:[6,8,242,439,440,517],reus:[3,502],rev:[6,13,67,75,101,118,122,152,153,166,216,246,252,254,267,269,270,274,292,297,307,310,315,320,331,335,338,340,341,346,381,395,403,404,405,408,412,413,414,417,418,423,428,435,436,437,438,440,445,450,454,461,471,473,474,475,478,485],revers:[2,6,8,96,189,227,250,269,295,296,306,324,339,340,346,384,434,499,511],review:[152,306,320,338,441,451,461,485,504,511,512],rewind:372,rewrap:202,rewrit:[5,12],rewritten:19,rezwanur:449,rfac0:[152,461],rfactor:331,rfile:315,rg0:329,rgb:206,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[445,472],rho0:[438,457,459,467,468],rho0_meam:438,rho:[2,3,41],rho_0:[467,468],rho_alpha_beta:412,rho_bkgd:438,rho_colloid:348,rho_e:343,rho_fin:342,rho_i:[439,440],rho_initi:342,rho_ref_meam:438,rho_wal:348,rhodo:[9,10],rhodopsin:[1,10],rhohi:301,rholo:301,rhosum:[2,111,463,465],rhot:237,ribier:381,richard:9,richardson:315,richi:[9,19],rick:[306,307,404,460],rick_and_stuart:307,ridg:[9,19],right:[3,6,11,12,42,154,178,196,197,201,203,224,227,250,255,266,295,356,376,405,490,493,500,512,517],rightmost:[42,224],rigid:[2,3,4],rigidifi:315,rii:[98,99],rij:[101,118,225,226,296,409,410,445,469],rin:[420,431,432],ring:[2,3,128,300],rino:[78,478],rinv:373,rirj:[349,418],risi:[152,461],risk:[8,314,499],rix:[98,99],rjk:[225,226],rjone:[7,9,13],rlo:[445,472],rmask:[3,517],rmass:[3,304],rmax:[76,179,225],rmdir:501,rmin0:[152,461],rmin:[76,179,226,428],rms:[373,374],rmsd:342,rnemd:6,robert:9,robin:206,robust:[380,381,382],rock:438,rockett:450,rod:315,rodata:12,rodnei:310,roi:7,role:[6,338],roll:12,ronchetti:118,room:[60,62],root:[11,96,98,99,204,338,342,389,412,497],rosati:40,rose:438,ross:438,rosski:298,rosybrown:206,rot:[6,100,298,314,338,518],rotat:[2,3,4,7,9,41,6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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 &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","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":225,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,241,244,245,250,252,253,254,255,256,258,264,267,269,270,274,292,293,297,298,301,302,303,304,305,307,310,312,313,315,316,331,333,338,339,340,341,344,346,348,350,354,367,371,373,374,376,377,380,381,383,385,386,387,389,392,395,397,414,435,436,441,443,452,453,469,470,485,486,487,490,491,493,495,497,498,499,502,504,506,507,508,509,510,516,518,520,521],"function":517,"long":[220,396,398,399,400,401,405,407,408,426,430,434,447,455,476],"new":8,"static":12,acceler:1,account:512,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,adding:512,addition:[12,13,512],addtorqu:213,adiabat:6,adjust_dt:321,adp:390,after:512,airebo:391,alloi:412,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,91,156,271,275,279,280,289],asphere:9,atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,304,517],atom_modifi:40,atom_styl:41,attract:5,aveforc:223,awpmd:[9,392],balanc:[42,224],barostat:6,basal:71,beck:393,berendsen:[302,334],between:6,binary2txt:13,bodi:[6,8,43,72,157,272,276,281,290,394],body:9,bond:[8,13,73,74,225,226,227,311],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:395,born:[396,407],boundari:[7,60],box:[6,61,228],branch:512,brownian:397,buck:[398,399,407,437],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:512,change_box:62,charmm:[6,20,184,400,434],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,357,401],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,348,403,481],colvar:[13,229],colvars:9,com:[79,80,159],comb3:404,comb:[307,404],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,517],compute_modifi:113,condit:7,conduct:[6,339],constant:[6,517],constraint:7,contact:[81,132],coord:82,core:6,coreshell:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:359,coul:[396,398,399,400,401,405,406,407,419,426,430,434,447,455],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:335,csvr:335,cubic:428,cuda:[9,14,121,124,155,165,212,223,238,243,247,269,278,317,318,334,336,347,396,398,400,401,412,418,419,426,427,429,432,444,471,473],custom:[8,202,203],cut:[50,392,398,401,405,408,414,416,426,427,434,442,447,476],cvff:360,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[405,426],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:24,deposit:231,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],diagnost:7,diel:406,dielectr:183,diffraction:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,29,87,408],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:361,distribut:[7,12],document:0,dpd:[9,89,90,409,410],drag:232,dreid:420,dreiding:6,drude:[6,9,163,233,234,253],dsf:[405,426],dsmc:411,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:306,eam:[13,412],echo:208,edip:413,eff:[9,13,107,108,162,164,169,254,270,282,293,337,414],efield:236,ehex:237,eim:415,elastic:6,emac:13,energi:[135,410],enforce2d:238,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:241,event:95,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,327,328,329,330,331,332,333,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,513,514,515,516,517,518,519,520,521,522],exp:[27,187],expand:[47,429],extend:[8,11],extern:242,fcc:296,fdt:410,featur:[7,8,512,517],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:306,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235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