From bcaafc27e6eacc87b5dd53e49c4a30c69eb85614 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 18 Aug 2015 23:22:43 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13894 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.txt | 6 +++--- doc/compute_xrd.html | 6 +++--- doc/compute_xrd.txt | 4 ++-- doc/fix_ave_chunk.html | 6 ++++++ doc/fix_ave_chunk.txt | 7 +++++++ doc/fix_ave_time.html | 10 ++++++++-- doc/fix_ave_time.txt | 11 +++++++++-- doc/searchindex.js | 2 +- 8 files changed, 39 insertions(+), 13 deletions(-) diff --git a/doc/Manual.txt b/doc/Manual.txt index f47482fdf2..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index e12b3c68fa..ab52cca0c1 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -159,15 +159,15 @@ compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual -
fix 1 all ave/histo/weights 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
-fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+
fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd

Description

Define a computation that calculates x-ray diffraction intensity as described -in (Coleman) on a mesh of reciprocal lattice nodes defined +in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using a simulated radiation of wavelength lambda.

The x-ray diffraction intensity, I, at each reciprocal lattice point, k, diff --git a/doc/compute_xrd.txt b/doc/compute_xrd.txt index 49d5a5d2fe..a59f2201db 100644 --- a/doc/compute_xrd.txt +++ b/doc/compute_xrd.txt @@ -37,8 +37,8 @@ keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre -fix 1 all ave/histo/weights 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd -fix 2 all ave/histo/weights 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre +fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd +fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file Deg2Theta.xrd :pre :pre diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html index bd87b28572..1cc86e2d26 100644 --- a/doc/fix_ave_chunk.html +++ b/doc/fix_ave_chunk.html @@ -173,6 +173,8 @@ v_name = per-atom vector calculated by an atom-style variable with name file arg = filename filename = file to write results to overwrite arg = none = overwrite output file with only latest output +format arg = string + string = C-style format string title1 arg = string string = text to print as 1st line of output file title2 arg = string @@ -437,6 +439,10 @@ quantities, as explained above.

The overwrite keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the ave running setting.

+

The format keyword sets the numeric format of each value when it is +printed to a file via the file keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g.

The title1 and title2 and title3 keywords allow specification of the strings that will be printed as the first 3 lines of the output file, assuming the file keyword was used. LAMMPS uses default diff --git a/doc/fix_ave_chunk.txt b/doc/fix_ave_chunk.txt index a8cdbe0fa8..7ba5269539 100644 --- a/doc/fix_ave_chunk.txt +++ b/doc/fix_ave_chunk.txt @@ -48,6 +48,8 @@ keyword = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite} {file} arg = filename filename = file to write results to {overwrite} arg = none = overwrite output file with only latest output + {format} arg = string + string = C-style format string {title1} arg = string string = text to print as 1st line of output file {title2} arg = string @@ -357,6 +359,11 @@ The {overwrite} keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the {ave running} setting. +The {format} keyword sets the numeric format of each value when it is +printed to a file via the {file} keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g. + The {title1} and {title2} and {title3} keywords allow specification of the strings that will be printed as the first 3 lines of the output file, assuming the {file} keyword was used. LAMMPS uses default diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 8beb62f4da..6194c9f630 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -166,6 +166,8 @@ v_name = global value calculated by an equal-style variable with name file arg = filename filename = name of file to output time averages to overwrite arg = none = overwrite output file with only latest output +format arg = string + string = C-style format string title1 arg = string string = text to print as 1st line of output file title2 arg = string @@ -336,6 +338,10 @@ array sections.

The overwrite keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the ave running setting.

+

The format keyword sets the numeric format of each value when it is +printed to a file via the file keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g.

The title1 and title2 and title3 keywords allow specification of the strings that will be printed as the first 2 or 3 lines of the output file, assuming the file keyword was used. LAMMPS uses @@ -403,8 +409,8 @@ the run command. Thi

Default

The option defaults are mode = scalar, ave = one, start = 0, no file -output, title 1,2,3 = strings as described above, and no off settings -for any input values.

+output, format = %g, title 1,2,3 = strings as described above, and no +off settings for any input values.

diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 26fc0bc0b0..a750c6929b 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -41,6 +41,8 @@ keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title {file} arg = filename filename = name of file to output time averages to {overwrite} arg = none = overwrite output file with only latest output + {format} arg = string + string = C-style format string {title1} arg = string string = text to print as 1st line of output file {title2} arg = string @@ -240,6 +242,11 @@ The {overwrite} keyword will continuously overwrite the output file with the latest output, so that it only contains one timestep worth of output. This option can only be used with the {ave running} setting. +The {format} keyword sets the numeric format of each value when it is +printed to a file via the {file} keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g. + The {title1} and {title2} and {title3} keywords allow specification of the strings that will be printed as the first 2 or 3 lines of the output file, assuming the {file} keyword was used. LAMMPS uses @@ -315,5 +322,5 @@ ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html, [Default:] The option defaults are mode = scalar, ave = one, start = 0, no file -output, title 1,2,3 = strings as described above, and no off settings -for any input values. +output, format = %g, title 1,2,3 = strings as described above, and no +off settings for any input values. diff --git a/doc/searchindex.js b/doc/searchindex.js index aca8ccd577..c6df5a253a 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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64,189,199,211,214,225,312,370,400,462,469],acceptor:390,access:[0,3,6,7,8,9,11,12,16,40,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,85,88,89,90,91,92,93,95,96,99,100,101,103,104,105,106,107,108,110,111,112,113,114,115,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,156,157,159,160,161,162,163,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,219,220,221,222,223,224,225,226,227,228,229,230,231,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,253,256,257,258,259,260,261,262,263,264,265,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,299,302,303,304,305,306,307,308,309,310,311,313,314,315,316,317,319,320,321,322,323,324,325,326,327,345,360,386,388,390,391,407,419,420,428,451,452,455,460,472,479],accidenti:339,accler:16,accommod:197,accomod:249,accompani:8,accomplish:[16,214,237,263],accord:[64,71,121,127,130,188,199,209,210,236,249,272,280,294,296,314,315,317,322,323,325,326,327,356,360,384,388,399,402,417,424,426,428,430,431,433,434,435,463,468,479],accordingli:[11,14,143,157,168,356,405,406],account:[3,6,9,87,118,162,163,172,183,202,203,219,230,231,233,249,254,255,266,267,269,271,275,281,290,291,293,302,303,304,305,308,309,310,313,317,320,335,354,376,388,396,400,405,406,407,451,468,480],accuml:[3,290,313,320],accumul:[1,6,8,15,71,192,202,233,290,294,319,343,360,460,478],accur:[1,3,6,15,17,38,41,56,147,208,247,285,290,293,305,313,320,326,328,346,366,384,387,388,411,421,436,438,439,441,468,479],accuraci:[1,3,6,12,41,187,189,208,227,249,282,293,318,328,345,346,352,384,411,419,420,438,444,463,468,474,479,482],ach:345,achiev:[1,3,6,16,17,18,41,208,227,249,250,272,273,280,345,391,463],achiv:18,acid:9,ackland1:382,ackland2:382,ackland:[],acknowledg:[],acml:12,aco:479,acolor:[188,189],acoust:272,acquir:[3,6,58,61,62,167,210,212,214,249,415,459,474],across:[1,2,3,6,9,12,13,15,41,57,61,65,68,69,71,79,92,107,108,115,117,152,166,168,201,203,204,205,208,219,229,290,291,295,313,317,320,326,330,355,360,449,454,457,458,462,471],act:[3,6,108,149,218,228,231,232,233,234,236,239,248,290,299,312,314,315,317,326,327,328,353,368,379,387,388,390,421,435],acta:[118,163,361],action:[2,6,11,12,71,226,231,315,474],activ:[5,8,11,12,13,14,55,59,87,162,199,213,226,230,233,239,248,270,290,297,316,343,404,436,448,476,479],actual:[1,3,6,8,12,56,62,122,147,187,189,193,194,207,209,210,218,233,234,267,271,277,285,294,305,307,308,309,310,312,318,327,328,345,356,387,389,399,405,406,451,452,463,464,472,479],adam:[345,346],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,40,42,71,87,91,102,114,117,119,162,164,165,187,188,192,193,194,195,196,198,200,201,202,203,204,205,206,210,213,218,220,223,227,228,229,231,233,235,236,240,247,248,249,250,251,252,253,254,255,266,267,268,269,271,279,289,290,292,293,302,304,308,310,311,315,316,317,319,321,322,326,328,346,348,352,354,362,367,369,372,376,384,391,396,407,411,414,420,422,452,454,455,460,462,464,466,474],add_molecul:198,add_speci:198,add_to_nodeset:198,addforc:[],addit:[],addition:[6,8,16,139,305,327,387,421],address:[7,8,11,188,232],addtorqu:[],adequ:[305,318,345,355,463],adher:29,adhikari:236,adiabat:[],adiam:[188,189],adjac:[39,164,355,411,438,439,468,469],adjiman:410,adjust:[2,3,6,16,17,41,59,118,143,144,147,148,151,152,157,158,163,168,187,188,201,208,212,214,230,233,237,241,245,246,249,250,253,267,271,274,276,277,280,281,282,283,288,290,297,305,309,313,318,320,321,322,324,325,327,345,346,353,355,360,362,381,405,406,441,464,480],adjust_dt:128,adjust_radiu:297,adjust_radius_factor:297,admiss:253,adof:[144,201],adopt:[289,474],adp:[],adri:[9,286,419,420],adust:158,advanc:[3,230,366,449,460],advantag:[1,6,8,11,14,18,39,40,41,208,360,383,463,468],advect:[3,6,305],advertis:8,advis:[355,418],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,88,117,141,148,162,168,189,194,201,202,203,204,205,206,209,210,211,212,214,215,223,229,231,233,239,246,250,251,252,254,255,261,266,267,269,290,291,303,317,327,339,345,351,352,353,355,356,357,360,384,405,406,411,451,452,454,457,459,462,464],affin:[16,17,18,214,360,375],afil:227,aforement:18,afresh:[278,462,479],afshar:380,after:[2,3,5,6,8,9,11,12,15,16,21,22,33,39,40,41,44,50,57,58,59,61,63,71,143,144,145,146,147,148,151,152,153,154,156,157,164,165,167,168,171,172,177,186,187,188,189,190,192,193,194,198,199,201,202,208,209,210,211,212,214,218,225,236,237,238,239,240,245,246,247,249,254,255,261,266,267,269,272,276,280,288,290,293,301,306,308,309,310,312,313,314,315,316,320,322,324,328,331,332,337,344,350,351,353,354,356,358,359,360,361,362,366,373,375,382,383,384,385,391,392,393,404,405,406,407,408,409,413,417,419,420,427,437,439,440,441,449,451,453,454,455,456,457,459,460,462,464,466,468,471,472,474,478,479,480,481,482,483],afterrun:462,afterward:3,afterword:41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,189,214,229,276,331,344,355,405,406,449,451,452,454,456,461,468,470,479,481],against:[11,12,13,64,215,355,419,420],aggreg:[6,12,65,68,69,79,92,108,115,229,245,288,290,303,449,480],aggress:[229,468],agilio:[9,13],agre:[3,8,184,353,362,393,420],agreement:[5,7],ahd:390,ahead:324,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:188,akohlmei:[7,9,13,190,230],aktulga:[7,9,283,420],al2o3_001:[118,291],al3:163,ala:236,alain:9,alat:[271,407],alb:[417,439,441],albeit:289,albert:9,alchem:[87,158],alcohol:320,alcu:[361,366],alcu_eam:417,alderton:379,alejandr:[249,250],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,189,198,208,211,214,236,238,239,261,273,290,293,312,313,317,320,325,351,352,353,357,360,384,406,424,426,449,451,468],alia:12,alias:[1,346],aliceblu:189,align:[6,12,29,41,71,166,184,204,208,231,348,454,457,474],alkali:384,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,242,244,245,247,249,250,251,252,253,254,255,256,257,258,259,260,261,262,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,301,302,304,305,306,307,308,309,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,331,332,335,340,343,344,345,346,347,348,350,353,354,355,356,357,359,360,361,362,363,365,366,367,369,370,371,372,373,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,451,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,471,472,474,478,479,480,481,482,483],allen:[29,87,379,387],allentildeslei:87,allign:3,allindex:329,alloc:[3,5,6,8,9,11,12,60,223,319,354,356,360,415,420,454,462],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,188,189,190,192,193,195,197,198,199,201,202,203,204,205,206,208,210,211,212,213,214,215,219,220,223,225,226,227,228,230,233,236,239,240,244,246,249,250,271,275,277,278,279,280,284,290,291,293,294,296,297,301,305,312,313,314,315,317,318,319,320,321,322,328,330,332,340,345,346,348,353,354,355,356,359,360,363,366,367,368,369,370,371,376,382,384,388,389,390,391,400,405,406,411,417,420,421,424,426,435,444,446,449,452,454,456,457,458,459,460,461,464,466,467,468,471,472,479,480],almost:[2,3,12,60,231,280,317,346,357,360,435],alo:376,alon:[6,7,211,286,419,420,452],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,188,211,231,236,237,241,246,248,280,290,293,294,298,302,303,312,316,317,323,326,328,348,351,352,353,355,376,379,388,391,394,396,400,407,419,420,438,454,457,464,465,479],alonso:[408,409],alpha:[6,51,193,236,272,280,285,353,361,364,367,376,380,382,383,385,390,395,396,407,412,416,440,442,472,474],alpha_:442,alpha_c:404,alpha_i:[427,442],alpha_ialpha_j:442,alpha_lj:404,alphabet:[2,3,22,37,44,55,63,172,183,192,332,340,354,373,436,454],alphanumer:[3,63,192,279,287,330,354,479],alreadi:[3,7,8,12,42,164,165,167,197,201,204,205,208,210,214,240,278,280,305,328,354,355,380,389,391,398,406,435,444,447,450,454,455,459,464,479],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,192,193,194,195,197,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,220,223,224,225,226,227,229,230,233,234,235,236,246,247,249,250,251,252,253,254,255,260,263,264,266,267,268,269,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,298,299,302,303,305,308,309,310,311,312,316,317,318,319,321,323,326,328,330,332,337,340,343,345,346,348,349,350,353,354,355,356,357,359,360,366,370,371,373,377,378,379,380,382,383,384,387,388,390,391,392,400,404,405,407,411,413,415,416,417,418,421,422,424,430,431,433,434,435,436,437,438,439,440,441,442,449,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,472,473,474,475,477,478,479,480,481,483],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,157,164,168,187,188,190,193,194,201,209,210,211,212,214,248,249,285,288,290,292,299,305,313,320,327,352,355,391,454,459,461,464,479,480,483],alter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70,76,77,116,122,140,239,271,293,303,354,413,419,420,454],centro:[],centroid:[3,273,443,464],cerda:345,ceriotti2:227,ceriotti:[13,227,232],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,188,200,201,202,203,204,205,206,211,223,224,290,292,306,319,330,337,344,356,391,411,420,442,456,460,474,479],certainli:231,cerutti:346,cfg:[3,6,7,13,187,188,189,190],cfile:420,cfl:[128,295],cfor:294,cg_type:422,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:293,ch2lmp:[],ch3:293,chain3:356,chain:[],challeng:[6,294],chalopin:285,champaign:[230,345,346,405],chandler:[361,382],chandrasekhar:[6,396],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,192,193,194,195,196,198,199,204,205,207,208,209,210,211,212,213,214,215,219,220,222,224,227,229,230,231,233,235,236,237,239,245,246,247,249,250,251,252,253,254,255,261,266,267,268,269,271,272,276,277,279,280,284,287,288,289,290,292,293,294,305,308,309,310,311,313,314,315,316,317,318,320,323,326,328,346,351,353,355,358,360,380,384,388,391,405,406,407,411,419,420,436,449,450,451,452,454,455,456,457,458,459,460,462,463,464,465,466,469,472,475,477,478,479,480,481],change_box:[],changeabl:187,channel:[4,195],chapter:[273,346],charact:[2,3,6,12,38,41,56,63,184,187,188,189,190,192,208,279,287,330,354,359,384,395,417,419,420,438,451,452,456,461,462,479,481,482,483],character:[6,67,70,116,140,427,449,468],characterist:[234,305,314],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,190,192,193,194,199,215,220,225,279,281,282,283,287,307,320,345,346,354,367,369,375,376,378,379,382,384,385,391,396,400,404,414,419,420,436,441,442,444,446,447,454,455,459,464,466,474,478,479],charmm2lammp:13,charmm:[],chartreus:189,cheap:305,cheaper:[219,387,421],check:[3,6,8,11,12,15,17,39,41,71,91,184,199,204,208,209,210,215,222,225,231,232,289,293,305,313,315,320,328,330,344,353,354,355,356,357,360,381,392,395,411,420,435,449,451,452,454,462,468,471,472],checkf:184,checkqeq:420,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,213,218,226,227,234,236,248,249,250,267,268,273,277,280,282,290,294,305,308,309,312,313,314,315,322,331,339,341,345,346,352,355,362,367,371,372,375,376,377,379,380,384,386,387,389,390,396,400,401,404,407,410,411,414,435,442,463,466,468,474],chemic:[9,118,158,163,187,198,199,225,281,286,287,312,346,419,420,431],chemistri:[9,280,281,283,366,384,419,420],chen:317,cheng:375,chenoweth:[419,420],chenoweth_2008:[419,420],chi:[92,153,186,271,281,283,385,387,480],chiefli:418,child:8,chip:[7,12,17,360,467],chipot:213,chiral:339,chmod:[11,12],cho:407,chocol:[7,189],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,201,204,205,208,211,214,215,227,233,236,247,249,273,281,290,312,340,346,351,352,355,357,360,391,404,411,415,454,463,464,467,468,473,474,478],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,188,209,210,211,212,215,222,233,236,247,249,251,252,253,254,255,277,305,309,323,345,346,352,444,449,451,463,469],chose:[439,441],chosen:[2,3,6,12,17,140,164,167,176,184,188,194,199,212,215,222,225,226,234,236,247,249,253,273,276,287,305,309,312,313,318,320,321,327,346,347,352,360,384,388,394,395,398,422,439,449,463,468,474],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,201],chute:[4,10,228],ciccotti:293,cieplak:[6,170,466],cii:202,cij:202,circl:301,circular:[3,6,143,185],circumst:18,circumv:285,citat:[],cite:[3,7,8,12,233],cko:2,cl1:163,clarendon:[29,379],clarifi:[7,439,441],clariti:330,clark:414,class2:[],classic:[0,3,5,6,7,8,9,223,273,280,285,317,341,384],classifi:[9,436],claus:452,clean:[6,12,14,15,17,462],cleanli:[453,482],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:458,click:[2,11,22,37,44,55,164,172,183,188,230,332,340,355,373,436],client:[230,232],climb:[248,355,468],clinic:[7,13],clo:[153,186,480],clock:[12,449,468],clockwis:323,close:[3,6,11,12,13,39,41,67,141,167,187,210,211,212,227,234,236,249,267,290,293,323,326,344,346,349,351,352,355,360,362,366,376,377,407,411,423,425,441,458,464,474,476],closer:[3,41,116,162,186,187,208,212,216,314,355],closest:[210,271,290,320,387,421,435,444],cloud:474,clovertown:18,clsuter:72,clump1:[275,290],clump2:[275,290],clump3:[275,290],clump:290,cluster:[],clutter:[3,9],cmap:454,cmatrix:227,cmax:407,cmd:[11,12,273,465],cmin:407,cmm:[],cn1:202,cn2:202,cna:[],cnn:202,cnr:[9,13],cnt:[391,458],co2:[40,163,293,354],coars:[7,9,29,36,40,54,176,275,290,305,389,422,466],coarser:[346,479],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,331,332,337,373,391,395,411,424,426,428,454,456],coeffcient:454,coeffici:[],coefficienct:380,coefficient0:382,coefficient1:382,coeffieci:[6,364],coeffincientn:382,coexist:[9,225,384],cohes:[6,385,407],coincid:[122,326,371,405,406,449],cold:[6,149,229,356,474],coldest:313,coleman8:9,coleman:[9,118,163,291],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,189,201,213,239,245,275,285,288,290,328,345,354,356,374,394,454,461,467,483],collid:[219,305,327],colliex:163,collinear:[3,275],collis:[3,236,305,323,327,381,388,447],colllis:305,colloid:[],colombo:39,colon:[190,328,455],color1:189,color2:189,color:[3,9,41,187,188,189,208,226,280,285],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,189,192,200,201,202,203,204,205,206,239,246,247,280,290,306,307,317,327,386,390,419,420,455,469,471,479],colvar:[],colvarmodul:12,com:[],comamnd:214,comand:[211,456],comannd:360,comb3:[],comb:[],comb_1:282,comb_2:282,combiant:377,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,188,198,203,230,239,249,273,279,309,318,326,329,331,345,346,348,352,360,374,376,377,384,385,391,403,404,427,437,439,441,446,457,462,474,479],come:[],comfort:[12,13],comm:[0,3,12,61,73,230,232,233,346,355,360,380,411,416,438],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,234,290,317,354,355,361,382,383,385,395,407,413,420,427,437,438,439,440,441,451,452,454,474,479],commerci:7,commmand:[3,6,12,59,107,268,448,449,451,468,482],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,188,190,341,389,398,427,439,441,454,457,466],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,188,189,208,209,210,212,213,214,230,232,236,238,239,240,249,272,279,281,282,283,290,305,317,328,345,356,357,358,360,381,415,451,452,456,463,464,481,483],communc:345,comp:[7,232,233,293,346,355,384,411,416,421,434,438,440],compact:[63,192,373,436],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,189,218,281,328,330,345,346,353,355,407,449,468,469,474,478],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,331,332,340,372,436],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,190,194,200,201,202,203,204,205,206,208,272,284,309,312,319,322,325,345,360,392,411,438,451,452,479],compens:[6,209,210,288,356,384],compet:316,competit:346,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,190,230,316,346,360,454,455,459],compl:17,complain:[12,17],complement:407,complementari:[7,376,396],complet:[3,6,9,12,15,41,59,71,189,204,208,213,239,273,276,279,305,316,318,330,344,355,360,385,424,426,443,449,454,459,462,466,468,471,474,479],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,236,301,326,343,355,384,438,452,454,457,479],compli:[312,316],complic:[6,7,9,12,13,199,225,452],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,188,189,195,196,200,201,202,203,204,205,206,207,211,212,214,215,220,223,228,232,233,236,239,241,245,246,248,249,250,253,254,255,266,267,269,270,272,273,274,277,288,290,292,293,294,298,299,302,305,308,309,310,312,319,320,325,326,327,345,348,352,353,354,355,360,380,384,388,405,406,424,426,427,454,455,464,472,479,480],componenet:6,composit:[6,199,236,382],compound:[375,384,385],compres:[71,114,201],compress:[3,6,59,71,114,167,187,188,189,201,214,247,253,277,280],compris:[40,326,394,421,443],compton:[118,163],comptu:[3,6],compuat:346,comput:[],computation:[3,6,209,210,317,366],computational:474,compute_arrai:8,compute_fep:[194,404],compute_group_group:225,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,291],compute_scalar:8,compute_temp:8,compute_ti:194,compute_vector:8,compute_xrd:163,concaten:[2,3,482],concav:326,concentr:382,concept:[6,144,154,201,463],conceptu:[3,6,71,152,212,214,355,376,391,407,459],concern:[6,73,87,226],concis:[11,316],conclud:12,concret:8,concurr:[9,16,346],conden:[317,439,441],condens:[6,146,317,362,378,382,396],condit:[],conducit:6,conduct:[],cone:457,confid:[3,468],config:[12,187,451],configfil:213,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,188,192,212,213,214,215,219,225,232,233,261,273,281,316,343,353,355,362,366,383,407,437,439,441,449,454,456,457,468],confin:[454,468],conflict:[3,40,411,452],conform:[3,6,13,59,211,212,248,289,294,316,339,355,384,466],confus:3,conjuct:380,conjug:[7,8,233,352,384,419,420],conjunct:[6,7,71,86,87,114,147,152,158,164,168,189,193,194,233,236,240,261,276,277,281,282,283,285,290,305,313,320,325,345,346,355,367,369,373,376,380,384,390,396,411,414,422,442,454,457,461,474,483],connect:[3,6,87,149,167,211,230,275,290,293,302,355,377,388,435,441,451,452,458,474],conput:3,consecut:[3,11,12,39,71,164,189,193,194,215,230,231,376,396,400,449,455,457],consequ:[1,6,317,395,468],conserv:[3,192,199,211,218,219,226,229,233,235,236,240,245,247,249,261,290,293,308,309,313,320,321,325,355,379,380,388,402,463,468],consid:[6,9,70,71,78,87,115,149,150,167,187,189,193,194,200,202,204,208,210,211,215,237,250,272,290,312,313,316,317,320,346,373,384,391,420,421,435,449,450,452,455,456,457,459,462,464,472,474,479],consider:[6,8,233,234,308,309,310,360,463],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,190,195,196,201,214,215,218,220,223,226,233,234,235,246,249,251,252,253,254,255,256,257,259,260,261,262,264,265,266,267,268,269,277,280,285,287,289,290,308,309,310,311,321,345,346,348,354,355,360,362,366,368,374,376,384,387,391,405,406,407,411,421,424,426,438,444,452,454,455,457,458,459,466,474,479],consistent_fe_initi:198,consit:290,constant:[],constitu:[3,6,239,290,322,326,374,421],constitut:[424,426],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,192,201,215,225,226,231,239,243,275,276,288,290,293,303,313,320,353,354,384,459,466,474],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,140,163,212,249,272,289,326,356,360,379,411,435,437,438,457,458,479],constructor:8,consult:420,consum:[1,285,415,479],consumpt:343,contact:[],contact_stiff:[423,425],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,188,189,190,192,193,194,198,200,201,202,203,204,205,206,208,213,215,220,227,231,232,233,234,236,247,261,271,272,275,276,278,280,283,287,290,291,295,305,312,316,317,326,327,330,344,346,354,355,358,359,361,362,363,366,375,376,379,382,383,384,391,392,407,413,417,418,419,420,427,437,438,439,440,441,442,449,450,451,452,454,455,456,457,459,461,463,466,468,471,472,474,479,481,483],content:[12,18,420,470,472],context:[3,6,8,12,17,117,189,209,210,215,275,287,321,352,446,454,461,470,478,479,480],contibut:70,contigu:451,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,189,192,193,194,199,201,202,203,204,205,206,208,211,212,213,214,215,225,226,227,229,230,231,233,234,235,241,246,247,249,251,252,253,254,255,266,267,268,269,274,276,279,280,290,291,294,304,305,307,314,315,317,323,326,330,344,359,360,366,380,381,398,401,419,420,421,424,426,440,449,452,454,456,457,462,468,471,472,479,481],continuum:[6,7,9,198,317,424,426],contour_integr:198,contract:[59,212,214,249,277,290],contradictori:3,contrain:293,contraint:261,contrari:[227,234],contrast:[1,6,42,55,64,149,214,328,424,426,446,482],contrib:317,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,194,199,200,201,202,203,204,205,206,212,225,233,236,239,240,244,250,267,268,275,276,284,287,290,291,293,319,345,353,355,363,380,381,382,384,391,405,406,411,419,420,466,472,474],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,173,187,188,192,198,199,208,212,213,214,229,230,233,234,249,251,252,253,254,255,277,282,290,296,297,308,309,310,317,321,343,345,357,384,387,419,420,423,425,437,441,449,451,463,469,470],control_typ:198,controlfil:420,convect:91,conveni:[6,12,29,187,190,206,291,348,427,479],convent:[3,8,9,29,175,182,183,189,289,302,329,382,384,479],converg:[3,6,41,88,187,188,190,195,208,211,212,220,223,253,280,282,285,289,293,351,352,353,355,375,376,396,449,461,468],convers:[3,8,140,188,189,199,202,277,345,376,377,378,384,396,400,404,414,452,468,478],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,188,189,206,247,328,331,333,336,339,348,355,361,382,439,441,447,452,454,455,456,461,471,474,478,479,481,483],convex:326,convinc:[7,12],cook:9,cooki:7,cool:[7,154,229,288],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,201,204,205],coord2:[3,114,201,204,205],coord3:[3,114,201,204,205],coord:[],coordiat:353,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,192,195,200,201,203,204,205,208,209,210,211,212,213,214,215,218,220,221,223,225,228,229,230,231,232,233,234,246,248,249,251,252,254,255,267,270,271,272,275,276,277,287,288,290,292,293,294,299,302,303,304,305,307,315,316,317,324,325,327,328,348,353,354,355,360,361,362,365,383,449,454,455,457,459,462,464,468,474,479,480],coordn:[114,201],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,188,317,355,373,419,452],copper:447,coproccesor:16,coprocessor:[1,4,7,9,16,17,360,467],coproprocessor:17,copy_arrai:8,copyright:[7,8,275],coral:189,core:[],core_shel:146,coreshel:[6,9,369,376,378],cornel:[6,170,466],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,188,326,327,348,443,454],cornflowerblu:189,cornsilk:189,corpor:16,corr:375,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,188,214,227,233,249,250,267,275,277,280,316,322,326,345,355,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,454,469,472,474],correction_max_iter:198,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,189,195,215,220,223,234,243,249,250,283,290,293,302,304,323,326,355,356,360,378,406,451,452,454,464,478,480],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,188,189,193,194,195,201,203,204,205,207,210,212,214,221,223,224,228,233,236,237,245,246,247,249,251,252,253,254,255,256,261,264,266,267,269,272,273,277,282,290,292,293,308,310,312,321,322,323,325,326,327,329,331,332,333,334,335,336,339,341,346,350,352,354,355,361,362,364,367,368,369,370,371,372,373,374,375,376,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,411,412,413,414,416,417,419,420,421,422,427,428,437,438,439,440,441,443,445,446,447,449,451,452,454,455,457,467,468,469,471,472,474,479],correspondingli:[405,406,463],cosin:[],cosineshift:27,cosmo:[227,232],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,188,189,201,204,205,208,209,210,222,249,282,317,345,346,358,376,396,400,411,437,451,463],costheta0:[437,439,441],costheta:417,costli:[11,88,227,356],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,188,189,193,194,199,201,202,204,208,214,223,232,279,280,281,285,288,290,292,305,306,312,316,317,318,322,326,328,330,337,342,344,351,353,356,360,363,386,390,391,419,420,450,451,452,454,456,458,461,462,470,474,479,480],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,281,283,318,345,346,353,360,367,369,370,371,372,375,376,377,378,379,384,388,389,391,396,400,404,411,414,419,420,422,436,441,442,446,459,466,472,474,478],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,195,196,199,201,203,204,205,207,208,215,220,222,225,231,249,261,276,293,308,309,326,346,353,354,355,357,360,386,390,411,472,479],counter:[323,449,460,462,468],counterbal:229,counterpart:[187,290,449],counterproduct:18,coupl:[],courant:295,cours:[3,8,126,128,158,187,193,194,226,289,302,316,322,324,325,327,328,346,405,428,451,454,467,474,479,481],coval:[6,29,384,407,474],covari:227,cover:[6,71,184,189,198,236,384,394,443],coverag:[71,204],cpc:232,cpp:[1,3,6,8,9,11,12,13,87,187,193,194,223,293],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,189,192,218,234,318,343,346,360,373,436,449,467,468,471,472],cpuremain:472,cr2:163,cr3:163,crack:[4,356],crada:[5,7],crai:[5,7,13,18,187],crash:[3,356,474],craympi:360,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:198,create_faceset:198,create_nodeset:198,createatom:[],creation:[],crimson:189,critchlei:275,criteria:[3,116,165,188,189,209,210,211,244,353,416,443,456,459,479],criterion:[41,121,162,164,167,199,208,211,225,261,282,295,323,328,353,355,375,384,388,459,468,469],criterioni:468,critic:[48,49,247,312,317,353],cross:[3,12,22,71,89,143,172,187,188,200,204,210,214,246,248,267,290,298,302,304,313,320,332,348,355,371,380,381,382,389,390,391,396,398,400,417,422,424,426,439,441,454,458,464,481],crossov:1,crossterm:454,crozier:[0,7,13],crucial:280,crystal:[4,6,13,73,271,272,315,356,458,472,474],crystallin:[6,272,348,440,474],crystallis:312,crystallogr:[118,163],crystallograph:[348,472],crystallographi:[118,163,348],cs1:163,cs_chunk:6,cs_im:[40,454],cs_re:[40,454],csanyi:[140,418,427],cscl:407,csequ:6,csh:[11,12,373],cshrc:[11,12],csic:[383,437,439,441],csinfo:6,csisi:[383,437,439,441],csld:[],cst:382,cstherm:6,cstyle:451,csvr:[],ctcm:[361,382],ctemp_cor:218,cterm:294,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:407,cube:[6,41,162,167,208,218,326,348,474],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:366,cummul:[3,6,206,209,210,211,213,222,227,233,235,305,308,309,310,311,313,320,390,472],cumul:[6,199,201,203,204,205,219,225,233,247,249,253,261,290,291,355],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,193,194,198,199,201,204,205,206,208,209,210,211,212,213,214,215,219,220,223,225,227,230,231,233,239,246,249,250,254,255,261,266,267,269,275,281,282,284,287,288,289,290,293,294,295,296,297,298,299,301,303,304,305,308,309,310,316,317,320,321,322,323,324,325,327,328,330,343,344,345,346,349,350,352,353,354,355,360,366,373,375,379,382,384,385,388,392,395,405,406,407,408,409,411,417,419,420,423,424,425,426,428,439,441,442,444,449,450,451,452,454,455,456,457,458,460,461,462,464,466,468,469,471,472,479,480,481,482,483],curv:[6,164,225,272],curvatur:[387,421,447],custom:[],cut0:452,cut1:463,cut2:463,cut:[],cuthi:[271,283],cutinn:[368,405,406],cutlo:[271,283],cutmax:417,cutoff1:[372,379,396,400,404,414,422],cutoff2:[367,369,370,372,378,379,396,400,404,414,422],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,210,211,216,271,280,281,283,285,287,290,305,318,322,326,328,345,346,353,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,452,456,459,463,474],cutoffa:383,cutoffc:383,cuu3:382,cval:163,cvd:312,cvel:294,cvff:[],cwiggl:[3,246,322,325,327,479],cyan:[2,188,189],cycl:[3,225,247,249,250,253],cyclic:[3,184],cygwin:12,cylind:[3,4,188,231,276,323,326,457],cylindr:[6,231,302,323],cypress:360,cyrot:366,cyrstal:272,d3q15:236,d3q19:236,d_double_doubl:15,d_e:317,d_flag2:279,d_flag:279,d_name:[113,187,279,307,464],d_single_doubl:15,d_single_singl:15,d_sx:279,d_sy:279,d_sz:279,daan:315,dai:12,daili:12,daivi:267,damag:[],dammak:285,damp:[3,6,192,197,233,234,235,240,249,250,253,277,280,285,290,308,309,321,323,324,352,353,355,367,369,371,376,379,384,388,396,404,414,422,436,442,468,474],damp_com:234,damp_drud:234,dampen:[290,474],dampflag:[323,388],dan:17,danger:[3,12,225,328,380,472],dangl:167,daniel:9,darden:[346,379],darkblu:189,darkcyan:189,darken:188,darkgoldenrod:189,darkgrai:189,darkgreen:189,darkkhaki:189,darkmagenta:189,darkolivegreen:189,darkorang:189,darkorchid:189,darkr:189,darksalmon:189,darkseagreen:189,darkslateblu:189,darkslategrai:189,darkturquois:189,darkviolet:189,dasgupta:281,dash:[388,471],dat:[6,91,184,198,450],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,291],dataset:291,datatyp:3,date:[0,6,12,13,419,420,479],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,202],davi:322,david:[9,19,345,346,439,441],daw:[382,417],dbg:14,dcd:[3,6,7,187,188,189,190,273,455,459],ddim:186,deactiv:404,dealt:232,debug:[6,7,11,12,13,14,17,118,122,163,164,273,278,343,345,360,392,411,444,452,453,456,461,464,471,479],deby:[],decai:[376,447],decid:[3,6,12,16,71,246,279,290,318,469],decipher:348,declin:305,decod:188,decompos:[87,427],decomposit:[3,5,7,18,62,198,273],decoupl:[6,474],decreas:[3,187,195,196,211,214,220,223,233,316,345],decrement:294,deepli:342,deeppink:189,deepskyblu:189,def:[12,13,452],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,218,219,220,223,224,225,228,231,232,233,234,235,236,244,246,248,249,250,251,252,253,254,255,257,258,259,262,264,265,266,267,268,269,271,272,273,275,276,277,279,281,283,288,290,291,292,293,295,299,303,305,307,308,309,310,311,313,314,315,317,319,320,322,323,324,325,326,327,328,330,331,332,333,334,335,336,339,340,341,343,345,346,348,350,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,376,377,379,380,381,383,384,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,410,411,412,413,414,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,454,455,457,458,459,460,463,464,465,466,468,469,471,472,474,475,476,477,478,479,480],definit:[2,3,6,8,12,13,78,80,116,140,189,201,202,203,204,205,206,214,231,253,291,307,319,322,325,327,329,340,343,354,363,366,374,384,394,417,424,426,427,443,452,454,456,463,465,478,479],defint:472,deform:[],deg2theta:163,deg:474,degener:[3,275],degrad:[8,18,272,346,463],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,188,201,211,218,225,227,228,233,234,239,249,250,253,254,255,266,267,269,273,275,289,290,293,308,309,310,315,331,333,336,339,341,353,379,382,390,464,472,474,480],degress:[144,201],del:468,delai:[3,6,12,356,381,472],deleg:391,delet:[2,3,7,8,12,54,57,60,63,162,167,168,192,201,202,203,204,205,206,209,211,222,225,249,291,308,309,328,330,344,354,356,359,411,454,455,457,465,466,471,475,477,479,480],delete_atom:[],delete_bond:[],delete_el:198,deli:186,delimit:[452,479],deloc:[250,384],delr:407,delt_lo:468,delta:[],delta_1:366,delta_3:366,delta_7:366,delta_conf:3,delta_ij:[407,417],delta_mu:[3,199],delta_pi:366,delta_r:417,delta_sigma:366,delx:186,delz:186,demand:285,demo:11,demon:270,demonstr:[280,407],den:276,dendrim:390,denniston:[9,236,238,239,240,272],denomin:[7,169],denot:[118,218,234,272,283,285,376,389,391,420,424,426],dens:[71,211,384],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,193,194,198,201,204,205,208,214,223,236,239,242,243,272,276,277,281,317,322,348,350,354,361,366,382,407,408,409,417,421,430,432,433,434,454,463,464,472,478],density_continu:426,density_summ:426,depart:[0,7],departur:[247,280],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,188,189,192,193,194,195,196,199,201,203,204,206,207,208,210,212,220,221,224,227,228,229,231,233,234,236,238,239,246,249,251,252,253,254,255,256,264,266,267,269,271,282,285,287,290,292,293,299,305,308,309,310,312,314,316,317,319,321,322,325,326,327,328,330,331,332,333,334,335,336,339,341,346,348,353,354,356,357,358,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,410,412,413,414,416,417,419,420,421,422,427,428,436,437,438,439,440,441,442,443,445,446,447,449,451,454,456,457,460,464,466,468,471,472,473,479,480],dependend:6,depflag:12,dephas:[449,468],depos:215,deposit:[],deprec:281,depth:[51,143,188,317,387,421],dequidt:9,der:[87,107,374,375,404,419,420,446,474],deriv:[6,7,8,38,56,63,87,140,158,184,202,212,214,225,233,246,249,251,252,253,254,255,271,277,281,285,314,315,317,322,323,326,352,354,362,366,374,379,384,385,389,398,402,403,407,419,420,436,438,446,474],derjagin:446,derlet:271,descend:189,descent:[7,352],descib:[40,281],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,192,193,194,201,202,203,204,205,206,208,211,212,213,214,215,217,218,226,227,230,231,232,233,234,235,236,238,239,240,244,248,249,250,253,260,268,271,273,278,279,280,281,282,283,290,294,302,305,306,307,308,309,310,311,312,313,314,315,320,322,323,325,330,345,346,348,351,352,353,354,355,359,362,363,365,367,368,369,371,372,373,374,375,376,379,382,384,385,387,388,389,391,396,397,398,399,400,401,402,403,404,405,406,407,410,416,417,418,419,420,421,422,427,428,435,436,437,438,439,440,441,442,445,446,447,449,451,452,454,455,457,458,464,467,468,471,479,480,481],descript:[],descriptor:[140,187,392],deserno:346,design:[0,3,6,7,8,11,13,14,15,17,118,146,149,163,198,211,217,218,249,250,271,272,291,312,317,363,364,365,368,371,376,378,384,404,405,406,408,409,417,420,438,463],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,199,212,214,223,225,226,233,234,235,239,249,267,275,276,277,278,281,285,290,293,305,308,309,310,311,316,323,337,342,345,346,348,351,353,354,355,380,382,390,405,406,437,439,441,450,451,452,454,458,463,468,469,471,472,479,480,481],desk:7,desktop:[4,6,7,10,12,17,188],despit:474,destabil:366,destre:339,destroi:[11,39,209,210],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,188,189,192,193,194,198,201,202,203,204,206,208,210,211,212,213,214,215,223,225,226,227,228,230,231,233,235,236,240,246,247,248,249,250,251,252,253,254,255,259,261,266,267,268,269,272,275,276,277,279,280,282,283,284,290,293,305,308,309,310,311,312,313,315,316,317,318,319,320,321,328,330,332,340,345,346,349,353,354,356,357,360,361,362,363,365,366,368,370,371,372,373,374,375,376,379,380,384,385,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,407,410,411,416,419,420,421,427,428,436,443,445,446,452,454,455,456,457,459,460,463,464,466,469,472,479,480,483],detect:[2,3,12,61,63,86,224,276,316,355,375,390,395,449,451,454,465,468,479],determ:360,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,188,189,190,191,195,196,197,200,201,202,203,204,205,206,207,208,212,214,215,218,220,225,228,229,231,233,234,239,244,246,247,249,254,255,266,267,269,271,273,277,280,287,288,289,290,291,292,295,297,299,305,308,309,310,312,318,319,322,323,324,325,326,327,328,340,345,346,348,354,356,357,360,362,363,370,375,379,381,382,386,388,391,392,400,407,411,420,421,435,438,442,446,451,454,455,457,459,461,464,468,470,471,478,479,480],detil:108,devan:[9,422],devanathan:441,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,230,253,275,280,281,284,362,366,384,409,456],devemi:9,deviat:[247,253,271,386],deviator:9,devic:[1,3,12,15,17,230,360],device_typ:360,devin:[282,375],devis:409,dfactor:188,dff:474,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,346],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,284],dhi:[59,186,214,276],dhug:[247,280],dhugoniot:[247,280],dia:407,diagnost:[],diagon:[3,6,83,140,141,212,249,277,290,320,424,426],diagonalstyl:427,diagram:[41,118,163,183,208,273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i:[3,8,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,189,203,204,205,213,280,328,354,366,383,407,413,420,427,437,438,439,440,441],entropi:468,entry1:[38,56,189,373,438],entry2:189,entryn:189,enumer:[165,187],enumuer:6,env:360,environ:[1,3,6,11,12,16,17,18,188,227,232,271,360,361,366,373,375,383,384,417,439,451,465,479],epair:[107,189,386,390,419,420,472],epen:[419,420],epfl:[227,232],epp:379,epq:379,eps0:446,eps14:404,epsilon0:441,epsilon:[3,6,36,45,46,50,53,54,87,170,193,194,225,290,305,322,326,351,353,365,371,372,374,376,377,378,379,387,389,390,391,394,395,396,397,398,399,400,401,402,403,404,410,414,421,422,431,437,443,445,446,463,474,478],epsilon_0:447,epsilon_14:371,epsilon_:421,epsilon_d:377,epsilon_i:[387,411,421],epsilon_i_:421,epsilon_i_a:[387,421],epsilon_i_b:[387,421],epsilon_i_c:[387,421],epsilon_ij:411,epsilon_j:[387,411,421],epsilon_j_:421,epsilon_j_a:[387,421],epsilon_j_b:[387,421],epsilon_j_c:[387,421],epsilon_lj:421,epton:416,eqch:159,eqeq:[419,420],eqp:379,eqq:379,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,188,189,192,193,194,195,196,199,202,203,206,207,208,212,214,215,220,225,226,228,229,231,233,234,236,239,240,246,247,253,263,271,273,276,278,280,281,282,285,287,289,290,292,294,299,301,308,309,310,313,314,315,317,319,320,322,325,327,328,330,344,353,355,356,357,359,360,375,380,386,387,390,405,410,417,419,420,421,423,424,425,427,428,438,443,447,450,451,452,454,456,457,461,462,465,468,470,472,479,480],equat:[3,6,7,8,9,91,112,118,163,172,183,192,212,218,219,227,233,234,236,239,247,248,249,250,253,267,271,273,280,281,285,293,305,313,317,320,322,323,325,327,339,345,346,374,379,380,384,385,388,393,405,406,407,411,421,424,426,430,431,433,434,442,447,474],equi:250,equidist:248,equil:[3,281,349,461,483],equilater:464,equilibr:[3,4,5,6,7,9,59,91,164,192,199,202,211,212,225,247,249,250,267,268,280,281,282,283,313,314,315,320,375,376,419,420,450,464],equilibria:320,equilibribum:[209,210],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,212,214,225,226,227,234,236,249,253,267,280,285,289,293,294,302,305,312,313,315,320,331,333,336,339,375,407,413,474],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:198,equival:[6,12,13,59,124,125,133,138,162,166,189,203,206,212,214,225,233,249,267,277,289,290,325,380,384,439,441,454,457,462,463,472,474],equlibrium:6,equliibr:[281,283],er3:163,eradiu:[40,113,384,454],eras:[292,314],erat:[214,406],erc:376,erfc:[376,396,411],erforc:113,erg:478,erhart:[199,382,439,441],ermscal:363,ernst:9,eror:3,eros:407,erose_form:407,erot:[],errata:[439,441],erratum:322,erron:3,error:[],erta:388,ervel:[113,454],escap:[215,474],especi:[8,11,16,152,164,192,199,208,225,280,285,288,289,360,451],espresso:[9,284],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,202,253,272,321,346,362,376,396,441,459,472],essex:29,establish:[87,229],estim:[1,3,6,10,12,38,41,56,91,141,198,208,219,247,305,312,345,346,351,411,420,438,468,472],esu:478,esub:407,eta:[6,236,249,280,281,283,321,383,385,387,417,440,478],eta_dot:249,eta_ij:417,eta_ji:385,etag:[40,454],etail:472,etap:249,etap_dot:249,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,188,189,192,198,199,200,201,203,204,205,206,209,210,214,215,223,225,226,233,249,276,287,291,317,318,326,330,344,345,353,354,355,356,358,382,383,391,404,406,415,419,420,437,439,441,449,452,454,455,456,461,463,464,468,470,471,472,474,478,479,481,483],ethernet:18,etol:[353,355,449,468],etot0:280,etot:[6,94,96,97,110,141,150,189,218,234,247,280,471,472],eu2:163,eu3:163,euler:[353,355],eulerian:198,euqat:429,europhi:236,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,188,189,193,194,195,196,198,200,201,202,203,204,205,206,207,214,220,226,228,229,231,232,233,234,272,278,281,292,295,299,308,309,310,319,322,325,327,328,330,345,346,351,353,360,411,417,423,425,438,449,450,452,456,457,459,461,462,463,464,468,470,472,479,480],evalut:[330,452],evan:[152,267],evanseck:[6,20,170,371,466],evapor:[],evaul:[8,353],evdwl:[107,419,420,472],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,189,192,193,194,199,200,201,203,204,205,206,208,209,210,212,214,215,218,231,234,247,249,250,272,285,287,290,291,301,305,313,317,320,322,326,328,338,345,351,353,355,360,365,384,385,388,391,411,421,444,454,455,457,459,460,461,463,464,466,469,471,472,474,483],evenli:[3,41,141,184,208,236,394,444,454],event:[],eventu:[3,6,12,15,166,281,468],ever:[54,56,232,305],evera:[374,387,421,436],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,192,193,194,195,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,219,222,223,225,227,229,230,231,236,237,245,249,250,253,270,271,272,276,277,278,279,280,281,282,283,285,287,288,290,291,293,294,305,307,308,309,310,311,312,313,316,317,318,319,320,328,330,344,346,355,356,357,360,380,381,391,404,419,420,432,448,449,450,454,456,458,459,461,462,463,468,469,470,472,479,483],everyth:[8,107],everywher:[116,398],eviri:384,evolut:[227,236,273,449],evolv:[236,273,318],ewald:[2,3,5,6,7,8,12,88,110,118,141,318,345,346,353,367,369,370,376,379,384,396,400,414,422,436,438,456],ewald_disp:379,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,208,211,226,227,233,234,235,276,285,286,305,317,332,345,373,456,461,468,481,483],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,193,194,203,208,214,219,226,233,234,235,250,260,261,268,272,280,305,310,311,324,360,373,380,382,388,391,394,405,411,438,456,457,464,468,479],exager:474,examin:[6,8,211,272],examp:[452,479],exampl:[],exce:[3,6,16,17,18,41,58,71,166,201,204,205,208,212,214,219,222,249,272,296,297,305,353,360,454,479],exceed:[3,41,59,208,214,249,305,462],excel:384,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,192,195,201,202,203,207,208,212,214,221,224,225,228,231,233,235,249,250,251,252,253,254,255,256,260,261,264,266,267,268,269,273,282,283,290,292,293,302,305,308,310,311,317,321,328,330,331,332,333,334,335,336,339,340,341,345,346,348,350,354,355,356,358,359,360,361,362,364,367,368,369,370,371,372,373,374,375,376,378,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,408,412,413,414,416,419,420,421,422,428,436,437,438,439,440,441,443,445,446,447,449,451,452,454,456,457,459,462,463,464,465,466,468,472,474,478,479,480,482],excess:384,exchang:[2,3,6,8,9,61,62,192,198,199,225,233,282,290,313,317,320,345,360,384,469],exchange:345,excit:[9,384],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,201,204,209,210,237,245,275,288,290,312,323,328,353,354,356,368,388,391,405,406,411,435,466],exclus:[1,3,9,12,16,87,360,375,411,463],excurs:449,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,188,230,284,330,344,347,359,450,452,462,465,468,479],exemplari:226,exemplifi:384,exert:[6,231,234,285,324,325,326,346],exhaust:[198,359,479],exhibit:[249,352,384,463],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,192,197,207,210,212,215,225,275,276,278,328,331,333,334,336,340,349,354,360,391,419,444,450,452,454,455,456,465,466,467,479,480,481],exit:[2,3,11,12,41,57,187,208,344,359,452,453,462,471,479],exlanatori:3,exp:[],expand:[],expans:[12,140,187,465],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,208,220,225,227,246,271,277,279,280,285,290,328,346,356,373,407,411,449,452,454,456,459,463,468,479],expens:[6,10,71,189,271,275,290,317,328,345,346,356,360,452],experi:[6,13,15,17,207,215,230,239,248,277,289,290,351,355,380,411,463,468],experienc:[6,12,238,239],experiment:[345,360,468],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,188,189,192,201,202,206,208,210,212,214,249,271,279,290,302,328,330,344,345,348,354,355,359,365,382,394,428,443,447,452,455,456,459,461,464,474,479,483],explan:[3,6,59,113,140,187,201,248,271,391,448,451,452,454,463],explanatori:[3,8,117,187,200,201,203,204,205,290,354,451,479],explantori:[3,286],explic:410,explicit:[6,9,11,22,44,77,87,113,116,158,172,193,194,214,296,297,332,350,362,363,366,371,373,382,384,395,405,442,448,451,455,458],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,189,195,204,207,214,221,224,226,228,233,249,251,252,253,254,255,256,264,266,267,269,279,280,282,290,292,293,308,310,311,317,321,331,333,334,335,336,339,341,354,360,361,362,364,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,388,389,390,391,394,395,396,397,398,399,400,401,402,403,404,405,408,411,412,413,414,416,421,422,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,445,446,447,454,456,463,464,466,467,474],explictli:[16,467],exploit:[9,15,17,273],explor:[118,163],expon:[3,281,283,382,387,390,404,410,422],exponenti:[87,417,437,447,468,479],expos:11,exposit:[198,380,381],express:[6,140,150,164,193,194,212,246,271,281,317,323,330,366,382,384,398,407,427,436,479],expressiont:366,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,192,195,196,199,206,207,213,216,220,223,224,225,227,228,229,231,233,235,247,249,253,261,271,272,288,289,290,292,294,299,302,304,308,309,310,311,312,314,315,317,319,322,326,327,387,407,420,421,427,471,472],extent:[1,3,41,45,57,71,162,166,187,197,204,208,231,324,327,345,348,362,423,425,438,451,454,457],exterior:[3,6,326],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,189,203,208,210,249,278,279,280,290,305,353,354,357,358,379,388,391,394,407,411,451,452,454,457,466,474,479],extract:[3,6,11,13,36,63,87,107,115,117,119,193,194,283,355,376,385,407,427,452,459,471],extract_atom:11,extract_comput:[11,452],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,188,212,214,249,315,384,440,474],extrema:404,extrins:198,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,319],f_a:[439,440,441],f_ave:117,f_c:440,f_f:441,f_fix_id:280,f_harm:315,f_i:417,f_id:[6,71,117,119,187,192,200,201,202,203,204,205,206,244,307,319,472,479],f_ij:417,f_indent:206,f_int:314,f_jj:91,f_k:417,f_langevin:317,f_max:[280,285],f_msst:247,f_r:[234,439,440,441],f_sigma:366,f_solid:315,f_ss:6,f_temp:234,face:[3,6,57,59,71,152,162,166,197,204,205,322,324,325,326,327,348,387,407,421,454,457],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,227,305,315,388,466],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,188,189,193,194,202,208,212,214,215,225,230,233,235,236,247,249,250,253,273,277,289,293,295,297,305,309,313,320,321,322,326,336,346,348,360,362,363,366,367,369,371,376,377,378,380,384,388,391,395,396,407,411,413,414,420,422,428,437,442,451,454,457,458,463,466,468,469,472,474,478,479],factori:[3,452],factoriz:345,fail:[3,11,12,59,168,212,215,345,353,355,378,420,452],failur:[121,424],fairli:[11,411,463,468],faken:73,falcon:230,fall:[3,6,189,203,276,452],fals:[86,328,330,479],fame:8,famili:451,familiar:[0,11],fan:417,far:[3,6,12,17,57,59,61,86,187,189,190,208,209,210,212,215,249,271,289,290,305,322,333,336,351,355,356,443,452,454,459,472],farago:233,farrel:[439,441],farther:187,fashion:[6,8,41,71,164,189,192,193,194,199,204,208,210,215,225,227,231,246,247,249,251,252,253,254,255,263,266,267,268,269,279,280,282,290,294,298,304,307,315,317,321,322,323,325,327,355,391,405,457,466,479,482],fasolino:393,fast:[6,7,9,12,13,17,39,187,258,280,318,345,346,368,405,406,436,438,456,461,463,472,480,483],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,189,192,195,207,208,221,224,228,232,233,249,251,252,253,254,255,256,264,266,267,269,277,281,282,290,292,293,305,308,310,312,314,317,321,331,333,334,335,336,339,341,345,346,357,358,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,436,437,438,439,440,441,443,445,446,447,449,463,467,474],fastest:[6,14,17,152,204,317,318,360,451],fatal:[3,471],fault:[70,420],faulti:12,fava:387,favor:211,favorit:7,fbmc:312,fcc:[],fcm:[263,479],fdirect:218,fdotr:392,fdti:87,fe2:163,fe3:163,fe_md_boundari:198,featu:8,featur:[],fecr:382,feedback:[7,230],feel:[7,230,231,239,271,326,328,355,411],felling:409,felt:326,femtosecond:478,fene:[],fennel:[376,396],fep:[],ferguson:[6,170,466],fermi:[1,12,15,150,360,441],fermion:[9,384],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,190,200,201,202,203,204,205,206,234,249,276,279,281,293,319,345,353,354,355,362,451,454,459,463,465,479,481],fewer:[1,3,11,15,16,61,239,463],fewest:3,fextern:223,feynman:273,fff:452,ffield:[375,385,419,420],ffmpeg:[3,12,188],ffplai:188,fft:[1,3,7,12,14,15,88,109,110,141,272,345,346,463],fft_inc:[12,346],fft_lib:12,fft_path:12,fftbench:345,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,195,196,220,223,227,273,289,376,396,400,435],field1:[455,459],field2:455,field:[],fifth:[302,413],figur:[1,3,8,11,12,280,451,452],fij:379,file0:271,file1:[11,13,271,316,330,354,459,461,465],file2:[11,13,316,330,354,459,461,465],file:[],filenam:[3,12,13,38,41,56,184,187,188,189,190,198,201,202,203,204,205,206,208,213,271,275,278,281,282,283,286,287,290,291,316,317,342,343,344,355,361,362,366,376,382,383,385,393,407,408,409,413,417,418,419,420,427,437,438,439,440,441,450,451,452,455,456,461,465,472,479,481,482,483],filennam:461,filep:[3,187,189,456,461,483],filepo:287,fill:[7,164,188,276,317,348,356,366,420,457],filter:[189,198],final_integr:8,final_integrate_respa:8,finchham:[6,146,378],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,190,199,211,212,222,225,248,271,277,285,289,351,353,355,356,376,391,396,400,407,436,438,474,479],find_custom:8,fine:[16,17,168,195,220,315,356,360,479],finer:[140,164,479],finest:345,finger:[164,186,246,457],finish:[6,11,41,208,330,342,344,345,357,359,360,443,459,479,480],finit:[],finni:[7,382,436],finvers:218,fiorin:[9,213],fire:[351,352,353,355,468],firebrick:189,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,192,199,201,202,203,204,205,206,208,211,214,225,226,231,236,246,247,248,249,271,273,278,279,280,282,287,290,293,294,302,303,305,306,307,314,315,316,317,319,323,328,330,331,337,348,353,354,355,356,359,360,361,362,365,366,367,369,371,373,375,376,382,384,385,388,389,392,393,395,396,400,405,406,407,409,411,413,417,419,420,427,435,437,438,439,440,441,449,450,451,452,454,455,456,459,461,463,466,467,468,471,472,474,479,480,481,483],fischer:[6,9,19,20,170,371,466],fit:[3,6,9,12,38,56,184,289,305,362,366,393,407,411,431,438,440,462,479],five:[73,150,280,354,366,408,454,468],fix:[],fix_adapt:[158,194,404],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,199,276],fix_evapor:199,fix_flux:198,fix_gcmc:[199,354],fix_gl:227,fix_gld:227,fix_grav:276,fix_id:[3,212,247,249,251,252,253,254,255,277,280],fix_modifi:[],fix_mov:[186,323],fix_nh:8,fix_npt:227,fix_nvt:[199,225],fix_poem:[3,6],fix_pour:[3,215],fix_qbmsst:9,fix_qeq:[3,375],fix_rattl:293,fix_reax_bond:419,fix_rigid:[239,365],fix_saed_vtk:291,fix_setforc:8,fix_shak:293,fix_srd:3,fix_styl:253,fix_temp_rescal:311,fixedpoint:[212,249],fixextern:223,fixid:198,fji:379,flag1:[217,358],flag2:[217,358],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,188,189,190,206,211,213,217,230,233,237,239,245,246,272,279,290,302,304,305,312,316,325,328,343,346,354,358,359,360,362,390,395,407,435,449,451,452,454,455,456,458,459,460,464,479],flag_buck:370,flag_coul:[370,379,400],flag_lj:[379,400],flagfld:[368,405,406],flaghi:[3,368,405,406],flaglog:[368,405,406],flagn:217,flagvf:[368,405,406],flat:[6,317,322,323,327],flavor:[2,7,12],fld:[9,322,368,405,406],flen:363,flex_press:363,flexibl:[3,6,8,165,188,201,204,213,227,250,313,320,384,440,472],flip:[3,6,214,249,324,325],floor:479,flop:12,floralwhit:189,flow:[],fluctuat:[6,64,87,212,225,226,233,236,249,253,271,272,315,317,339],fluid:[],fluid_veloc:240,flush:[3,189,471],flux:[],flv:188,fly:[7,9,12,41,188,192,198,215,218,290,293,318,366,472,474],fmackai:9,fmag:216,fmass:273,fmax:[353,472],fmomentum:218,fmsec:[2,189,233,234,246,249,277,290,308,309,463,473,478,480],fname:344,fno:12,fnorm:[353,472],fnpt:218,fnvt:218,foce:391,fock:363,focu:293,fogarti:[9,283,420],foil:[140,271,427],fold:[303,463],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,192,198,199,200,201,202,203,204,205,206,208,213,214,215,218,219,223,225,226,227,230,232,233,234,236,239,247,249,253,254,255,266,267,269,272,273,275,278,279,280,281,283,285,287,289,290,291,293,307,308,309,310,313,314,315,316,317,319,320,328,329,333,334,335,336,339,341,343,348,350,353,354,355,360,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,437,438,439,440,441,442,443,445,446,447,449,451,452,454,455,456,457,459,461,462,463,466,468,469,470,474,479,480,482],foo:[4,8,11,12,187,188,223,452,465,479],foot:6,footprint:[12,360],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:239,forcefield:[289,390],forcegroup:236,forcezero:351,ford:379,forestgreen:189,forev:71,forget:[234,474],forgiv:249,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,189,192,193,194,210,226,227,233,235,239,246,267,272,283,285,289,290,317,322,326,331,332,339,350,352,354,355,362,363,366,373,382,384,386,390,391,395,407,409,413,414,417,419,420,421,427,428,436,438,439,440,441,446,448,451,452,454,459,464,471,474,479],formal:[6,78,80,91,226,227,233,249,273,305,313],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,201,203,204,205,206,208,210,272,275,279,281,283,286,290,291,301,316,317,328,329,332,350,354,355,361,362,366,373,382,385,395,407,409,418,419,420,422,427,438,444,451,452,454,455,456,459,470,471,472,479,481],former:[6,12,16,39,41,189,208,317,321,366,368,460,466,479],formerli:[7,13],formul:[1,40,64,141,195,220,233,249,267,281,283,289,293,316,345,362,366,382,384,387,407,416],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,193,194,195,196,201,202,203,206,207,214,220,228,229,231,233,234,246,271,272,278,287,292,299,303,305,308,309,310,319,322,325,327,328,330,331,332,334,340,348,354,362,363,365,366,371,372,373,374,379,380,382,383,387,388,389,390,392,395,396,398,399,400,402,403,405,406,407,410,411,412,421,422,428,436,437,439,440,441,445,446,447,450,454,457,464,471,472,478,479,480],forth:[1,6,11,12,13,14,15,359,452,457,461],fortran:[3,6,9,11,12,13,223,382,391,407,419,420],fortun:8,forward:[3,8,87,344,355,360],foster:[366,416,417],foul:167,found:[3,6,9,12,73,158,187,211,213,225,230,236,272,312,318,330,344,356,373,376,379,449,455,456,471],four:[6,11,54,81,103,104,140,160,247,317,339,354,355,449],fourier:[],fo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17,119,307],input2:[65,68,69,79,92,108,113,114,115,117,119,307],input:[],input_doubl:3,inquir:295,insensit:12,insert:[3,5,7,8,12,59,164,192,215,225,231,276,345,427,435,452,458,474],insid:[2,3,6,8,11,71,129,135,164,187,189,200,204,205,215,216,222,225,231,236,239,276,290,305,322,324,325,326,327,328,343,348,398,452,453,454,456,457,464,468,479],insight:[6,13],instabl:[236,379,426],instal:[],instanc:[6,11,213,227,324,386,391,411,417,452,474],instantan:[6,63,211,212,226,227,249,253,272,277,280,285,287,290,312,460,472],instanti:[6,11,12,198,391,451],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,143,146,168,184,187,194,201,203,204,205,206,208,212,213,233,236,239,240,272,278,288,290,307,325,343,345,346,349,356,360,369,370,382,395,397,404,407,449,457,461,468,470,474,479],institut:[9,230,275],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,142,151,162,170,171,173,174,175,176,178,179,181,182,184,185,188,195,207,221,224,228,233,249,251,252,253,254,255,256,264,266,267,269,282,290,292,293,308,310,321,331,333,334,335,336,339,341,346,360,361,362,364,367,368,369,370,371,372,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447,463,474],insuffici:[3,6,12],insult:249,insur:[3,6,11,12,17,39,40,61,73,102,104,164,165,184,187,188,189,195,209,210,215,220,221,222,223,225,228,233,245,278,279,288,290,305,317,322,326,327,328,330,344,354,356,360,374,387,391,415,421,438,451,452,454,455,459,462,463,471,472,479,480],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,140,162,164,167,168,170,174,175,179,184,186,187,188,189,199,201,204,205,209,210,211,215,217,223,225,226,227,230,233,234,235,236,272,275,276,279,280,285,290,305,307,309,312,316,317,335,345,348,368,380,381,394,407,419,420,424,426,427,449,451,452,454,462,463,464,468,471,479,480],integr:[],integrate_ulsph:296,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,226,418,454],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,161,163,192,201,202,203,204,205,206,208,209,210,211,219,222,229,239,247,249,253,287,290,291,305,313,317,319,320,471,472],intepol:479,inter:[14,18,42,61,62,144,167,168,187,211,233,235,248,282,290,345,355,366,464,474,479,481,483],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,122,123,124,125,127,128,129,130,131,132,133,135,136,137,138,140,141,143,157,158,162,165,166,167,168,169,170,172,176,177,183,187,192,193,194,209,210,211,224,225,230,231,233,235,239,261,271,273,275,281,283,289,290,296,297,305,306,312,317,321,322,323,326,327,332,333,334,336,340,345,346,353,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,420,421,422,424,426,427,428,435,436,437,439,440,441,442,443,444,445,446,447,449,452,454,456,458,459,463,464,466,471,472,474,481],interatom:[3,4,7,164,187,248,314,315,361,366,382,384,392,407,440,479],intercept:118,interchang:6,interconnect:18,interconvert:384,intereract:39,interesect:326,interest:[1,5,7,8,9,11,13,71,163,273,312,315,346,383,406,419,420,452,479],interf:360,interfac:[],interfer:[249,362],interg:[6,474],intergr:[463,467],interi:406,interior:[3,6,41,326,457],interlac:407,interleav:[6,164,462],intermedi:[6,12,59,188,248,271,339,355,452,453,462,466],intermix:449,intermolecular:362,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,141,144,146,163,171,184,188,189,192,193,194,198,210,214,218,230,242,243,247,249,253,272,290,294,331,333,336,339,343,353,354,429,430,438,452,454,456,459,468,471,472,478,479,480,481],internal_element_set:198,internal_quadratur:198,internet:232,interpenetr:407,interpentr:[430,431,433],interpol:[6,15,38,56,100,184,188,189,198,236,271,345,346,355,366,411,420,432,438,439],interpret:[2,6,11,188,203,388,428,449,452,468,479],interrupt:280,intersect:[3,6,118,189,326,328,457],intersert:326,interspers:353,interstiti:162,intertia:[3,93],interv:[3,6,91,202,233,280,285,286,297,432,449,468,479],intestieti:118,intial:[6,360,362],intiial:[41,459],intiti:[3,304],intra:290,intra_energi:225,intramolecular:[29,225],introduc:[6,9,188,249,280,285,290,339,345,361,376,384,396,400,404,437,468],introduct:[],intsal:16,intuit:348,inv:[118,163,291],invalid:[3,12,71,89,167,261,355,405,406,456],invari:[133,138,140],invent:293,invers:[],invert:[6,168,272],invis:326,invoc:[162,211,360,424,426,452],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,142,151,158,159,162,164,165,167,168,170,171,173,174,175,176,178,179,181,182,184,187,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12,142,143,147,151,157,162,164,165,166,167,168,170,171,173,174,175,176,178,179,181,182,184,186,187,188,195,198,202,203,206,207,209,210,211,212,215,221,224,225,228,230,233,246,249,251,252,253,254,255,256,264,266,267,269,276,279,282,288,290,292,293,294,307,308,310,313,317,319,320,321,322,323,326,327,328,331,333,334,335,336,339,341,346,348,354,355,356,359,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,416,417,419,420,421,422,428,437,438,439,440,441,443,445,446,447,448,451,452,454,456,457,458,461,462,463,464,465,466,467,471,472,478,479,481,483],yourself:[6,8,12,13,212,354],yplane:323,ypo:164,ysu:[3,187,455],yuan:9,yukawa:[],yukawa_1_1:444,yxz:451,yzx:451,z_i:[384,441,447],z_j:[441,447],z_meam:407,zachari:13,zannoni:387,zbl:[],zblcut:441,zblcutinn:427,zblcutout:427,zblexpscal:441,zblz:427,zcm:290,zcylind:323,zepeda:199,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,75,87,88,90,93,102,103,104,105,106,108,109,110,112,113,114,115,116,117,118,121,140,141,143,144,145,152,153,156,157,159,161,162,163,164,166,167,168,170,173,182,184,186,187,188,189,192,193,194,195,197,199,200,201,202,203,204,205,206,207,208,209,210,212,214,219,220,221,222,224,225,226,227,229,233,234,235,236,237,239,245,246,247,249,253,261,264,273,278,279,280,281,282,285,287,288,290,291,292,293,296,297,299,305,307,312,313,315,317,320,321,322,323,324,325,327,328,329,330,335,348,351,353,354,355,356,360,363,366,367,369,370,371,374,376,379,380,384,387,389,390,391,392,396,398,400,401,404,406,407,411,416,420,421,422,435,438,442,447,449,450,451,454,455,457,459,461,462,463,464,468,469,472,474,479,480,481,483],zeta:[3,236,281,385],zfactor:188,zflag:[151,152,237,239,245,290,312],zhang:[290,313,388],zhi:[3,6,166,187,197,316,322,325,327,454,457,472],zhi_bound:[6,187],zhou:[13,366,385,417,439,441],zhu:434,ziegenhain:13,ziegler:[275,407,436,441,447],zimmerman2004:198,zimmerman2010:198,zimmerman:[9,70,198,366],zlat:[214,231,472],zlo:[3,6,166,187,197,316,322,324,325,327,454,457,472],zlo_bound:[6,187],zmax:[197,236,479],zmin:[236,479],zn2:163,zone:[118,291],zoom:[3,187,188,189],zplane:323,zr4:163,zrest:304,zsu:[3,187,455],zwall:322,zwall_veloc:236,zxy:451,zybin:420,zyx:451},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","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","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local 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/local command","compute dilatation/atom command","compute displace/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 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 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 temp command","compute temp/asphere 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","dimension command","displace_atoms command","dump 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/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/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 smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style 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","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style 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 meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style 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_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl 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","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":209,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,188,189,190,191,193,194,195,197,198,199,201,204,205,206,209,210,212,213,214,215,219,222,225,226,231,233,234,235,236,237,239,244,247,249,250,253,267,268,272,273,276,277,278,279,280,282,285,287,288,290,291,305,307,312,313,314,315,318,320,322,324,328,340,343,345,346,348,349,351,352,354,356,357,358,360,363,366,368,384,405,406,411,419,420,435,436,449,450,451,454,455,457,459,461,462,463,466,468,470,471,472,473,478,480,481,482],"function":479,"long":[367,369,370,371,372,376,378,379,396,400,404,414,422],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[193,194],addforc:195,addit:[12,13],addtorqu:196,adiabat:6,adjust_dt:295,adp:361,airebo:362,alloi:382,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:197,arrai:6,aspher:[6,82,143,251,254,257,258,266],atc:[9,198],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,197,199,200,279,479],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:207,awpmd:[9,363],balanc:[41,208],barostat:6,basal:67,beck:364,berendsen:[277,308],between:6,binary2txt:13,bodi:[6,8,42,68,259,365],bond:[8,13,69,209,210,211,286],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:366,born:[367,378],boundari:[7,57],box:[6,58,212],brownian:368,buck:[369,370,378],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,371,404],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,201],citat:7,class2:[21,43,171,331,372],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[322,374,446],colvar:[9,13,213],com:[74,75,145],comb3:375,comb:[282,375],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,479],compute_modifi:102,condit:7,conduct:[6,313],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:202,cosin:[23,24,25,26,27,28,173],cossq:333,coul:[367,369,370,371,372,376,377,378,389,396,400,404,414,422],coupl:6,creat:210,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:309,csvr:309,cubic:398,cuda:[9,14,109,112,142,151,195,207,221,224,228,249,256,292,293,308,310,321,367,369,371,372,382,388,389,396,397,399,402,412,437,439],custom:8,cut:[49,363,369,372,376,379,384,386,396,397,404,410,414],cvff:334,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[376,396],deform:[147,148,214],delete_atom:167,delete_bond:168,delta:24,deposit:215,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],diagnost:7,diel:377,dielectr:169,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:172,dihedral_styl:[2,170,171,173,174,175,176,177,178,179,180,181,182,183,184],dilat:80,dimens:185,dipol:[6,29,379],direct:218,discuss:6,disp:6,displac:[81,86],displace_atom:186,distribut:[7,12],document:0,dpd:380,drag:216,dreid:[6,390],drude:[6,9,149,217,218,234],dsf:[376,396],dsmc:381,dump:[6,8,187,188,190],dump_modifi:189,dynam:281,eam:[13,382],echo:191,edip:383,eff:[9,13,96,97,148,150,155,235,250,260,268,311,384],efield:220,eim:385,elast:6,emac:13,enforce2d:221,ensembl:7,erot:[82,83,84,85],error:3,evapor:222,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],exp:[27,173],expand:[46,399],extend:[8,11],extern:223,fcc:271,featur:[7,8],fene:[45,46],fep:[9,13,87,194],field:[6,7],file:6,finit:6,fix:[2,6,8,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,479],fix_modifi:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],flow:6,fluid:236,flux:91,forc:[6,7,306],fourier:[30,31,174,335],freez:224,from:[6,11],futur:5,gauss:386,gaybern:387,gcmc:225,gener:[1,6,7,13],get:12,gld:226,gle:227,global:6,gpu:[15,364,367,369,371,372,374,376,379,380,382,386,387,389,396,397,399,410,412,421,422,428,437,438,445,446],gran:[323,388],granular:6,graviti:228,gromac:389,group2ndx:329,group:[88,328,479],gyrat:[89,90],harmon:[32,47,48,49,175,178,322,336,413],hbond:390,heat:[91,229],heatconduct:429,helix:176,hertz:[388,423],histo:203,histori:[5,388],hook:388,hourglass_error:122,how:6,hybrid:[33,50,177,337,391],idealga:430,imag:[187,188],imd:230,implicit:371,improp:[8,92],improper_coeff:332,improper_styl:[2,331,333,334,335,336,337,338,339,340,341],includ:342,inclus:8,indent:231,indic:0,individu:2,induc:6,inertia:93,info:[0,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,343],input:[2,6,8],instal:11,integr:[6,7],integrate_tlsph:296,integrate_ulsph:297,intel:[9,16,371,387,396,437],interfac:[6,11],internal_energi:123,introduct:7,invers:218,ipi:232,ipp:13,jul:[],jump:344,kate:13,keyword:411,kim:392,kokko:17,kspace:[2,8,318],kspace_modifi:345,kspace_styl:[6,346],label:347,lammp:[0,1,2,6,7,8,11,12],langevin:[233,234,235],lattic:348,lcbop:393,librari:[6,11,12],limit:[261,310],line:[12,262,394],linear:403,lineforc:241,list:[2,395],lj1043:322,lj126:322,lj93:322,lj96:397,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:349,lubric:405,lubricateu:406,make:12,mass:350,math:479,matlab:13,meam:[407,408,409],measur:1,meso:[242,243],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:410,min_modifi:351,min_styl:352,minim:[8,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,353],misc:9,mod:[317,440],model:[6,7],modifi:8,molecul:354,molfil:[9,187,190],moltempl:13,momentum:[237,245],morri:434,mors:[51,390,412],move:246,move_tri_surf:298,movi:[187,188],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[367,369,371,376,396],msst:247,multi:[6,7,178],multipl:6,nb3b:413,neb:[248,355],neigh_modifi:356,neighbor:357,nemd:6,newton:358,next:359,nharmon:179,noforc:[258,263],non:[6,7],none:[34,52,180,338,415],nongauss:105,nonlinear:53,nph:[249,250,251,252,290],nphug:253,npt:[249,250,254,255,290],nve:[256,257,258,259,260,261,262,263,264,265,290],nvt:[249,250,266,267,268,269,290],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,170,171,173,174,175,176,178,179,181,182,184,228,249,251,252,253,254,255,256,264,266,267,269,282,331,333,334,335,336,339,341,361,362,364,367,368,369,370,371,372,374,375,376,377,379,380,382,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447],onewai:270,open:7,oper:479,opl:181,opt:[19,371,382,396,400,412],optim:1,option:[6,8,12],orient:271,orthogon:6,other:6,output:[6,7,8,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],overlai:391,overview:11,packag:[1,9,12,14,15,16,17,18,19,360],pair:[6,107,108],pair_coeff:373,pair_modifi:411,pair_styl:[2,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447],pair_writ:444,pairwis:8,parallel:11,paramet:6,pars:2,partial:151,particl:[6,7,42],partit:448,past:5,per:6,perform:[1,10],peri:416,period:25,phonon:[9,13,272],pimd:273,piston:324,pla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7,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,462],run_styl:463,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,422],self:304,serial:11,set:[6,464],setforc:292,setvel:299,shake:293,share:[11,12],shell:[6,465],shield:281,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:281,slice:119,sllod:[267,268],small:290,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,294,295,296,297,298,299,301,423,424,425,426],smooth:[402,403],sna:140,snad:140,snap:427,snapshot:6,snav:140,soft:[404,428],solver:2,sourc:7,spatial:[204,205],spc:6,speci:287,special:[7,411,479],special_bond:466,sph:[9,429,430,431,432,433,434],sphere:[84,85,157,205,239,252,255,264,269],spheric:6,spline:[408,409],spring:[302,303,304,315],squar:28,srd:[305,327],srp:435,standard:9,start:[12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],state:307,stationari:243,stop:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],store:[306,307],strategi:1,streitz:376,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:467,summari:6,swap:[199,211],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],system:6,tabl:[0,6,38,56,184,438,439],tad:468,taitwat:[433,434],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,308,309,310,311],temper:469,temperatur:6,tersoff:[439,440,441],test:11,tfmc:312,thermal:[6,313],thermo:[6,470],thermo_modifi:471,thermo_styl:472,thermodynam:[6,8],thermostat:6,thole:442,time:[6,206],timestep:473,tip3p:6,tip4p:[6,376,396,400,404],tip:12,tlsph:424,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:316,tool:13,torqu:159,transform:218,tri:[265,443],tri_surfac:425,triangle_mesh_vertic:134,triclin:6,tstat:380,ttm:317,tune:318,type:7,ulsph:426,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:341,uncomput:475,undump:476,unfix:477,unit:478,user:[9,12,14,16,18],vacf:160,valu:[6,479],variabl:[6,8,479],variou:1,vcm:161,vector:[6,319,479],veloc:480,version:[0,5,12],via: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\ No newline at end of file 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,229,276,331,344,355,405,406,449,451,452,454,456,461,468,470,479,481],against:[11,12,13,64,215,355,419,420],aggreg:[6,12,65,68,69,79,92,108,115,229,245,288,290,303,449,480],aggress:[229,468],agilio:[9,13],agre:[3,8,184,353,362,393,420],agreement:[5,7],ahd:390,ahead:324,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:188,akohlmei:[7,9,13,190,230],aktulga:[7,9,283,420],al2o3_001:[118,291],al3:163,ala:236,alain:9,alat:[271,407],alb:[417,439,441],albeit:289,albert:9,alchem:[87,158],alcohol:320,alcu:[361,366],alcu_eam:417,alderton:379,alejandr:[249,250],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,189,198,208,211,214,236,238,239,261,273,290,293,312,313,317,320,325,351,352,353,357,360,384,406,424,426,449,451,468],alia:12,alias:[1,346],aliceblu:189,align:[6,12,29,41,71,166,184,204,208,231,348,454,457,474],alkali:384,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,242,244,245,247,249,250,251,252,253,254,255,256,257,258,259,260,261,262,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,301,302,304,305,306,307,308,309,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,331,332,335,340,343,344,345,346,347,348,350,353,354,355,356,357,359,360,361,362,363,365,366,367,369,370,371,372,373,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,451,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,471,472,474,478,479,480,481,482,483],allen:[29,87,379,387],allentildeslei:87,allign:3,allindex:329,alloc:[3,5,6,8,9,11,12,60,223,319,354,356,360,415,420,454,462],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,188,189,190,192,193,195,197,198,199,201,202,203,204,205,206,208,210,211,212,213,214,215,219,220,223,225,226,227,228,230,233,236,239,240,244,246,249,250,271,275,277,278,279,280,284,290,291,293,294,296,297,301,305,312,313,314,315,317,318,319,320,321,322,328,330,332,340,345,346,348,353,354,355,356,359,360,363,366,367,368,369,370,371,376,382,384,388,389,390,391,400,405,406,411,417,420,421,424,426,435,444,446,449,452,454,456,457,458,459,460,461,464,466,467,468,471,472,479,480],almost:[2,3,12,60,231,280,317,346,357,360,435],alo:376,alon:[6,7,211,286,419,420,452],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,188,211,231,236,237,241,246,248,280,290,293,294,298,302,303,312,316,317,323,326,328,348,351,352,353,355,376,379,388,391,394,396,400,407,419,420,438,454,457,464,465,479],alonso:[408,409],alpha:[6,51,193,236,272,280,285,353,361,364,367,376,380,382,383,385,390,395,396,407,412,416,440,442,472,474],alpha_:442,alpha_c:404,alpha_i:[427,442],alpha_ialpha_j:442,alpha_lj:404,alphabet:[2,3,22,37,44,55,63,172,183,192,332,340,354,373,436,454],alphanumer:[3,63,192,279,287,330,354,479],alreadi:[3,7,8,12,42,164,165,167,197,201,204,205,208,210,214,240,278,280,305,328,354,355,380,389,391,398,406,435,444,447,450,454,455,459,464,479],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,192,193,194,195,197,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,220,223,224,225,226,227,229,230,233,234,235,236,246,247,249,250,251,252,253,254,255,260,263,264,266,267,268,269,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,298,299,302,303,305,308,309,310,311,312,316,317,318,319,321,323,326,328,330,332,337,340,343,345,346,348,349,350,353,354,355,356,357,359,360,366,370,371,373,377,378,379,380,382,383,384,387,388,390,391,392,400,404,405,407,411,413,415,416,417,418,421,422,424,430,431,433,434,435,436,437,438,439,440,441,442,449,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,472,473,474,475,477,478,479,480,481,483],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,157,164,168,187,188,190,193,194,201,209,210,211,212,214,248,249,285,288,290,292,299,305,313,320,327,352,355,391,454,459,46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timet:478,central:[3,61,70,76,77,116,122,140,239,271,293,303,354,413,419,420,454],centro:[],centroid:[3,273,443,464],cerda:345,ceriotti2:227,ceriotti:[13,227,232],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,188,200,201,202,203,204,205,206,211,223,224,290,292,306,319,330,337,344,356,391,411,420,442,456,460,474,479],certainli:231,cerutti:346,cfg:[3,6,7,13,187,188,189,190],cfile:420,cfl:[128,295],cfor:294,cg_type:422,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:293,ch2lmp:[],ch3:293,chain3:356,chain:[],challeng:[6,294],chalopin:285,champaign:[230,345,346,405],chandler:[361,382],chandrasekhar:[6,396],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,192,193,194,195,196,198,199,204,205,207,208,209,210,211,212,213,214,215,219,220,222,224,227,229,230,231,233,235,236,237,239,245,246,247,249,250,251,252,253,254,255,261,266,267,268,269,271,272,276,277,279,280,284,287,288,289,290,292,293,294,305,308,309,310,311,313,314,315,316,317,318,320,323,326,328,346,351,353,355,358,360,380,384,388,391,405,406,407,411,419,420,436,449,450,451,452,454,455,456,457,458,459,460,462,463,464,465,466,469,472,475,477,478,479,480,481],change_box:[],changeabl:187,channel:[4,195],chapter:[273,346],charact:[2,3,6,12,38,41,56,63,184,187,188,189,190,192,208,279,287,330,354,359,384,395,417,419,420,438,451,452,456,461,462,479,481,482,483],character:[6,67,70,116,140,427,449,468],characterist:[234,305,314],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,190,192,193,194,199,215,220,225,279,281,282,283,287,307,320,345,346,354,367,369,375,376,378,379,382,384,385,391,396,400,404,414,419,420,436,441,442,444,446,447,454,455,459,464,466,474,478,479],charmm2lammp:13,charmm:[],chartreus:189,cheap:305,cheaper:[219,387,421],check:[3,6,8,11,12,15,17,39,41,71,91,184,199,204,208,209,210,215,222,225,231,232,289,293,305,313,315,320,328,330,344,353,354,355,356,357,360,381,392,395,411,420,435,449,451,452,454,462,468,471,472],checkf:184,checkqeq:420,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,213,218,226,227,234,236,248,249,250,267,268,273,277,280,282,290,294,305,308,309,312,313,314,315,322,331,339,341,345,346,352,355,362,367,371,372,375,376,377,379,380,384,386,387,389,390,396,400,401,404,407,410,411,414,435,442,463,466,468,474],chemic:[9,118,158,163,187,198,199,225,281,286,287,312,346,419,420,431],chemistri:[9,280,281,283,366,384,419,420],chen:317,cheng:375,chenoweth:[419,420],chenoweth_2008:[419,420],chi:[92,153,186,271,281,283,385,387,480],chiefli:418,child:8,chip:[7,12,17,360,467],chipot:213,chiral:339,chmod:[11,12],cho:407,chocol:[7,189],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,201,204,205,208,211,214,215,227,233,236,247,249,273,281,290,312,340,346,351,352,355,357,360,391,404,411,415,454,463,464,467,468,473,474,478],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,188,209,210,211,212,215,222,233,236,247,249,251,252,253,254,255,277,305,309,323,345,346,352,444,449,451,463,469],chose:[439,441],chosen:[2,3,6,12,17,140,164,167,176,184,188,194,199,212,215,222,225,226,234,236,247,249,253,273,276,287,305,309,312,313,318,320,321,327,346,347,352,360,384,388,394,395,398,422,439,449,463,468,474],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,201],chute:[4,10,228],ciccotti:293,cieplak:[6,170,466],cii:202,cij:202,circl:301,circular:[3,6,143,185],circumst:18,circumv:285,citat:[],cite:[3,7,8,12,233],cko:2,cl1:163,clarendon:[29,379],clarifi:[7,439,441],clariti:330,clark:414,class2:[],classic:[0,3,5,6,7,8,9,223,273,280,285,317,341,384],classifi:[9,436],claus:452,clean:[6,12,14,15,17,462],cleanli:[453,482],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:458,click:[2,11,22,37,44,55,164,172,183,188,230,332,340,355,373,436],client:[230,232],climb:[248,355,468],clinic:[7,13],clo:[153,186,480],clock:[12,449,468],clockwis:323,close:[3,6,11,12,13,39,41,67,141,167,187,210,211,212,227,234,236,249,267,290,293,323,326,344,346,349,351,352,355,360,362,366,376,377,407,411,423,425,441,458,464,474,476],closer:[3,41,116,162,186,187,208,212,216,314,355],closest:[210,271,290,320,387,421,435,444],cloud:474,clovertown:18,clsuter:72,clump1:[275,290],clump2:[275,290],clump3:[275,290],clump:290,cluster:[],clutter:[3,9],cmap:454,cmatrix:227,cmax:407,cmd:[11,12,273,465],cmin:407,cmm:[],cn1:202,cn2:202,cna:[],cnn:202,cnr:[9,13],cnt:[391,458],co2:[40,163,293,354],coars:[7,9,29,36,40,54,176,275,290,305,389,422,466],coarser:[346,479],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,331,332,337,373,391,395,411,424,426,428,454,456],coeffcient:454,coeffici:[],coefficienct:380,coefficient0:382,coefficient1:382,coeffieci:[6,364],coeffincientn:382,coexist:[9,225,384],cohes:[6,385,407],coincid:[122,326,371,405,406,449],cold:[6,149,229,356,474],coldest:313,coleman8:9,coleman:[9,118,163,291],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,189,201,213,239,245,275,285,288,290,328,345,354,356,374,394,454,461,467,483],collid:[219,305,327],colliex:163,collinear:[3,275],collis:[3,236,305,323,327,381,388,447],colllis:305,colloid:[],colombo:39,colon:[190,328,455],color1:189,color2:189,color:[3,9,41,187,188,189,208,226,280,285],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,189,192,200,201,202,203,204,205,206,239,246,247,280,290,306,307,317,327,386,390,419,420,455,469,471,479],colvar:[],colvarmodul:12,com:[],comamnd:214,comand:[211,456],comannd:360,comb3:[],comb:[],comb_1:282,comb_2:282,combiant:377,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,188,198,203,230,239,249,273,279,309,318,326,329,331,345,346,348,352,360,374,376,377,384,385,391,403,404,427,437,439,441,446,457,462,474,479],come:[],comfort:[12,13],comm:[0,3,12,61,73,230,232,233,346,355,360,380,411,416,438],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,234,290,317,354,355,361,382,383,385,395,407,413,420,427,437,438,439,440,441,451,452,454,474,479],commerci:7,commmand:[3,6,12,59,107,268,448,449,451,468,482],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,188,190,341,389,398,427,439,441,454,457,466],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,188,189,208,209,210,212,213,214,230,232,236,238,239,240,249,272,279,281,282,283,290,305,317,328,345,356,357,358,360,381,415,451,452,456,463,464,481,483],communc:345,comp:[7,232,233,293,346,355,384,411,416,421,434,438,440],compact:[63,192,373,436],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,189,218,281,328,330,345,346,353,355,407,449,468,469,474,478],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,331,332,340,372,436],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,190,194,200,201,202,203,204,205,206,208,272,284,309,312,319,322,325,345,360,392,411,438,451,452,479],compens:[6,209,210,288,356,384],compet:316,competit:346,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,190,230,316,346,360,454,455,459],compl:17,complain:[12,17],complement:407,complementari:[7,376,396],complet:[3,6,9,12,15,41,59,71,189,204,208,213,239,273,276,279,305,316,318,330,344,355,360,385,424,426,443,449,454,459,462,466,468,471,474,479],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,236,301,326,343,355,384,438,452,454,457,479],compli:[312,316],complic:[6,7,9,12,13,199,225,452],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,188,189,195,196,200,201,202,203,204,205,206,207,211,212,214,215,220,223,228,232,233,236,239,241,245,246,248,249,250,253,254,255,266,267,269,270,272,273,274,277,288,290,292,293,294,298,299,302,305,308,309,310,312,319,320,325,326,327,345,348,352,353,354,355,360,380,384,388,405,406,424,426,427,454,455,464,472,479,480],componenet:6,composit:[6,199,236,382],compound:[375,384,385],compres:[71,114,201],compress:[3,6,59,71,114,167,187,188,189,201,214,247,253,277,280],compris:[40,326,394,421,443],compton:[118,163],comptu:[3,6],compuat:346,comput:[],computation:[3,6,209,210,317,366],computational:474,compute_arrai:8,compute_fep:[194,404],compute_group_group:225,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,291],compute_scalar:8,compute_temp:8,compute_ti:194,compute_vector:8,compute_xrd:163,concaten:[2,3,482],concav:326,concentr:382,concept:[6,144,154,201,463],conceptu:[3,6,71,152,212,214,355,376,391,407,459],concern:[6,73,87,226],concis:[11,316],conclud:12,concret:8,concurr:[9,16,346],conden:[317,439,441],condens:[6,146,317,362,378,382,396],condit:[],conducit:6,conduct:[],cone:457,confid:[3,468],config:[12,187,451],configfil:213,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,188,192,212,213,214,215,219,225,232,233,261,273,281,316,343,353,355,362,366,383,407,437,439,441,449,454,456,457,468],confin:[454,468],conflict:[3,40,411,452],conform:[3,6,13,59,211,212,248,289,294,316,339,355,384,466],confus:3,conjuct:380,conjug:[7,8,233,352,384,419,420],conjunct:[6,7,71,86,87,114,147,152,158,164,168,189,193,194,233,236,240,261,276,277,281,282,283,285,290,305,313,320,325,345,346,355,367,369,373,376,380,384,390,396,411,414,422,442,454,457,461,474,483],connect:[3,6,87,149,167,211,230,275,290,293,302,355,377,388,435,441,451,452,458,474],conput:3,consecut:[3,11,12,39,71,164,189,193,194,215,230,231,376,396,400,449,455,457],consequ:[1,6,317,395,468],conserv:[3,192,199,211,218,219,226,229,233,235,236,240,245,247,249,261,290,293,308,309,313,320,321,325,355,379,380,388,402,463,468],consid:[6,9,70,71,78,87,115,149,150,167,187,189,193,194,200,202,204,208,210,211,215,237,250,272,290,312,313,316,317,320,346,373,384,391,420,421,435,449,450,452,455,456,457,459,462,464,472,474,479],consider:[6,8,233,234,308,309,310,360,463],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,190,195,196,201,214,215,218,220,223,226,233,234,235,246,249,251,252,253,254,255,256,257,259,260,261,262,264,265,266,267,268,269,277,280,285,287,289,290,308,309,310,311,321,345,346,348,354,355,360,362,366,368,374,376,384,387,391,405,406,407,411,421,424,426,438,444,452,454,455,457,458,459,466,474,479],consistent_fe_initi:198,consit:290,constant:[],constitu:[3,6,239,290,322,326,374,421],constitut:[424,426],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,192,201,215,225,226,231,239,243,275,276,288,290,293,303,313,320,353,354,384,459,466,474],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,140,163,212,249,272,289,326,356,360,379,411,435,437,438,457,458,479],constructor:8,consult:420,consum:[1,285,415,479],consumpt:343,contact:[],contact_stiff:[423,425],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,188,189,190,192,193,194,198,200,201,202,203,204,205,206,208,213,215,220,227,231,232,233,234,236,247,261,271,272,275,276,278,280,283,287,290,291,295,305,312,316,317,326,327,330,344,346,354,355,358,359,361,362,363,366,375,376,379,382,383,384,391,392,407,413,417,418,419,420,427,437,438,439,440,441,442,449,450,451,452,454,455,456,457,459,461,463,466,468,471,472,474,479,481,483],content:[12,18,420,470,472],context:[3,6,8,12,17,117,189,209,210,215,275,287,321,352,446,454,461,470,478,479,480],contibut:70,contigu:451,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,189,192,193,194,199,201,202,203,204,205,206,208,211,212,213,214,215,225,226,227,229,230,231,233,234,235,241,246,247,249,251,252,253,254,255,266,267,268,269,274,276,279,280,290,291,294,304,305,307,314,315,317,323,326,330,344,359,360,366,380,381,398,401,419,420,421,424,426,440,449,452,454,456,457,462,468,471,472,479,481],continuum:[6,7,9,198,317,424,426],contour_integr:198,contract:[59,212,214,249,277,290],contradictori:3,contrain:293,contraint:261,contrari:[227,234],contrast:[1,6,42,55,64,149,214,328,424,426,446,482],contrib:317,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,194,199,200,201,202,203,204,205,206,212,225,233,236,239,240,244,250,267,268,275,276,284,287,290,291,293,319,345,353,355,363,380,381,382,384,391,405,406,411,419,420,466,472,474],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,173,187,188,192,198,199,208,212,213,214,229,230,233,234,249,251,252,253,254,255,277,282,290,296,297,308,309,310,317,321,343,345,357,384,387,419,420,423,425,437,441,449,451,463,469,470],control_typ:198,controlfil:420,convect:91,conveni:[6,12,29,187,190,206,291,348,427,479],convent:[3,8,9,29,175,182,183,189,289,302,329,382,384,479],converg:[3,6,41,88,187,188,190,195,208,211,212,220,223,253,280,282,285,289,293,351,352,353,355,375,376,396,449,461,468],convers:[3,8,140,188,189,199,202,277,345,376,377,378,384,396,400,404,414,452,468,478],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,188,189,206,247,328,331,333,336,339,348,355,361,382,439,441,447,452,454,455,456,461,471,474,478,479,481,483],convex:326,convinc:[7,12],cook:9,cooki:7,cool:[7,154,229,288],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,201,204,205],coord2:[3,114,201,204,205],coord3:[3,114,201,204,205],coord:[],coordiat:353,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,192,195,200,201,203,204,205,208,209,210,211,212,213,214,215,218,220,221,223,225,228,229,230,231,232,233,234,246,248,249,251,252,254,255,267,270,271,272,275,276,277,287,288,290,292,293,294,299,302,303,304,305,307,315,316,317,324,325,327,328,348,353,354,355,360,361,362,365,383,449,454,455,457,459,462,464,468,474,479,480],coordn:[114,201],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,188,317,355,373,419,452],copper:447,coproccesor:16,coprocessor:[1,4,7,9,16,17,360,467],coproprocessor:17,copy_arrai:8,copyright:[7,8,275],coral:189,core:[],core_shel:146,coreshel:[6,9,369,376,378],cornel:[6,170,466],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,188,326,327,348,443,454],cornflowerblu:189,cornsilk:189,corpor:16,corr:375,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,188,214,227,233,249,250,267,275,277,280,316,322,326,345,355,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,454,469,472,474],correction_max_iter:198,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,189,195,215,220,223,234,243,249,250,283,290,293,302,304,323,326,355,356,360,378,406,451,452,454,464,478,480],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,188,189,193,194,195,201,203,204,205,207,210,212,214,221,223,224,228,233,236,237,245,246,247,249,251,252,253,254,255,256,261,264,266,267,269,272,273,277,282,290,292,293,308,310,312,321,322,323,325,326,327,329,331,332,333,334,335,336,339,341,346,350,352,354,355,361,362,364,367,368,369,370,371,372,373,374,375,376,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,411,412,413,414,416,417,419,420,421,422,427,428,437,438,439,440,441,443,445,446,447,449,451,452,454,455,457,467,468,469,471,472,474,479],correspondingli:[405,406,463],cosin:[],cosineshift:27,cosmo:[227,232],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,188,189,201,204,205,208,209,210,222,249,282,317,345,346,358,376,396,400,411,437,451,463],costheta0:[437,439,441],costheta:417,costli:[11,88,227,356],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,188,189,193,194,199,201,202,204,208,214,223,232,279,280,281,285,288,290,292,305,306,312,316,317,318,322,326,328,330,337,342,344,351,353,356,360,363,386,390,391,419,420,450,451,452,454,456,458,461,462,470,474,479,480],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,281,283,318,345,346,353,360,367,369,370,371,372,375,376,377,378,379,384,388,389,391,396,400,404,411,414,419,420,422,436,441,442,446,459,466,472,474,478],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,195,196,199,201,203,204,205,207,208,215,220,222,225,231,249,261,276,293,308,309,326,346,353,354,355,357,360,386,390,411,472,479],counter:[323,449,460,462,468],counterbal:229,counterpart:[187,290,449],counterproduct:18,coupl:[],courant:295,cours:[3,8,126,128,158,187,193,194,226,289,302,316,322,324,325,327,328,346,405,428,451,454,467,474,479,481],coval:[6,29,384,407,474],covari:227,cover:[6,71,184,189,198,236,384,394,443],coverag:[71,204],cpc:232,cpp:[1,3,6,8,9,11,12,13,87,187,193,194,223,293],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,189,192,218,234,318,343,346,360,373,436,449,467,468,471,472],cpuremain:472,cr2:163,cr3:163,crack:[4,356],crada:[5,7],crai:[5,7,13,18,187],crash:[3,356,474],craympi:360,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:198,create_faceset:198,create_nodeset:198,createatom:[],creation:[],crimson:189,critchlei:275,criteria:[3,116,165,188,189,209,210,211,244,353,416,443,456,459,479],criterion:[41,121,162,164,167,199,208,211,225,261,282,295,323,328,353,355,375,384,388,459,468,469],criterioni:468,critic:[48,49,247,312,317,353],cross:[3,12,22,71,89,143,172,187,188,200,204,210,214,246,248,267,290,298,302,304,313,320,332,348,355,371,380,381,382,389,390,391,396,398,400,417,422,424,426,439,441,454,458,464,481],crossov:1,crossterm:454,crozier:[0,7,13],crucial:280,crystal:[4,6,13,73,271,272,315,356,458,472,474],crystallin:[6,272,348,440,474],crystallis:312,crystallogr:[118,163],crystallograph:[348,472],crystallographi:[118,163,348],cs1:163,cs_chunk:6,cs_im:[40,454],cs_re:[40,454],csanyi:[140,418,427],cscl:407,csequ:6,csh:[11,12,373],cshrc:[11,12],csic:[383,437,439,441],csinfo:6,csisi:[383,437,439,441],csld:[],cst:382,cstherm:6,cstyle:451,csvr:[],ctcm:[361,382],ctemp_cor:218,cterm:294,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:407,cube:[6,41,162,167,208,218,326,348,474],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:366,cummul:[3,6,206,209,210,211,213,222,227,233,235,305,308,309,310,311,313,320,390,472],cumul:[6,199,201,203,204,205,219,225,233,247,249,253,261,290,291,355],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,193,194,198,199,201,204,205,206,208,209,210,211,212,213,214,215,219,220,223,225,227,230,231,233,239,246,249,250,254,255,261,266,267,269,275,281,282,284,287,288,289,290,293,294,295,296,297,298,299,301,303,304,305,308,309,310,316,317,320,321,322,323,324,325,327,328,330,343,344,345,346,349,350,352,353,354,355,360,366,373,375,379,382,384,385,388,392,395,405,406,407,408,409,411,417,419,420,423,424,425,426,428,439,441,442,444,449,450,451,452,454,455,456,457,458,460,461,462,464,466,468,469,471,472,479,480,481,482,483],curv:[6,164,225,272],curvatur:[387,421,447],custom:[],cut0:452,cut1:463,cut2:463,cut:[],cuthi:[271,283],cutinn:[368,405,406],cutlo:[271,283],cutmax:417,cutoff1:[372,379,396,400,404,414,422],cutoff2:[367,369,370,372,378,379,396,400,404,414,422],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,210,211,216,271,280,281,283,285,287,290,305,318,322,326,328,345,346,353,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,452,456,459,463,474],cutoffa:383,cutoffc:383,cuu3:382,cval:163,cvd:312,cvel:294,cvff:[],cwiggl:[3,246,322,325,327,479],cyan:[2,188,189],cycl:[3,225,247,249,250,253],cyclic:[3,184],cygwin:12,cylind:[3,4,188,231,276,323,326,457],cylindr:[6,231,302,323],cypress:360,cyrot:366,cyrstal:272,d3q15:236,d3q19:236,d_double_doubl:15,d_e:317,d_flag2:279,d_flag:279,d_name:[113,187,279,307,464],d_single_doubl:15,d_single_singl:15,d_sx:279,d_sy:279,d_sz:279,daan:315,dai:12,daili:12,daivi:267,damag:[],dammak:285,damp:[3,6,192,197,233,234,235,240,249,250,253,277,280,285,290,308,309,321,323,324,352,353,355,367,369,371,376,379,384,388,396,404,414,422,436,442,468,474],damp_com:234,damp_drud:234,dampen:[290,474],dampflag:[323,388],dan:17,danger:[3,12,225,328,380,472],dangl:167,daniel:9,darden:[346,379],darkblu:189,darkcyan:189,darken:188,darkgoldenrod:189,darkgrai:189,darkgreen:189,darkkhaki:189,darkmagenta:189,darkolivegreen:189,darkorang:189,darkorchid:189,darkr:189,darksalmon:189,darkseagreen:189,darkslateblu:189,darkslategrai:189,darkturquois:189,darkviolet:189,dasgupta:281,dash:[388,471],dat:[6,91,184,198,450],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,291],dataset:291,datatyp:3,date:[0,6,12,13,419,420,479],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,202],davi:322,david:[9,19,345,346,439,441],daw:[382,417],dbg:14,dcd:[3,6,7,187,188,189,190,273,455,459],ddim:186,deactiv:404,dealt:232,debug:[6,7,11,12,13,14,17,118,122,163,164,273,278,343,345,360,392,411,444,452,453,456,461,464,471,479],deby:[],decai:[376,447],decid:[3,6,12,16,71,246,279,290,318,469],decipher:348,declin:305,decod:188,decompos:[87,427],decomposit:[3,5,7,18,62,198,273],decoupl:[6,474],decreas:[3,187,195,196,211,214,220,223,233,316,345],decrement:294,deepli:342,deeppink:189,deepskyblu:189,def:[12,13,452],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,218,219,220,223,224,225,228,231,232,233,234,235,236,244,246,248,249,250,251,252,253,254,255,257,258,259,262,264,265,266,267,268,269,271,272,273,275,276,277,279,281,283,288,290,291,292,293,295,299,303,305,307,308,309,310,311,313,314,315,317,319,320,322,323,324,325,326,327,328,330,331,332,333,334,335,336,339,340,341,343,345,346,348,350,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,376,377,379,380,381,383,384,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,410,411,412,413,414,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,454,455,457,458,459,460,463,464,465,466,468,469,471,472,474,475,476,477,478,479,480],definit:[2,3,6,8,12,13,78,80,116,140,189,201,202,203,204,205,206,214,231,253,291,307,319,322,325,327,329,340,343,354,363,366,374,384,394,417,424,426,427,443,452,454,456,463,465,478,479],defint:472,deform:[],deg2theta:163,deg:474,degener:[3,275],degrad:[8,18,272,346,463],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,188,201,211,218,225,227,228,233,234,239,249,250,253,254,255,266,267,269,273,275,289,290,293,308,309,310,315,331,333,336,339,341,353,379,382,390,464,472,474,480],degress:[144,201],del:468,delai:[3,6,12,356,381,472],deleg:391,delet:[2,3,7,8,12,54,57,60,63,162,167,168,192,201,202,203,204,205,206,209,211,222,225,249,291,308,309,328,330,344,354,356,359,411,454,455,457,465,466,471,475,477,479,480],delete_atom:[],delete_bond:[],delete_el:198,deli:186,delimit:[452,479],deloc:[250,384],delr:407,delt_lo:468,delta:[],delta_1:366,delta_3:366,delta_7:366,delta_conf:3,delta_ij:[407,417],delta_mu:[3,199],delta_pi:366,delta_r:417,delta_sigma:366,delx:186,delz:186,demand:285,demo:11,demon:270,demonstr:[280,407],den:276,dendrim:390,denniston:[9,236,238,239,240,272],denomin:[7,169],denot:[118,218,234,272,283,285,376,389,391,420,424,426],dens:[71,211,384],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,193,194,198,201,204,205,208,214,223,236,239,242,243,272,276,277,281,317,322,348,350,354,361,366,382,407,408,409,417,421,430,432,433,434,454,463,464,472,478],density_continu:426,density_summ:426,depart:[0,7],departur:[247,280],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,188,189,192,193,194,195,196,199,201,203,204,206,207,208,210,212,220,221,224,227,228,229,231,233,234,236,238,239,246,249,251,252,253,254,255,256,264,266,267,269,271,282,285,287,290,292,293,299,305,308,309,310,312,314,316,317,319,321,322,325,326,327,328,330,331,332,333,334,335,336,339,341,346,348,353,354,356,357,358,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,410,412,413,414,416,417,419,420,421,422,427,428,436,437,438,439,440,441,442,443,445,446,447,449,451,454,456,457,460,464,466,468,471,472,473,479,480],dependend:6,depflag:12,dephas:[449,468],depos:215,deposit:[],deprec:281,depth:[51,143,188,317,387,421],dequidt:9,der:[87,107,374,375,404,419,420,446,474],deriv:[6,7,8,38,56,63,87,140,158,184,202,212,214,225,233,246,249,251,252,253,254,255,271,277,281,285,314,315,317,322,323,326,352,354,362,366,374,379,384,385,389,398,402,403,407,419,420,436,438,446,474],derjagin:446,derlet:271,descend:189,descent:[7,352],descib:[40,281],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,192,193,194,201,202,203,204,205,206,208,211,212,213,214,215,217,218,226,227,230,231,232,233,234,235,236,238,239,240,244,248,249,250,253,260,268,271,273,278,279,280,281,282,283,290,294,302,305,306,307,308,309,310,311,312,313,314,315,320,322,323,325,330,345,346,348,351,352,353,354,355,359,362,363,365,367,368,369,371,372,373,374,375,376,379,382,384,385,387,388,389,391,396,397,398,399,400,401,402,403,404,405,406,407,410,416,417,418,419,420,421,422,427,428,435,436,437,438,439,440,441,442,445,446,447,449,451,452,454,455,457,458,464,467,468,471,479,480,481],descript:[],descriptor:[140,187,392],deserno:346,design:[0,3,6,7,8,11,13,14,15,17,118,146,149,163,198,211,217,218,249,250,271,272,291,312,317,363,364,365,368,371,376,378,384,404,405,406,408,409,417,420,438,463],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,199,201,206,212,214,223,225,226,233,234,235,239,249,267,275,276,277,278,281,285,290,293,305,308,309,310,311,316,323,337,342,345,346,348,351,353,354,355,380,382,390,405,406,437,439,441,450,451,452,454,458,463,468,469,471,472,479,480,481],desk:7,desktop:[4,6,7,10,12,17,188],despit:474,destabil:366,destre:339,destroi:[11,39,209,210],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,188,189,192,193,194,198,201,202,203,204,206,208,210,211,212,213,214,215,223,225,226,227,228,230,231,233,235,236,240,246,247,248,249,250,251,252,253,254,255,259,261,266,267,268,269,272,275,276,277,279,280,282,283,284,290,293,305,308,309,310,311,312,313,315,316,317,318,319,320,321,328,330,332,340,345,346,349,353,354,356,357,360,361,362,363,365,366,368,370,371,372,373,374,375,376,379,380,384,385,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,407,410,411,416,419,420,421,427,428,436,443,445,446,452,454,455,456,457,459,460,463,464,466,469,472,479,480,483],detect:[2,3,12,61,63,86,224,276,316,355,375,390,395,449,451,454,465,468,479],determ:360,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,188,189,190,191,195,196,197,200,201,202,203,204,205,206,207,208,212,214,215,218,220,225,228,229,231,233,234,239,244,246,247,249,254,255,266,267,269,271,273,277,280,287,288,289,290,291,292,295,297,299,305,308,309,310,312,318,319,322,323,324,325,326,327,328,340,345,346,348,354,356,357,360,362,363,370,375,379,381,382,386,388,391,392,400,407,411,420,421,435,438,442,446,451,454,455,457,459,461,464,468,470,471,478,479,480],detil:108,devan:[9,422],devanathan:441,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,230,253,275,280,281,284,362,366,384,409,456],devemi:9,deviat:[247,253,271,386],deviator:9,devic:[1,3,12,15,17,230,360],device_typ:360,devin:[282,375],devis:409,dfactor:188,dff:474,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,346],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,284],dhi:[59,186,214,276],dhug:[247,280],dhugoniot:[247,280],dia:407,diagnost:[],diagon:[3,6,83,140,141,212,249,277,290,320,424,426],diagonalstyl:427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1,293,294,305,307,308,309,310,311,312,313,316,317,318,319,320,328,330,344,346,355,356,357,360,380,381,391,404,419,420,432,448,449,450,454,456,458,459,461,462,463,468,469,470,472,479,483],everyth:[8,107],everywher:[116,398],eviri:384,evolut:[227,236,273,449],evolv:[236,273,318],ewald:[2,3,5,6,7,8,12,88,110,118,141,318,345,346,353,367,369,370,376,379,384,396,400,414,422,436,438,456],ewald_disp:379,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,208,211,226,227,233,234,235,276,285,286,305,317,332,345,373,456,461,468,481,483],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,193,194,203,208,214,219,226,233,234,235,250,260,261,268,272,280,305,310,311,324,360,373,380,382,388,391,394,405,411,438,456,457,464,468,479],exager:474,examin:[6,8,211,272],examp:[452,479],exampl:[],exce:[3,6,16,17,18,41,58,71,166,201,204,205,208,212,214,219,222,249,272,296,297,305,353,360,454,479],exceed:[3,41,59,208,214,249,305,462],excel:384,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,192,195,201,202,203,207,208,212,214,221,224,225,228,231,233,235,249,250,251,252,253,254,255,256,260,261,264,266,267,268,269,273,282,283,290,292,293,302,305,308,310,311,317,321,328,330,331,332,333,334,335,336,339,340,341,345,346,348,350,354,355,356,358,359,360,361,362,364,367,368,369,370,371,372,373,374,375,376,378,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,408,412,413,414,416,419,420,421,422,428,436,437,438,439,440,441,443,445,446,447,449,451,452,454,456,457,459,462,463,464,465,466,468,472,474,478,479,480,482],excess:384,exchang:[2,3,6,8,9,61,62,192,198,199,225,233,282,290,313,317,320,345,360,384,469],exchange:345,excit:[9,384],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,201,204,209,210,237,245,275,288,290,312,323,328,353,354,356,368,388,391,405,406,411,435,466],exclus:[1,3,9,12,16,87,360,375,411,463],excurs:449,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,188,230,284,330,344,347,359,450,452,462,465,468,479],exemplari:226,exemplifi:384,exert:[6,231,234,285,324,325,326,346],exhaust:[198,359,479],exhibit:[249,352,384,463],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,192,197,207,210,212,215,225,275,276,278,328,331,333,334,336,340,349,354,360,391,419,444,450,452,454,455,456,465,466,467,479,480,481],exit:[2,3,11,12,41,57,187,208,344,359,452,453,462,471,479],exlanatori:3,exp:[],expand:[],expans:[12,140,187,465],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,208,220,225,227,246,271,277,279,280,285,290,328,346,356,373,407,411,449,452,454,456,459,463,468,479],expens:[6,10,71,189,271,275,290,317,328,345,346,356,360,452],experi:[6,13,15,17,207,215,230,239,248,277,289,290,351,355,380,411,463,468],experienc:[6,12,238,239],experiment:[345,360,468],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,188,189,192,201,202,206,208,210,212,214,249,271,279,290,302,328,330,344,345,348,354,355,359,365,382,394,428,443,447,452,455,456,459,461,464,474,479,483],explan:[3,6,59,113,140,187,201,248,271,391,448,451,452,454,463],explanatori:[3,8,117,187,200,201,203,204,205,290,354,451,479],explantori:[3,286],explic:410,explicit:[6,9,11,22,44,77,87,113,116,158,172,193,194,214,296,297,332,350,362,363,366,371,373,382,384,395,405,442,448,451,455,458],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,189,195,204,207,214,221,224,226,228,233,249,251,252,253,254,255,256,264,266,267,269,279,280,282,290,292,293,308,310,311,317,321,331,333,334,335,336,339,341,354,360,361,362,364,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,388,389,390,391,394,395,396,397,398,399,400,401,402,403,404,405,408,411,412,413,414,416,421,422,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,445,446,447,454,456,463,464,466,467,474],explictli:[16,467],exploit:[9,15,17,273],explor:[118,163],expon:[3,281,283,382,387,390,404,410,422],exponenti:[87,417,437,447,468,479],expos:11,exposit:[198,380,381],express:[6,140,150,164,193,194,212,246,271,281,317,323,330,366,382,384,398,407,427,436,479],expressiont:366,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,192,195,196,199,206,207,213,216,220,223,224,225,227,228,229,231,233,235,247,249,253,261,271,272,288,289,290,292,294,299,302,304,308,309,310,311,312,314,315,317,319,322,326,327,387,407,420,421,427,471,472],extent:[1,3,41,45,57,71,162,166,187,197,204,208,231,324,327,345,348,362,423,425,438,451,454,457],exterior:[3,6,326],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,189,203,208,210,249,278,279,280,290,305,353,354,357,358,379,388,391,394,407,411,451,452,454,457,466,474,479],extract:[3,6,11,13,36,63,87,107,115,117,119,193,194,283,355,376,385,407,427,452,459,471],extract_atom:11,extract_comput:[11,452],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,188,212,214,249,315,384,440,474],extrema:404,extrins:198,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,319],f_a:[439,440,441],f_ave:117,f_c:440,f_f:441,f_fix_id:280,f_harm:315,f_i:417,f_id:[6,71,117,119,187,192,200,201,202,203,204,205,206,244,307,319,472,479],f_ij:417,f_indent:206,f_int:314,f_jj:91,f_k:417,f_langevin:317,f_max:[280,285],f_msst:247,f_r:[234,439,440,441],f_sigma:366,f_solid:315,f_ss:6,f_temp:234,face:[3,6,57,59,71,152,162,166,197,204,205,322,324,325,326,327,348,387,407,421,454,457],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,227,305,315,388,466],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,188,189,193,194,202,208,212,214,215,225,230,233,235,236,247,249,250,253,273,277,289,293,295,297,305,309,313,320,321,322,326,336,346,348,360,362,363,366,367,369,371,376,377,378,380,384,388,391,395,396,407,411,413,414,420,422,428,437,442,451,454,457,458,463,466,468,469,472,474,478,479],factori:[3,452],factoriz:345,fail:[3,11,12,59,168,212,215,345,353,355,378,420,452],failur:[121,424],fairli:[11,411,463,468],faken:73,falcon:230,fall:[3,6,189,203,276,452],fals:[86,328,330,479],fame:8,famili:451,familiar:[0,11],fan:417,far:[3,6,12,17,57,59,61,86,187,189,190,208,209,210,212,215,249,271,289,290,305,322,333,336,351,355,356,443,452,454,459,472],farago:233,farrel:[439,441],farther:187,fashion:[6,8,41,71,164,189,192,193,194,199,204,208,210,215,225,227,231,246,247,249,251,252,253,254,255,263,266,267,268,269,279,280,282,290,294,298,304,307,315,317,321,322,323,325,327,355,391,405,457,466,479,482],fasolino:393,fast:[6,7,9,12,13,17,39,187,258,280,318,345,346,368,405,406,436,438,456,461,463,472,480,483],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,189,192,195,207,208,221,224,228,232,233,249,251,252,253,254,255,256,264,266,267,269,277,281,282,290,292,293,305,308,310,312,314,317,321,331,333,334,335,336,339,341,345,346,357,358,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,436,437,438,439,440,441,443,445,446,447,449,463,467,474],fastest:[6,14,17,152,204,317,318,360,451],fatal:[3,471],fault:[70,420],faulti:12,fava:387,favor:211,favorit:7,fbmc:312,fcc:[],fcm:[263,479],fdirect:218,fdotr:392,fdti:87,fe2:163,fe3:163,fe_md_boundari:198,featu:8,featur:[],fecr:382,feedback:[7,230],feel:[7,230,231,239,271,326,328,355,411],felling:409,felt:326,femtosecond:478,fene:[],fennel:[376,396],fep:[],ferguson:[6,170,466],fermi:[1,12,15,150,360,441],fermion:[9,384],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,190,200,201,202,203,204,205,206,234,249,276,279,281,293,319,345,353,354,355,362,451,454,459,463,465,479,481],fewer:[1,3,11,15,16,61,239,463],fewest:3,fextern:223,feynman:273,fff:452,ffield:[375,385,419,420],ffmpeg:[3,12,188],ffplai:188,fft:[1,3,7,12,14,15,88,109,110,141,272,345,346,463],fft_inc:[12,346],fft_lib:12,fft_path:12,fftbench:345,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,195,196,220,223,227,273,289,376,396,400,435],field1:[455,459],field2:455,field:[],fifth:[302,413],figur:[1,3,8,11,12,280,451,452],fij:379,file0:271,file1:[11,13,271,316,330,354,459,461,465],file2:[11,13,316,330,354,459,461,465],file:[],filenam:[3,12,13,38,41,56,184,187,188,189,190,198,201,202,203,204,205,206,208,213,271,275,278,281,282,283,286,287,290,291,316,317,342,343,344,355,361,362,366,376,382,383,385,393,407,408,409,413,417,418,419,420,427,437,438,439,440,441,450,451,452,455,456,461,465,472,479,481,482,483],filennam:461,filep:[3,187,189,456,461,483],filepo:287,fill:[7,164,188,276,317,348,356,366,420,457],filter:[189,198],final_integr:8,final_integrate_respa:8,finchham:[6,146,378],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,190,199,211,212,222,225,248,271,277,285,289,351,353,355,356,376,391,396,400,407,436,438,474,479],find_custom:8,fine:[16,17,168,195,220,315,356,360,479],finer:[140,164,479],finest:345,finger:[164,186,246,457],finish:[6,11,41,208,330,342,344,345,357,359,360,443,459,479,480],finit:[],finni:[7,382,436],finvers:218,fiorin:[9,213],fire:[351,352,353,355,468],firebrick:189,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,192,199,201,202,203,204,205,206,208,211,214,225,226,231,236,246,247,248,249,271,273,278,279,280,282,287,290,293,294,302,303,305,306,307,314,315,316,317,319,323,328,330,331,337,348,353,354,355,356,359,360,361,362,365,366,367,369,371,373,375,376,382,384,385,388,389,392,393,395,396,400,405,406,407,409,411,413,417,419,420,427,435,437,438,439,440,441,449,450,451,452,454,455,456,459,461,463,466,467,468,471,472,474,479,480,481,483],fischer:[6,9,19,20,170,371,466],fit:[3,6,9,12,38,56,184,289,305,362,366,393,407,411,431,438,440,462,479],five:[73,150,280,354,366,408,454,468],fix:[],fix_adapt:[158,194,404],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,199,276],fix_evapor:199,fix_flux:198,fix_gcmc:[199,354],fix_gl:227,fix_gld:227,fix_grav:276,fix_id:[3,212,247,249,251,252,253,254,255,277,280],fix_modifi:[],fix_mov:[186,323],fix_nh:8,fix_npt:227,fix_nvt:[199,225],fix_poem:[3,6],fix_pour:[3,215],fix_qbmsst:9,fix_qeq:[3,375],fix_rattl:293,fix_reax_bond:419,fix_rigid:[239,365],fix_saed_vtk:291,fix_setforc:8,fix_shak:293,fix_srd:3,fix_styl:253,fix_temp_rescal:311,fixedpoint:[212,249],fixextern:223,fixid:198,fji:379,flag1:[217,358],flag2:[217,358],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,188,189,190,206,211,213,217,230,233,237,239,245,246,272,279,290,302,304,305,312,316,325,328,343,346,354,358,359,360,362,390,395,407,435,449,451,452,454,455,456,458,459,460,464,479],flag_buck:370,flag_coul:[370,379,400],flag_lj:[379,400],flagfld:[368,405,406],flaghi:[3,368,405,406],flaglog:[368,405,406],flagn:217,flagvf:[368,405,406],flat:[6,317,322,323,327],flavor:[2,7,12],fld:[9,322,368,405,406],flen:363,flex_press:363,flexibl:[3,6,8,165,188,201,204,213,227,250,313,320,384,440,472],flip:[3,6,214,249,324,325],floor:479,flop:12,floralwhit:189,flow:[],fluctuat:[6,64,87,212,225,226,233,236,249,253,271,272,315,317,339],fluid:[],fluid_veloc:240,flush:[3,189,471],flux:[],flv:188,fly:[7,9,12,41,188,192,198,215,218,290,293,318,366,472,474],fmackai:9,fmag:216,fmass:273,fmax:[353,472],fmomentum:218,fmsec:[2,189,233,234,246,249,277,290,308,309,463,473,478,480],fname:344,fno:12,fnorm:[353,472],fnpt:218,fnvt:218,foce:391,fock:363,focu:293,fogarti:[9,283,420],foil:[140,271,427],fold:[303,463],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,192,198,199,200,201,202,203,204,205,206,208,213,214,215,218,219,223,225,226,227,230,232,233,234,236,239,247,249,253,254,255,266,267,269,272,273,275,278,279,280,281,283,285,287,289,290,291,293,307,308,309,310,313,314,315,316,317,319,320,328,329,333,334,335,336,339,341,343,348,350,353,354,355,360,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,437,438,439,440,441,442,443,445,446,447,449,451,452,454,455,456,457,459,461,462,463,466,468,469,470,474,479,480,482],foo:[4,8,11,12,187,188,223,452,465,479],foot:6,footprint:[12,360],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:239,forcefield:[289,390],forcegroup:236,forcezero:351,ford:379,forestgreen:189,forev:71,forget:[234,474],forgiv:249,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,189,192,193,194,210,226,227,233,235,239,246,267,272,283,285,289,290,317,322,326,331,332,339,350,352,354,355,362,363,366,373,382,384,386,390,391,395,407,409,413,414,417,419,420,421,427,428,436,438,439,440,441,446,448,451,452,454,459,464,471,474,479],formal:[6,78,80,91,226,227,233,249,273,305,313],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,201,203,204,205,206,208,210,272,275,279,281,283,286,290,291,301,316,317,328,329,332,350,354,355,361,362,366,373,382,385,395,407,409,418,419,420,422,427,438,444,451,452,454,455,456,459,470,471,472,479,481],former:[6,12,16,39,41,189,208,317,321,366,368,460,466,479],formerli:[7,13],formul:[1,40,64,141,195,220,233,249,267,281,283,289,293,316,345,362,366,382,384,387,407,416],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,193,194,195,196,201,202,203,206,207,214,220,228,229,231,233,234,246,271,272,278,287,292,299,303,305,308,309,310,319,322,325,327,328,330,331,332,334,340,348,354,362,363,365,366,371,372,373,374,379,380,382,383,387,388,389,390,392,395,396,398,399,400,402,403,405,406,407,410,411,412,421,422,428,436,437,439,440,441,445,446,447,450,454,457,464,471,472,478,479,480],forth:[1,6,11,12,13,14,15,359,452,457,461],fortran:[3,6,9,11,12,13,223,382,391,407,419,420],fortun:8,forward:[3,8,87,344,355,360],foster:[366,416,417],foul:167,found:[3,6,9,12,73,158,187,211,213,225,230,236,272,312,318,330,344,356,373,376,379,449,455,456,471],four:[6,11,54,81,103,104,140,160,247,31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input1:[65,68,69,79,92,108,113,114,115,117,119,307],input2:[65,68,69,79,92,108,113,114,115,117,119,307],input:[],input_doubl:3,inquir:295,insensit:12,insert:[3,5,7,8,12,59,164,192,215,225,231,276,345,427,435,452,458,474],insid:[2,3,6,8,11,71,129,135,164,187,189,200,204,205,215,216,222,225,231,236,239,276,290,305,322,324,325,326,327,328,343,348,398,452,453,454,456,457,464,468,479],insight:[6,13],instabl:[236,379,426],instal:[],instanc:[6,11,213,227,324,386,391,411,417,452,474],instantan:[6,63,211,212,226,227,249,253,272,277,280,285,287,290,312,460,472],instanti:[6,11,12,198,391,451],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,143,146,168,184,187,194,201,203,204,205,206,208,212,213,233,236,239,240,272,278,288,290,307,325,343,345,346,349,356,360,369,370,382,395,397,404,407,449,457,461,468,470,474,479],institut:[9,230,275],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,142,151,162,170,171,173,174,175,176,178,179,181,182,184,185,188,195,207,221,224,228,233,249,251,252,253,254,255,256,264,266,267,269,282,290,292,293,308,310,321,331,333,334,335,336,339,341,346,360,361,362,364,367,368,369,370,371,372,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447,463,474],insuffici:[3,6,12],insult:249,insur:[3,6,11,12,17,39,40,61,73,102,104,164,165,184,187,188,189,195,209,210,215,220,221,222,223,225,228,233,245,278,279,288,290,305,317,322,326,327,328,330,344,354,356,360,374,387,391,415,421,438,451,452,454,455,459,462,463,471,472,479,480],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,140,162,164,167,168,170,174,175,179,184,186,187,188,189,199,201,204,205,209,210,211,215,217,223,225,226,227,230,233,234,235,236,272,275,276,279,280,285,290,305,307,309,312,316,317,335,345,348,368,380,381,394,407,419,420,424,426,427,449,451,452,454,462,463,464,468,471,479,480],integr:[],integrate_ulsph:296,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,226,418,454],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,161,163,192,201,202,203,204,205,206,208,209,210,211,219,222,229,239,247,249,253,287,290,291,305,313,317,319,320,471,472],intepol:479,inter:[14,18,42,61,62,144,167,168,187,211,233,235,248,282,290,345,355,366,464,474,479,481,483],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,122,123,124,125,127,128,129,130,131,132,133,135,136,137,138,140,141,143,157,158,162,165,166,167,168,169,170,172,176,177,183,187,192,193,194,209,210,211,224,225,230,231,233,235,239,261,271,273,275,281,283,289,290,296,297,305,306,312,317,321,322,323,326,327,332,333,334,336,340,345,346,353,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,420,421,422,424,426,427,428,435,436,437,439,440,441,442,443,444,445,446,447,449,452,454,456,458,459,463,464,466,471,472,474,481],interatom:[3,4,7,164,187,248,314,315,361,366,382,384,392,407,440,479],intercept:118,interchang:6,interconnect:18,interconvert:384,intereract:39,interesect:326,interest:[1,5,7,8,9,11,13,71,163,273,312,315,346,383,406,419,420,452,479],interf:360,interfac:[],interfer:[249,362],interg:[6,474],intergr:[463,467],interi:406,interior:[3,6,41,326,457],interlac:407,interleav:[6,164,462],intermedi:[6,12,59,188,248,271,339,355,452,453,462,466],intermix:449,intermolecular:362,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,141,144,146,163,171,184,188,189,192,193,194,198,210,214,218,230,242,243,247,249,253,272,290,294,331,333,336,339,343,353,354,429,430,438,452,454,456,459,468,471,472,478,479,480,481],internal_element_set:198,internal_quadratur:198,internet:232,interpenetr:407,interpentr:[430,431,433],interpol:[6,15,38,56,100,184,188,189,198,236,271,345,346,355,366,411,420,432,438,439],interpret:[2,6,11,188,203,388,428,449,452,468,479],interrupt:280,intersect:[3,6,118,189,326,328,457],intersert:326,interspers:353,interstiti:162,intertia:[3,93],interv:[3,6,91,202,233,280,285,286,297,432,449,468,479],intestieti:118,intial:[6,360,362],intiial:[41,459],intiti:[3,304],intra:290,intra_energi:225,intramolecular:[29,225],introduc:[6,9,188,249,280,285,290,339,345,361,376,384,396,400,404,437,468],introduct:[],intsal:16,intuit:348,inv:[118,163,291],invalid:[3,12,71,89,167,261,355,405,406,456],invari:[133,138,140],invent:293,invers:[],invert:[6,168,272],invis:326,invoc:[162,211,360,424,426,452],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,142,151,158,159,162,164,165,167,168,170,171,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5,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,107,109,112,142,143,147,151,157,162,164,165,166,167,168,170,171,173,174,175,176,178,179,181,182,184,186,187,188,195,198,202,203,206,207,209,210,211,212,215,221,224,225,228,230,233,246,249,251,252,253,254,255,256,264,266,267,269,276,279,282,288,290,292,293,294,307,308,310,313,317,319,320,321,322,323,326,327,328,331,333,334,335,336,339,341,346,348,354,355,356,359,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,396,397,398,399,400,401,402,403,404,405,407,408,409,411,412,413,414,416,417,419,420,421,422,428,437,438,439,440,441,443,445,446,447,448,451,452,454,456,457,458,461,462,463,464,465,466,467,471,472,478,479,481,483],yourself:[6,8,12,13,212,354],yplane:323,ypo:164,ysu:[3,187,455],yuan:9,yukawa:[],yukawa_1_1:444,yxz:451,yzx:451,z_i:[384,441,447],z_j:[441,447],z_meam:407,zachari:13,zannoni:387,zbl:[],zblcut:441,zblcutinn:427,zblcutout:427,zblexpscal:441,zblz:427,zcm:290,zcylind:323,zepeda:199,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,75,87,88,90,93,102,103,104,105,106,108,109,110,112,113,114,115,116,117,118,121,140,141,143,144,145,152,153,156,157,159,161,162,163,164,166,167,168,170,173,182,184,186,187,188,189,192,193,194,195,197,199,200,201,202,203,204,205,206,207,208,209,210,212,214,219,220,221,222,224,225,226,227,229,233,234,235,236,237,239,245,246,247,249,253,261,264,273,278,279,280,281,282,285,287,288,290,291,292,293,296,297,299,305,307,312,313,315,317,320,321,322,323,324,325,327,328,329,330,335,348,351,353,354,355,356,360,363,366,367,369,370,371,374,376,379,380,384,387,389,390,391,392,396,398,400,401,404,406,407,411,416,420,421,422,435,438,442,447,449,450,451,454,455,457,459,461,462,463,464,468,469,472,474,479,480,481,483],zeta:[3,236,281,385],zfactor:188,zflag:[151,152,237,239,245,290,312],zhang:[290,313,388],zhi:[3,6,166,187,197,316,322,325,327,454,457,472],zhi_bound:[6,187],zhou:[13,366,385,417,439,441],zhu:434,ziegenhain:13,ziegler:[275,407,436,441,447],zimmerman2004:198,zimmerman2010:198,zimmerman:[9,70,198,366],zlat:[214,231,472],zlo:[3,6,166,187,197,316,322,324,325,327,454,457,472],zlo_bound:[6,187],zmax:[197,236,479],zmin:[236,479],zn2:163,zone:[118,291],zoom:[3,187,188,189],zplane:323,zr4:163,zrest:304,zsu:[3,187,455],zwall:322,zwall_veloc:236,zxy:451,zybin:420,zyx:451},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","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","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local 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/local command","compute dilatation/atom command","compute displace/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 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 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 temp command","compute temp/asphere 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","dimension command","displace_atoms command","dump 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/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/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 smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style 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","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style 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 meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style 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_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl 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","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":209,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,188,189,190,191,193,194,195,197,198,199,201,204,205,206,209,210,212,213,214,215,219,222,225,226,231,233,234,235,236,237,239,244,247,249,250,253,267,268,272,273,276,277,278,279,280,282,285,287,288,290,291,305,307,312,313,314,315,318,320,322,324,328,340,343,345,346,348,349,351,352,354,356,357,358,360,363,366,368,384,405,406,411,419,420,435,436,449,450,451,454,455,457,459,461,462,463,466,468,470,471,472,473,478,480,481,482],"function":479,"long":[367,369,370,371,372,376,378,379,396,400,404,414,422],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[193,194],addforc:195,addit:[12,13],addtorqu:196,adiabat:6,adjust_dt:295,adp:361,airebo:362,alloi:382,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:197,arrai:6,aspher:[6,82,143,251,254,257,258,266],atc:[9,198],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,197,199,200,279,479],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:207,awpmd:[9,363],balanc:[41,208],barostat:6,basal:67,beck:364,berendsen:[277,308],between:6,binary2txt:13,bodi:[6,8,42,68,259,365],bond:[8,13,69,209,210,211,286],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:366,born:[367,378],boundari:[7,57],box:[6,58,212],brownian:368,buck:[369,370,378],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,371,404],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,201],citat:7,class2:[21,43,171,331,372],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[322,374,446],colvar:[9,13,213],com:[74,75,145],comb3:375,comb:[282,375],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,479],compute_modifi:102,condit:7,conduct:[6,313],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:202,cosin:[23,24,25,26,27,28,173],cossq:333,coul:[367,369,370,371,372,376,377,378,389,396,400,404,414,422],coupl:6,creat:210,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:309,csvr:309,cubic:398,cuda:[9,14,109,112,142,151,195,207,221,224,228,249,256,292,293,308,310,321,367,369,371,372,382,388,389,396,397,399,402,412,437,439],custom:8,cut:[49,363,369,372,376,379,384,386,396,397,404,410,414],cvff:334,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[376,396],deform:[147,148,214],delete_atom:167,delete_bond:168,delta:24,deposit:215,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],diagnost:7,diel:377,dielectr:169,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:172,dihedral_styl:[2,170,171,173,174,175,176,177,178,179,180,181,182,183,184],dilat:80,dimens:185,dipol:[6,29,379],direct:218,discuss:6,disp:6,displac:[81,86],displace_atom:186,distribut:[7,12],document:0,dpd:380,drag:216,dreid:[6,390],drude:[6,9,149,217,218,234],dsf:[376,396],dsmc:381,dump:[6,8,187,188,190],dump_modifi:189,dynam:281,eam:[13,382],echo:191,edip:383,eff:[9,13,96,97,148,150,155,235,250,260,268,311,384],efield:220,eim:385,elast:6,emac:13,enforce2d:221,ensembl:7,erot:[82,83,84,85],error:3,evapor:222,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],exp:[27,173],expand:[46,399],extend:[8,11],extern:223,fcc:271,featur:[7,8],fene:[45,46],fep:[9,13,87,194],field:[6,7],file:6,finit:6,fix:[2,6,8,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,479],fix_modifi:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],flow:6,fluid:236,flux:91,forc:[6,7,306],fourier:[30,31,174,335],freez:224,from:[6,11],futur:5,gauss:386,gaybern:387,gcmc:225,gener:[1,6,7,13],get:12,gld:226,gle:227,global:6,gpu:[15,364,367,369,371,372,374,376,379,380,382,386,387,389,396,397,399,410,412,421,422,428,437,438,445,446],gran:[323,388],granular:6,graviti:228,gromac:389,group2ndx:329,group:[88,328,479],gyrat:[89,90],harmon:[32,47,48,49,175,178,322,336,413],hbond:390,heat:[91,229],heatconduct:429,helix:176,hertz:[388,423],histo:203,histori:[5,388],hook:388,hourglass_error:122,how:6,hybrid:[33,50,177,337,391],idealga:430,imag:[187,188],imd:230,implicit:371,improp:[8,92],improper_coeff:332,improper_styl:[2,331,333,334,335,336,337,338,339,340,341],includ:342,inclus:8,indent:231,indic:0,individu:2,induc:6,inertia:93,info:[0,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,343],input:[2,6,8],instal:11,integr:[6,7],integrate_tlsph:296,integrate_ulsph:297,intel:[9,16,371,387,396,437],interfac:[6,11],internal_energi:123,introduct:7,invers:218,ipi:232,ipp:13,jul:[],jump:344,kate:13,keyword:411,kim:392,kokko:17,kspace:[2,8,318],kspace_modifi:345,kspace_styl:[6,346],label:347,lammp:[0,1,2,6,7,8,11,12],langevin:[233,234,235],lattic:348,lcbop:393,librari:[6,11,12],limit:[261,310],line:[12,262,394],linear:403,lineforc:241,list:[2,395],lj1043:322,lj126:322,lj93:322,lj96:397,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:349,lubric:405,lubricateu:406,make:12,mass:350,math:479,matlab:13,meam:[407,408,409],measur:1,meso:[242,243],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:410,min_modifi:351,min_styl:352,minim:[8,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,353],misc:9,mod:[317,440],model:[6,7],modifi:8,molecul:354,molfil:[9,187,190],moltempl:13,momentum:[237,245],morri:434,mors:[51,390,412],move:246,move_tri_surf:298,movi:[187,188],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[367,369,371,376,396],msst:247,multi:[6,7,178],multipl:6,nb3b:413,neb:[248,355],neigh_modifi:356,neighbor:357,nemd:6,newton:358,next:359,nharmon:179,noforc:[258,263],non:[6,7],none:[34,52,180,338,415],nongauss:105,nonlinear:53,nph:[249,250,251,252,290],nphug:253,npt:[249,250,254,255,290],nve:[256,257,258,259,260,261,262,263,264,265,290],nvt:[249,250,266,267,268,269,290],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,170,171,173,174,175,176,178,179,181,182,184,228,249,251,252,253,254,255,256,264,266,267,269,282,331,333,334,335,336,339,341,361,362,364,367,368,369,370,371,372,374,375,376,377,379,380,382,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447],onewai:270,open:7,oper:479,opl:181,opt:[19,371,382,396,400,412],optim:1,option:[6,8,12],orient:271,orthogon:6,other:6,output:[6,7,8,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],overlai:391,overview:11,packag:[1,9,12,14,15,16,17,18,19,360],pair:[6,107,108],pair_coeff:373,pair_modifi:411,pair_styl:[2,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447],pair_writ:444,pairwis:8,parallel:11,paramet:6,pars:2,partial:151,particl:[6,7,42],partit:448,past:5,per:6,perform:[1,10],peri:416,period:25,phonon:[9,13,272],pimd:273,piston:324,pla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7,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,462],run_styl:463,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,422],self:304,serial:11,set:[6,464],setforc:292,setvel:299,shake:293,share:[11,12],shell:[6,465],shield:281,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:281,slice:119,sllod:[267,268],small:290,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,294,295,296,297,298,299,301,423,424,425,426],smooth:[402,403],sna:140,snad:140,snap:427,snapshot:6,snav:140,soft:[404,428],solver:2,sourc:7,spatial:[204,205],spc:6,speci:287,special:[7,411,479],special_bond:466,sph:[9,429,430,431,432,433,434],sphere:[84,85,157,205,239,252,255,264,269],spheric:6,spline:[408,409],spring:[302,303,304,315],squar:28,srd:[305,327],srp:435,standard:9,start:[12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],state:307,stationari:243,stop:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],store:[306,307],strategi:1,streitz:376,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:467,summari:6,swap:[199,211],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],system:6,tabl:[0,6,38,56,184,438,439],tad:468,taitwat:[433,434],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,308,309,310,311],temper:469,temperatur:6,tersoff:[439,440,441],test:11,tfmc:312,thermal:[6,313],thermo:[6,470],thermo_modifi:471,thermo_styl:472,thermodynam:[6,8],thermostat:6,thole:442,time:[6,206],timestep:473,tip3p:6,tip4p:[6,376,396,400,404],tip:12,tlsph:424,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:316,tool:13,torqu:159,transform:218,tri:[265,443],tri_surfac:425,triangle_mesh_vertic:134,triclin:6,tstat:380,ttm:317,tune:318,type:7,ulsph:426,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:341,uncomput:475,undump:476,unfix:477,unit:478,user:[9,12,14,16,18],vacf:160,valu:[6,479],variabl:[6,8,479],variou:1,vcm:161,vector:[6,319,479],veloc:480,version:[0,5,12],via:12,vim:13,viscos:[6,320],viscou:[240,321],visual:6,vol:139,voronoi:162,vtk:291,wall:[6,322,323,324,325,326,327],wall_surfac:301,warn:3,water:6,weight:203,what:[7,12],wolf:[367,376],wrapper:11,write:6,write_data:481,write_dump:482,write_restart:483,xmgrace:13,xmovi:13,xrd:163,yukawa:[445,446],zbl:[441,447]}}) 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