From 1c05f57bcd94da185a1e81137f42872f5e2337c9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 27 Jun 2016 22:32:39 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15218 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Section_commands.html | 2 +- doc/html/_sources/Section_commands.txt | 2 +- doc/html/_sources/fix_qeq_reax.txt | 30 ++++++++++++++++++ doc/html/_sources/pair_reax_c.txt | 44 ++++++++++++++++++++++++-- doc/html/fix_orient.html | 4 +-- doc/html/fix_qeq_reax.html | 20 ++++++++++++ doc/html/genindex.html | 2 +- doc/html/pair_reax_c.html | 33 +++++++++++++++++-- doc/html/searchindex.js | 2 +- doc/src/Section_commands.txt | 2 +- 10 files changed, 130 insertions(+), 11 deletions(-) diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index ec03d7a33c..07beb934a2 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -1230,7 +1230,7 @@ if multi/lucy/rx quip -reax/c +reax/c (k) smd/hertz smd/tlsph diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt index 699fbdc0f1..b49001ce94 100644 --- a/doc/html/_sources/Section_commands.txt +++ b/doc/html/_sources/Section_commands.txt @@ -665,7 +665,7 @@ if :ref:`LAMMPS is built with the appropriate package `. +-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ | :doc:`mgpt ` | :doc:`morse/smooth/linear ` | :doc:`morse/soft ` | :doc:`multi/lucy ` | +-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ -| :doc:`multi/lucy/rx ` | :doc:`quip ` | :doc:`reax/c ` | :doc:`smd/hertz ` | +| :doc:`multi/lucy/rx ` | :doc:`quip ` | :doc:`reax/c (k) ` | :doc:`smd/hertz ` | +-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ | :doc:`smd/tlsph ` | :doc:`smd/triangulated/surface ` | :doc:`smd/ulsph ` | :doc:`smtbq ` | +-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+ diff --git a/doc/html/_sources/fix_qeq_reax.txt b/doc/html/_sources/fix_qeq_reax.txt index f2ad1cadd0..afdb10a19c 100644 --- a/doc/html/_sources/fix_qeq_reax.txt +++ b/doc/html/_sources/fix_qeq_reax.txt @@ -3,6 +3,9 @@ fix qeq/reax command ==================== +fix qeq/reax/kk command +======================= + Syntax """""" @@ -69,6 +72,33 @@ be used with the *start/stop* keywords of the :doc:`run ` command. This fix is invoked during :doc:`energy minimization `. + +---------- + + +Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + Restrictions """""""""""" diff --git a/doc/html/_sources/pair_reax_c.txt b/doc/html/_sources/pair_reax_c.txt index 8b73c1de3c..3b42f4cbd2 100644 --- a/doc/html/_sources/pair_reax_c.txt +++ b/doc/html/_sources/pair_reax_c.txt @@ -3,6 +3,9 @@ pair_style reax/c command ========================= +pair_style reax/c/kk command +============================ + Syntax """""" @@ -46,6 +49,14 @@ the most up-to-date version of ReaxFF as of summer 2010. For more technical details about the pair reax/c implementation of ReaxFF, see the :ref:`(Aktulga) ` paper. +The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that is +derived from the *reax/c* style. The Kokkos version can run on GPUs and +can also use OpenMP multithreading. For more information about the Kokkos package, +see :ref:`Section_packages ` and :doc:`Section_accelerate `. +One important consideration when using the *reax/c/kk* style is the choice of either +half or full neighbor lists. This setting can be changed using the Kokkos :doc:`package ` +command. + The *reax/c* style differs from the :doc:`pair_style reax ` command in the lo-level implementation details. The *reax* style is a Fortran library, linked to LAMMPS. The *reax/c* style was initially @@ -124,9 +135,11 @@ control file. Note: Force field files are different for the original or lg corrected pair styles, using wrong ffield file generates an error message. Optional keywords *safezone* and *mincap* are used for allocating -reax/c arrays. Increase these values can avoid memory problems, such +reax/c arrays. Increasing these values can avoid memory problems, such as segmentation faults and bondchk failed errors, that could occur under -certain conditions. +certain conditions. These keywords aren't used by the Kokkos version, which +instead uses a more robust memory allocation scheme that checks if the sizes of +the arrays have been exceeded and automatically allocates more memory. The thermo variable *evdwl* stores the sum of all the ReaxFF potential energy contributions, with the exception of the Coulombic and charge @@ -287,6 +300,33 @@ This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the *inner*\ , *middle*\ , *outer* keywords. + +---------- + + +Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + Restrictions """""""""""" diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html index a94305b2f5..74dd4d3477 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -155,7 +155,7 @@ grain boundary which can be used to induce grain boundary migration (in the direction perpendicular to the grain boundary plane). The motivation and explanation of this force and its application are -described in (Janssens). The adaptiation to bcc crystals +described in (Janssens). The adaptiation to bcc crystals is described in (Wicaksono1). The computed force is only applied to atoms in the fix group.

The basic idea is that atoms in one grain (on one side of the @@ -175,7 +175,7 @@ system can displace during the simulation, and such motion should be accounted for in measuring the grain boundary velocity.

The potential energy added to atom I is given by these formulas

_images/fix_orient_fcc.jpg -

which are fully explained in (Janssens). For fcc crystals +

which are fully explained in (Janssens). For fcc crystals this order parameter Xi for atom I in equation (1) is a sum over the 12 nearest neighbors of atom I. For bcc crystals it is the corresponding sum of the 8 nearest neighbors. Rj is the vector from diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html index 9057d42102..cc02c2516a 100644 --- a/doc/html/fix_qeq_reax.html +++ b/doc/html/fix_qeq_reax.html @@ -126,6 +126,9 @@

fix qeq/reax command

+
+
+

fix qeq/reax/kk command

Syntax

fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params
@@ -184,7 +187,24 @@ of this fix are hard-coded to be A, eV, and electronic charge.

 quantities are stored by this fix for access by various output commands.  No parameter of this fix can
 be used with the start/stop keywords of the run command.

 
This fix is invoked during energy minimization.

+

+
Styles with a gpu, intel, kk, omp, or opt suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in Section_accelerate
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.

+
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the Making LAMMPS section for more info.

+
You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
+use the suffix command in your input script.

+
See Section_accelerate of the manual for
+more instructions on how to use the accelerated styles effectively.
+

Restrictions

This fix is part of the USER-REAXC package. It is only enabled if diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 19bfd5d8b8..b381f9e6fd 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -1296,7 +1296,7 @@ -

fix orient/fcc, [1] +
fix orient/fcc
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html index 2019b8ecd1..bd96471c6b 100644 --- a/doc/html/pair_reax_c.html +++ b/doc/html/pair_reax_c.html @@ -126,6 +126,9 @@

pair_style reax/c command

+
+
+

pair_style reax/c/kk command

Syntax

pair_style reax/c cfile keyword value
@@ -164,6 +167,13 @@ supplemental information of the following paper: (Aktulga) paper.

+
The reax/c/kk style is a Kokkos version of the ReaxFF potential that is
+derived from the reax/c style. The Kokkos version can run on GPUs and
+can also use OpenMP multithreading. For more information about the Kokkos package,
+see Section_packages and Section_accelerate.
+One important consideration when using the reax/c/kk style is the choice of either
+half or full neighbor lists. This setting can be changed using the Kokkos package
+command.

 
The reax/c style differs from the pair_style reax
 command in the lo-level implementation details.  The reax style is a
 Fortran library, linked to LAMMPS.  The reax/c style was initially
@@ -234,9 +244,11 @@ recommended value for parameter thb is 0.01, which can be set in the
 control file.  Note: Force field files are different for the original
 or lg corrected pair styles, using wrong ffield file generates an error message.

 
Optional keywords safezone and mincap are used for allocating
-reax/c arrays.  Increase these values can avoid memory problems, such
+reax/c arrays.  Increasing these values can avoid memory problems, such
 as segmentation faults and bondchk failed errors, that could occur under
-certain conditions.

+certain conditions. These keywords aren’t used by the Kokkos version, which
+instead uses a more robust memory allocation scheme that checks if the sizes of
+the arrays have been exceeded and automatically allocates more memory.

 
The thermo variable evdwl stores the sum of all the ReaxFF potential
 energy contributions, with the exception of the Coulombic and charge
 equilibration contributions which are stored in the thermo variable
@@ -361,7 +373,24 @@ script that reads a restart file.

 
This pair style can only be used via the pair keyword of the
 run_style respa command.  It does not support the
 inner, middle, outer keywords.

+

+
Styles with a gpu, intel, kk, omp, or opt suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in Section_accelerate
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.

+
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the Making LAMMPS section for more info.

+
You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can
+use the suffix command in your input script.

+
See Section_accelerate of the manual for
+more instructions on how to use the accelerated styles effectively.
+

Restrictions

This pair style is part of the USER-REAXC package. It is only enabled diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 0b582816bd..a888505429 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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6,125,158,166,173,175,178,202,203,206,218,229,259,266,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[235,335,357],colliex:177,collinear:[3,302],collis:[3,256,335,353,357,415,423,489],colllis:335,colloid:[],colombo:39,colon:[207,358,498,516],color1:206,color2:206,color:[3,9,41,202,205,206,224,246,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:230,comand:227,comannd:393,comb3:[],comb:[],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,204,250,252,253,378,388,393,413,448,455,478,479,499],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,184,198,202,240,241,254,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,294,429,491,492,494,511,528],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,180,202,205,207,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,204,252,253,286,292,321,378,388,418,448,455,460,474,478,479,481],compact:[65,209,406,476],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,130,161,177,186,197,206,234,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:[],comparison_of_nvidia_graphics_processing_unit:[],compart:382,compass:[7,9,20,21,36,43,44,55,185,186,197,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,202,207,211,217,218,219,221,222,224,237,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,225,226,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,202,204,205,207,250,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,206,224,229,259,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,256,286,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,216,245,495],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,216,256,416],compound:[408,418,419,485],compres:[75,125,218],compress:[],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[],computation:[3,6,225,226,347,399],computational:518,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,319],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,528],concav:356,concentr:[75,241,318,416,420,451,479],concept:[6,158,168,218,506],conceptu:[3,6,75,166,228,230,388,409,426,443,502],concern:[6,77,95,204,246],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[],conducit:6,conduct:[],cone:500,confer:446,confid:[3,511],config:[12,202,494],configfil:229,configur:[1,2,6,12,14,16,37,61,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,519],confin:[497,511],conflict:[3,12,40,203,448,495,519],conform:[3,6,13,61,227,228,269,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,253,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,206,210,211,253,256,260,284,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,414,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,227,250,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,206,210,211,231,250,251,409,431,435,492,498,500],consequ:[1,6,216,347,430,511],conserv:[3,9,28,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,317,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,253,254,338,339,340,393,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:215,consit:317,constant:[],constantli:237,constitu:[3,6,259,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,228,270,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:459,consum:[1,312,454,524],consumpt:375,contact:[],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,16,127,128,206,225,226,231,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,215,347,463,465],contour_integr:215,contract:[61,228,230,270,304,317],contradictori:3,contrain:321,contraint:284,contrari:[247,254],contrast:[1,6,42,55,66,160,163,203,230,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:215,controlfil:459,convect:99,conveni:[6,12,28,202,207,222,319,380,467,483,519,524],convent:[3,8,28,189,196,197,203,206,316,331,359,416,418,524],converg:[3,6,41,96,202,203,205,207,212,224,227,228,236,243,275,286,292,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511],convers:[3,8,152,205,206,216,219,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,202,205,206,219,222,268,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,315],cooordin:[202,203],cooper:[5,7],coord123:125,coord1:[3,125,218],coord2:[3,125,218],coord3:[3,125,218],coord:[],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,218],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,205,347,388,406,458,495,519],copper:489,coproccesor:15,coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:206,core:[],core_shel:160,cores:518,coreshel:[4,6,9],coreshell:[],cornel:[6,184,509],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,205,356,357,380,484,497,519],cornflowerblu:206,cornsilk:206,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,160,165,172,184,203,205,230,237,245,247,253,270,271,293,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:215,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,297,299,300,304,309,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[],cosineshift:26,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,205,206,218,224,225,226,242,270,309,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,96,247,389],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:245,counterbal:[237,249],counterbalanc:28,counterclockwis:184,counterpart:[202,492],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:324,cours:[3,8,138,140,172,202,210,211,246,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:247,cover:[6,12,75,198,206,215,256,418,484],coverag:75,cpc:252,cpp:[1,3,6,8,9,11,12,13,95,202,210,211,243,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,206,220,234,254,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,202],crash:[3,12,389,518],craympi:393,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:302,criteria:[3,127,179,205,206,225,226,227,265,386,455,484,499,502,524],criterion:[12,41,133,178,181,216,224,227,245,284,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,268,342,347,386],crmax:75,crmin:75,cross:[3,12,21,75,97,129,156,176,186,202,203,205,217,226,230,267,269,293,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,77,117,297,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[],cst:416,cstherm:6,cstyle:494,csvr:[],ctcm:[394,416],ctemp_core:234,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,234,356,380,518],cubes:[41,224],cubic:[],cuda:[],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cufft:[],cuh:399,cummul:[3,6,222,225,226,227,229,242,247,253,255,335,338,339,340,341,343,350,425,515],cumul:[6,216,218,221,235,245,253,268,270,275,284,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,265,267,270,271,276,277,278,284,286,290,291,292,293,295,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,414,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,245,286,292,299],curvatur:[422,460,489],custom:[],cut0:495,cut1:506,cut2:506,cut:[],cuthi:[297,298,310],cutinn:[401,440,441],cutlo:[297,298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,226,227,232,240,241,297,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[],cwiggl:[3,267,352,355,357,524],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,75,205,218,251,292,303,353,356,382,500],cylinder_d:382,cylindr:[6,251,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:256,d3q19:256,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,202,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:293,damag:[],dammak:312,damp:[3,6,209,214,253,254,255,260,270,271,275,292,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:254,damp_drud:254,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,245,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:308,dash:[423,514],dat:[6,99,198,215,493],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,319],dataset:319,datatyp:3,date:[0,4,6,12,13,201,458,459,524],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,202,219],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dbg:[],dcd:[3,6,7,202,204,205,206,207,300,498,502],dcs:9,ddim:201,deactiv:439,dealt:252,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[],decai:[100,409,489],decid:[3,6,12,15,75,267,306,317,348,512,519],decipher:380,deck:306,declar:204,declin:335,decod:205,decompos:[95,467],decomposit:[3,5,7,17,64,215,300,322],decoupl:[6,518],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,346,377],decrement:323,deepli:374,deeppink:206,deepskyblu:206,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,206,218,219,220,221,222,230,239,251,275,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:198,degress:[158,218],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,209,218,219,221,222,225,227,242,245,270,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[318,495,524],dellago:[6,237],deloc:[271,418,466],delr:443,delt_lo:511,delta:[],delta_1:399,delta_3:399,delta_7:399,delta_conf:3,delta_ij:[443,456],delta_pi:399,delta_r:456,delta_sigma:399,deltah_f:241,delx:201,delz:201,demand:312,demo:11,demon:296,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,256,258,259,260,299],denomin:[7,183],denot:[130,234,237,254,299,310,312,409,424,426,459,463,465],dens:[75,227,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[268,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,298,309,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:231,deposit:[],deprec:[3,308,458],deprect:218,depth:[51,156,205,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:[297,298],descend:206,descent:[7,385],descib:[40,205,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[],descriptor:[152,202,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,215,227,233,234,270,271,297,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,205],despit:518,destabil:399,destre:370,destroi:[9,11,39,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,244,303,346,388,408,425,430,492,494,497,508,511,524],determ:[],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,250,275,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[268,275,297,298,421],deviator:9,devic:[1,3,12,14,16,250,393],device_typ:393,devin:[309,408],devis:445,dfactor:205,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,201,230,303],dhug:[268,307],dhugoniot:[268,307],dia:443,diagnost:[],diagon:[3,6,91,129,152,153,154,228,270,304,317,350,463,465],diagonalstyl:467,diagram:[41,130,177,197,224,300],diallo:425,diam:[205,206,303,387],diamet:[3,6,40,42,124,178,202,203,205,206,210,211,253,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,198,318,377,409,456,481],difficult:[228,300,393,425,506],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[],diffuse:[4,6],digit:[2,3,206,360,446,524],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:418,dij:321,dilat:[],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,201,230,251,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:206,dimstr:[41,224],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,202,203,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,268,297,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[],directli:[3,6,8,9,11,12,95,124,129,152,154,202,203,204,205,212,236,247,251,256,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directoi:[],directori:[],disabl:[3,12,15,347,430,495,510,524],disadvantag:[6,224],disallow:[202,230,270],disappear:499,discard:[2,3,41,75,220,224,348,356,494,499,500],discontinu:[198,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,205,206,253,256,292],discuss:[],disk:[6,92,93,100,171,200,231,245,303,495],disloc:[74,446],disord:[39,74,446],disp:[],dispar:460,disperion:[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,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,487,488,489,495,498,499,500,504,506,516,524,529],enclos:[2,6,12,180,202,305,360,443,466,493,495,505,524],encod:[13,39,42,202,205,206,306,426],encompass:[3,6,40,42,59,61,127,179,330,349,476,500],encount:[3,8,12,61,117,221,392,502,524],encourag:[7,8,311,333],end12i:124,end12x:124,end12z:124,end1i:124,end1x:124,end1z:124,end2i:124,end2x:124,end2z:124,end:[1,2,3,5,6,8,11,12,14,15,16,17,18,37,40,41,42,57,59,61,75,124,181,182,185,201,202,203,205,206,207,210,211,219,221,222,227,230,237,246,251,253,255,269,270,271,284,292,304,316,317,323,335,338,339,340,341,343,346,347,350,354,357,358,376,377,387,388,392,393,413,416,422,429,442,446,460,463,465,467,468,486,492,495,497,498,499,500,502,504,505,509,513,515,518,524,529],end_of_step:8,endbondtors:[3,185,191,497],endif:8,energet:[227,395,459],energi:[],energy_compon:466,energy_update_freq:459,enforc:[6,9,59,60,114,201,202,203,204,205,207,209,216,227,230,270,296,299,309,317,321,360,377,431,494,524,525],enforce2d:[],eng:[11,68,73,119,202,243,358,360,408,445],eng_previ:360,engiliti:9,engilitycorp:9,engin:230,engineer:[215,302,323,344,416],enginer:444,enhanc:[211,215,237,492],enlarg:[61,205],enough:[3,40,63,94,178,179,181,182,224,254,303,307,312,317,348,352,353,356,389,393,409,454,497,501,502],enpub:416,ensembl:[],ensight:6,ensur:[3,6,152,202,203,216,220,228,245,246,270,324,346,378,399,415,439,477,485],enter:[59,168,419,446,485,511],enthalpi:[135,272,273,274,318,416,514,515,524],entir:[0,2,3,6,11,14,41,42,65,88,89,96,120,121,123,127,129,130,153,158,177,178,206,209,210,211,218,224,227,229,237,242,245,246,249,253,254,266,270,272,273,274,275,276,277,278,297,298,300,302,315,317,318,333,347,349,360,393,412,435,448,478,479,497,505,506],entireti:484,entiti:[6,8,40,42,202,317],entri:[3,8,12,37,42,56,68,73,84,102,119,126,129,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,229,240,241,307,358,387,399,417,443,450,451,452,459,467,477,478,479,480,481,482,485,524],entries:206,entropi:511,entry1:[37,56,206,406,450,451,478,479],entry2:206,entryn:206,enumer:[179,202,490],enumuer:6,env:393,environ:[1,3,6,11,12,15,16,17,205,247,252,297,298,393,394,399,406,408,417,418,456,480,494,508,524],eos:[9,240,241],epair:[118,206,395,421,425,458,459,515],epen:[458,459],epfl:[247,252],epp:412,epq:412,eps0:488,eps14:439,eps:[455,476],epsilon0:482,epsilon:[3,6,35,45,46,50,53,54,95,184,210,211,245,317,335,352,356,384,386,398,404,405,407,409,410,411,412,420,422,424,425,426,429,430,431,432,433,434,435,436,437,438,439,442,447,453,460,461,471,477,483,484,487,488,506,518,523],epsilon_0:489,epsilon_14:404,epsilon_:460,epsilon_d:410,epsilon_i:[422,448,460],epsilon_i_:460,epsilon_i_a:[422,460],epsilon_i_b:[422,460],epsilon_i_c:[422,460],epsilon_ij:448,epsilon_j:[422,448,460],epsilon_j_:460,epsilon_j_a:[422,460],epsilon_j_b:[422,460],epsilon_j_c:[422,460],epsilon_lj:460,epton:455,eqch:173,eqeq:[458,459],eqp:412,eqq:412,equal:[2,3,6,8,11,12,16,39,41,54,65,68,71,73,75,80,84,94,95,99,102,119,121,126,128,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,222,223,224,228,230,231,236,245,246,248,249,251,253,254,256,259,260,267,268,275,286,287,297,298,300,303,305,307,308,309,312,314,316,317,318,320,323,328,330,338,339,340,343,344,345,347,349,350,352,355,357,358,360,376,380,386,388,389,390,392,393,395,408,413,414,421,422,425,429,440,446,447,456,458,459,460,462,463,464,466,467,468,478,479,484,485,489,493,494,495,497,499,500,504,505,508,511,513,515,524,525],equat:[3,6,7,8,9,99,117,123,130,177,186,197,209,228,234,235,237,239,240,241,247,253,254,256,259,268,269,270,271,275,293,297,298,300,307,308,312,318,321,322,335,343,347,350,352,353,355,357,377,378,382,407,412,413,414,418,419,420,423,428,440,441,443,448,451,460,463,465,470,471,473,474,479,489,518],equation:[247,297,298,370],equi:271,equidist:269,equil:[3,308,381,504,529],equilater:507,equilibr:[3,4,5,6,7,9,61,99,178,209,216,219,227,228,245,268,270,271,293,294,304,307,308,309,310,343,344,345,350,408,409,458,459,493,507],equilibria:350,equilibribum:[225,226],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,228,230,245,246,247,254,256,270,275,293,307,308,312,316,321,323,331,335,342,343,345,350,361,363,367,370,408,443,452,466,518],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,28,61,63,136,137,145,150,176,180,206,221,222,228,230,245,253,270,293,304,316,317,355,395,413,418,466,480,482,483,497,500,505,506,515,518],equlibrium:6,equliibr:[308,310],er3:177,eradiu:[40,124,203,418,497],eras:[320,344],erat:[230,441],erc:409,erfc:[409,431,448],erforc:[124,203],erg:523,erhart:[216,416,480,482],ermscal:396,ernst:9,eror:3,eros:443,erose_form:443,erot:[],errata:[480,482],erratum:352,erron:3,error:[],erta:423,ervel:[124,203,497],escap:[231,518],especi:[8,15,166,178,209,216,224,245,307,312,315,316,393,494],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,219,299,351,378,395,409,431,482,502,515],essential:[8,275],essex:28,establish:[95,249],estim:[1,3,6,10,12,37,41,56,99,153,215,224,235,268,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,256,270,307,308,310,351,417,419,422,456,481,485,523],eta_dot:270,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:270,etap_dot:270,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,243,245,246,253,270,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,206,234,254,268,307,514,515],eu2:177,eu3:177,euler:[386,388],eulerian:215,euqat:469,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,299,305,308,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,293],evanseck:[6,19,184,404,509],evapor:[],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,198,224,256,429,486],event:[],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,252,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[237,247,256,300,492],evolv:[256,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,224,227,246,247,253,254,255,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,227,299],examp:[495,524],exampl:[],exce:[3,6,15,16,17,41,60,75,180,217,218,221,222,224,228,230,235,242,270,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,224,230,270,335,505],excel:418,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[220,418],exchang:[2,3,6,8,63,64,209,215,216,237,245,249,253,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,202,218,225,226,257,266,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[270,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,205,250,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:246,exemplifi:418,exert:[6,251,254,286,312,354,355,356,378],exhaust:[215,392,524],exhibit:[100,237,249,270,385,418,506],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,134,178,179,197,204,205,206,209,214,223,226,228,231,245,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,202,224,376,392,495,496,505,514,516,524],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,152,202,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,198,224,236,245,247,267,297,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,206,297,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,223,231,250,259,269,304,316,317,384,388,413,448,506,511],experienc:[6,12,258,259],experiment:[16,245,377,393,511],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,202,203,218,269,297,298,426,491,494,495,497,506],explanatori:[3,8,128,202,203,217,218,221,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,210,211,230,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,306,307,309,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,420,456,477,485,489,511,524],expos:11,exposit:[215,413,415],express:[6,152,164,178,210,211,228,267,297,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,209,515],extent:[1,3,41,42,45,59,75,176,180,202,214,224,251,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,305,306,307,317,335,386,387,390,391,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,210,211,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,205,220,228,230,270,345,418,481,518],extrema:439,extreme:418,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,202,203,209,217,218,219,220,221,222,265,337,349,515,524],f_ij:456,f_indent:222,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:268,f_r:[254,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,214,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,247,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,228,231,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:250,fall:[3,6,206,221,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,202,203,206,207,224,225,226,228,231,270,297,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:253,farrel:[480,482],farther:202,fashion:[6,8,41,75,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,16,39,202,203,281,307,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,304,308,309,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:227,favorit:7,fbmc:342,fcc:[],fcm:[287,524],fcold:237,fdirect:234,fdotr:427,fdt:[],fdti:95,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:416,feedback:[7,250],feel:[7,250,251,259,297,298,356,358,388,448],felling:445,felt:356,femtosecond:523,fene:[],fennel:[409,431],fep:[],ferguson:[6,184,509],fermi:[1,9,10,12,14,164,393,482],fermion:418,fernando:442,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,207,217,218,219,221,222,237,254,270,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,259,506],fewest:3,fextern:243,feynman:300,fff:495,ffield:[408,419,458,459,466],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:475,fictiti:[6,212,213,236,243,247,300,316,409,431,435,475],field1:[498,502],field2:498,field:[],fifth:[6,331,420,452],figshar:297,figur:[1,3,8,12,307,494,495,519],fij:412,file0:[297,298],file1:[11,13,241,297,298,346,360,387,502,504,508],file2:[11,13,241,346,360,387,502,504,508],file:[],file_from:204,filen:387,filenam:[3,12,13,37,41,56,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,202,203,206,499,504,529],filepo:314,fill:[7,9,178,205,303,347,380,389,399,446,459,500,519],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,198,207,216,227,228,240,241,242,245,269,297,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,212,236,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,201,267,500],finish:[6,11,41,224,360,374,376,377,390,392,393,484,502,524,525],finit:[],finni:[7,416,476],finverse:234,fiorin:[9,229],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,353,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,198,240,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[],fix_deposit:3,fix_ehex07:[],fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,304,307],fix_manifoldforc:519,fix_modifi:[],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:412,flag1:[233,391],flag2:[233,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:233,flagvf:[401,440,441],flat:[6,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,205,218,229,247,271,343,350,418,481,515],flip:[3,6,230,270,354,355],floor:524,flop:12,floralwhit:206,flow:[],fluctuat:[6,66,95,228,245,246,253,256,270,275,297,298,299,304,322,345,347,370,414],fluid:[],fluid_veloc:260,flush:[3,206,514],flux:[],flv:205,fly:[7,9,12,41,205,209,215,220,231,234,317,321,348,399,446,515,518],fmackai:9,fmag:232,fmass:300,fmax:[386,515],fmomentum:234,fmsec:[2,206,253,254,267,270,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:234,fnve:237,fnvt:234,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,297,298,467],fold:[333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,202,205,243,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,15,17],forc:[],force_uvm:16,forceatom:259,forcefield:[316,425],forcegroup:256,forcezero:384,ford:412,forestgreen:206,forev:75,forget:[254,518],forgiv:270,fork:[],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,246,247,253,270,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:241,former:[6,12,15,39,41,206,224,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,212,236,253,270,293,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,299,305,314,320,328,333,335,338,339,340,349,352,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,243,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,202,227,229,237,245,250,256,262,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,268,347,370,387,388,446,492],fourier:[],fourth:[6,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:252,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,201,205,206,216,225,226,227,228,268,303,307,314,315,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,250,314],fraig:42,frame:[91,152,206,215,268,307,354,422],framer:[205,206],framework:[5,247,394,467],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,210,211,297,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[6,237,245,345],freq:214,frequenc:[3,6,15,39,113,206,220,284,299,300,307,312,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,206,225,226,237,242,343,350,448,483,504,516],fri:[268,307],friction:[4,5,6,9,10,42,209,247,253,307,312,317,347,351,353,423,507],friedrich:324,from:[],front:[268,307,354],frontend:[205,311],frozen:[6,123,182,244,246,254,389,421],fs2:[6,99],fscale:250,fstr:524,fstring:495,ftol:[386,388,492,511],fuchsia:206,fuction:409,fudg:321,fugac:245,fugacity_coeff:245,fulfil:6,full:[1,2,3,6,9,12,16,37,39,40,99,205,219,220,229,237,256,297,298,318,377,378,393,399,416,418,419,422,483,497,499,504,505,509,511,516,518,528],full_energi:[3,245],fuller:386,fulli:[3,6,82,247,252,297,298,386,388,409,456,457,497,519,526,527],fulton:416,fumi:400,func:[495,524],funcfl:416,functionaliri:229,fund:[0,7],fundament:[335,523],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337,354,494,495,497,499,511,524,528],immediat:[330,524],immens:3,immers:[256,317],impact:[1,4,6,8,9,235,342,395,516],impart:[3,6,248,335,357],impei:[6,431],implement:[1,3,6,8,9,12,16,17,26,82,88,89,95,117,130,160,166,177,178,186,187,197,218,229,233,237,239,247,249,250,253,256,258,259,260,268,270,293,296,299,300,306,307,310,311,312,318,321,322,323,335,342,347,351,370,376,377,378,386,388,393,394,396,399,408,409,411,413,414,416,417,418,426,431,435,439,443,455,458,459,460,480,482,494,495,506,511,518,524,526,527],impli:[3,6,40,61,95,153,201,205,210,211,212,230,236,253,316,338,340,341,377,380,406,495],implicit:[],implicitli:8,implict:410,imporop:387,important:345,impos:[2,6,75,123,167,201,209,212,213,223,236,237,238,243,248,251,260,261,269,284,297,298,301,320,328,331,332,334,335,342,343,344,345,350,351,352,355,356,357,386,388,390,491,505,516],impose:248,imposs:[1,3,306,497],improp:[],improper:[3,8,362,368,370,371,387,497],improper_coeff:[],improper_styl:[],impropercoeff:[3,373],impropertyp:226,imprortant:107,improtant:[210,211],improv:[0,1,9,15,39,41,206,224,237,249,270,299,393,425,431,446,448,459,477,481],imrop:369,in3:177,inaccur:[1,3,6,181,268,377],inaccuraci:356,inact:425,inappropri:178,incid:[130,177,231],includ:[],include:[12,374],includelink:9,includig:[360,376],inclus:[],inclusion:12,incom:250,incompat:[3,11,262,286,292,427],incomplet:[3,11,497],incompress:[271,418],inconsist:[3,182,227,498],inconveni:380,incorpor:[307,399,410,519],incorrect:[3,161,253,443],incorrectli:[3,380,423,524],increas:[1,3,6,17,37,56,59,61,120,130,153,198,202,203,205,206,220,225,226,227,230,237,240,241,245,253,304,315,316,317,343,346,350,377,378,388,393,395,418,422,450,451,459,478,479,481,495,506,511,524],increasingli:418,increment:[3,11,140,212,213,223,224,231,236,242,270,303,323,324,358,376,392,429,466,492,495,509,511,524],incur:[16,218,242,347,494],inde:161,indefatig:7,indefinit:344,indent:[],independ:[4,6,9,11,12,15,16,41,61,65,86,99,128,131,164,178,201,209,217,218,219,221,222,224,227,228,229,230,231,246,248,253,254,256,259,270,299,304,308,312,317,319,323,334,345,347,380,423,446,492,495,514,525],indetermin:[202,203,206],index:[0,3,6,8,11,12,37,39,40,56,57,71,73,128,129,131,176,198,202,206,217,219,240,241,250,252,300,319,347,358,359,360,383,392,448,450,451,458,459,478,479,486,497,512,524],indianr:206,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,198,202,205,210,211,228,270,299,317,347,358,361,370,377,387,389,408,415,419,426,443,446,448,452,458,459,466,480,482,494,496,497,499,515,519,524],indigo:206,indirectli:[6,306,524],indistinguish:253,indium:467,individu:[],induc:[],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,152,166,205,230,270,299,377,390],inelig:216,inerti:441,inertia:[],inertiai:129,inertiax:129,inertiaz:129,inexpens:[247,506],inf:[2,3,12,350,500],infer:[3,104,106,107,172,212,213,224,225,226,236,250,302,335,343,350,380,406,419,497,509,515],infil:[3,13,317,494],infin:[3,386,502,515],infininti:205,infinit:[3,231,244,251,253,256,299,335,347,353,354,378,380,418,497,501,523],infinitesim:6,inflect:[410,433,476],influenc:[3,9,41,85,160,267,303,377,378,448,480,481,482],inform:[0,1,2,3,6,7,8,9,11,12,13,14,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,242,243,244,245,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,269,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,324,331,332,333,335,336,338,339,340,341,342,343,344,346,349,350,351,352,354,355,356,357,359,375,377,378,381,385,386,387,388,389,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,494,495,497,498,499,501,502,504,509,511,512,514,516,524,526,527,528,529],informat:[8,12,498],infrequ:[6,270,413,492,511,516],infti:[410,440,441],ingtegr:399,inher:[377,386,448],inherit:[6,483],inhomogen:[17,347,448],inidividu:386,init:[3,8,315,466],init_fil:347,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,241,245,246,250,251,252,253,254,256,261,266,267,268,269,270,275,284,286,299,300,301,306,307,312,315,316,317,320,322,332,334,335,337,342,344,345,346,347,348,349,352,353,354,355,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,202,251,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:259,innermost:[37,56,75,391,478,479,506],innernod:259,innner:437,inordin:348,inorgan:[6,485],inp:[229,360,467,485],input1:[68,71,73,84,102,119,124,125,126,128,129,131,337],input2:[68,71,73,84,102,119,124,125,126,128,129,131,337],input:[],input_doubl:3,inquir:324,insensit:12,insert:[3,5,7,8,9,12,61,178,209,231,245,251,303,377,467,475,495,501,518],insertion:[3,231,245,303],insid:[2,3,6,8,11,75,129,141,147,178,202,203,206,217,231,232,237,242,245,251,256,259,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[256,433,495,511],insight:[6,13],instabl:[256,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,202,204,205,207,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[],instanc:[6,9,11,210,229,247,354,421,426,448,456,495,518],instantan:[6,65,227,228,246,247,270,275,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,215,426,494],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,198,202,203,211,218,221,222,224,228,229,245,253,256,259,260,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,476,483,492,500,504,511,513,518,524],institut:[9,250,302],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,309,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:270,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,198,202,203,205,206,212,225,226,231,236,238,242,243,245,248,253,266,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,243,245,246,247,250,253,254,255,256,299,302,303,306,307,312,317,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[],integral:[300,450,451],integrate_ulsph:[],intel:[],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,220,246,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,242,249,259,268,270,275,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,209,515],intepol:524,inter:[17,42,63,64,158,181,182,202,227,253,255,269,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,244,245,250,251,253,255,259,284,297,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,202,269,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[],interfer:[12,270,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,205,269,297,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],intern:[],internal:[3,205,211,303,524],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:252,interpenetr:443,interpentr:[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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[220,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[210,211],addforc:212,adding:519,addition:[12,13,519],addtorqu:213,adiabat:6,adjust_dt:324,adp:394,after:519,airebo:395,alloi:416,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:214,arrai:6,aspher:[6,90,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,214,216,217,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:223,awpmd:[9,396],axel:519,balanc:[41,224],barostat:6,basal:70,bcc:297,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,273,277,282,291,398],body:9,bond:[8,13,72,73,225,226,227,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,228],branch:519,brownian:401,buck:[402,403,411,442],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:519,change_box:61,charmm:[6,19,184,404,439],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,218,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,229],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[219,220],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,cuda:[],custom:[8,202,203],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,431],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:23,deposit:231,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],diagnost:7,diel:410,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:85,dimens:200,dipol:[6,28,86,412],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:201,distanc:365,distribut:[7,12],document:0,dpd:[9,88,89,413,414],drag:232,dreid:425,dreiding:6,drude:[6,9,163,233,234,254,518],dsf:[409,431],dsmc:415,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:308,eam:[13,416],echo:208,edip:417,eff:[9,13,106,107,162,164,169,255,271,283,294,341,418],efield:236,ehex:237,eim:419,elastic:6,emac:13,energi:[135,414],enforce2d:238,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:242,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],exp6:420,exp:[26,187],expand:[46,434],extend:[8,11],extern:243,fcc:[297,298],fdt:414,featur:[7,8,519,524],fene:[45,46],fep:[9,13,95,211],field:[6,7],file:6,finit:6,fire:308,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,2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,316,341,345,357,359,392,417,422,465,476,494,498,506,523],"try":[1,3,8,12,16,18,218,250,256,342,343,344,349,494,518,523],"var":[3,11,12,178,357,375,507,523],"void":[4,6,7,8,41,181,224,243,499],"while":[1,3,9,11,12,13,17,75,115,152,161,176,189,202,207,216,228,230,234,246,247,252,253,254,256,262,270,293,306,307,311,313,347,377,385,392,398,409,415,457,458,479,481,484,491,494,505,510,517],a10:359,a123:359,a12:459,a2m:[6,99],a_0:[256,346,398],a_0_real:256,a_1:346,a_2:346,a_3:346,a_4:346,a_c:406,a_cc:406,a_f:481,a_ij:398,a_pi:398,a_sigma:398,a_ss:406,aat:185,aatom1:126,aatom2:126,aatom3:126,ab_23_cd:359,abbrevi:12,abc:[3,12,359,494,523],aberdeen:[88,89,239,321],abf:229,abf_integr:13,abi:207,abil:[3,228,270,303,316,417],abl:[3,8,9,11,12,39,94,202,207,227,236,244,286,342,349,392,494,523,527],ablat:346,abort:511,about:[0,1,3,6,8,9,11,12,13,16,39,41,42,63,65,82,119,126,127,130,172,178,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,234,235,236,237,238,242,243,244,245,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,264,266,269,275,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,300,301,302,303,304,305,307,308,309,310,311,312,313,314,315,316,318,319,320,330,331,332,334,335,337,338,339,340,341,342,343,344,345,346,348,349,350,351,353,354,355,356,357,374,377,384,385,387,392,397,403,408,425,454,458,487,494,497,498,503,504,506,511,515,518,523,526,528],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,35,37,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,59,65,66,71,74,75,76,77,80,81,94,95,97,98,99,103,104,106,107,123,125,127,130,152,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,176,177,178,180,181,184,185,186,187,188,189,190,191,192,193,195,196,198,202,203,204,205,206,209,210,211,212,213,218,219,221,222,224,227,228,230,231,236,240,243,245,249,251,253,254,255,259,269,270,275,299,302,304,309,315,316,317,322,330,334,337,338,339,340,357,359,360,361,362,363,364,365,366,367,369,371,377,379,382,386,387,391,392,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,428,430,431,432,433,434,435,436,437,438,439,440,441,442,445,446,447,448,449,450,452,454,455,457,458,459,460,465,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,489,490,491,492,493,494,496,497,498,499,500,503,504,505,506,507,510,511,514,517,518,523,524,527,528],abscissa:[449,450,477,478],absenc:213,absent:517,absolut:[3,206,216,229,230,234,322,336,376,377,385,422,430,497],absorb:346,absoult:377,ac3:177,academ:245,acc:341,acceler:0,accelri:[6,13],accept:[7,12,95,176,178,206,227,230,245,341,402,434,504,511,518],acceptanc:216,acceptor:424,access:[0,3,6,7,8,9,11,12,15,38,40,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,93,96,97,98,99,100,101,102,103,105,106,109,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,128,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,173,174,175,176,177,199,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,231,232,235,236,237,238,242,243,244,245,246,247,248,249,250,251,253,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,275,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,318,319,320,322,327,330,331,332,333,334,335,336,337,338,339,340,342,343,344,345,346,348,349,350,351,352,353,354,355,356,372,376,392,394,420,422,424,425,442,457,458,467,493,494,497,502,514,523],accident:518,accidenti:369,accler:[9,12,15],accommod:214,accomod:270,accompani:8,accomplish:[15,230,257,287],accord:[6,66,75,88,133,139,142,160,205,216,225,226,241,256,270,286,298,306,322,324,343,344,346,351,352,354,355,356,388,417,422,433,436,455,462,464,465,467,469,470,472,473,474,510,523],accordingli:[11,112,156,157,171,176,182,388,439,440,474],account:[3,6,95,130,160,176,177,186,197,219,221,235,237,250,251,253,270,276,277,278,290,291,293,295,297,301,307,316,318,320,330,332,333,334,337,338,339,342,346,349,365,386,408,413,422,430,434,439,440,442,445,465,493,510],accuml:[3,316,342,349],accumul:[6,8,14,75,88,154,209,219,220,253,316,322,348,374,392,502,522],accur:[1,3,6,9,14,16,37,41,56,161,224,268,311,316,317,320,334,342,349,355,357,377,398,417,421,422,447,459,475,477,478,479,481,510,515,523],accuraci:[1,3,6,12,41,201,202,206,224,237,247,270,308,320,347,357,376,377,384,394,417,447,449,450,457,458,477,478,485,505,510,515,517,523,527],accuractli:515,ach:376,achiev:[1,3,6,9,10,15,16,17,28,41,224,237,245,247,270,271,286,298,299,306,376,425,505],achiv:17,acid:9,ackag:[212,223,238,244,320],ackland1:415,ackland2:415,ackland:2,acknowledg:0,acml:12,aco:523,acolor:[205,206],acoust:298,acquir:[3,6,60,63,64,181,182,226,228,230,270,453,489,501,517],across:[1,2,3,6,9,12,13,14,41,59,63,68,71,73,75,84,102,119,126,128,166,180,182,218,221,224,235,249,316,318,323,342,346,349,355,359,387,392,491,496,499,500,504,513,515],act:[3,6,119,129,163,234,248,251,252,253,254,256,259,269,316,327,341,343,344,346,355,356,357,385,400,411,421,422,424,459,474],acta:[130,177,393],actinid:[9,445],action:[2,6,11,12,75,246,251,344,517],activ:[5,8,11,12,13,55,61,95,176,229,246,250,253,259,265,269,296,316,317,325,345,374,438,475,505,517,520,523],active:[265,490],actual:[1,3,6,8,12,56,64,134,161,202,203,206,210,211,223,225,226,234,253,254,293,297,302,303,311,314,322,334,337,338,339,341,347,356,357,376,388,421,423,428,433,439,440,474,493,494,505,506,514,523],actualli:336,adam:[376,377],adapt:[2,3,6,9,95,172,209],adapti:297,adaptiv:[9,229,394],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,40,42,75,95,99,112,125,128,129,131,176,178,179,202,203,204,205,209,210,211,212,213,215,217,218,219,221,222,226,229,234,236,237,243,247,248,249,251,253,255,256,260,268,269,270,271,272,273,274,275,276,277,278,290,291,293,294,295,297,305,315,316,319,320,330,331,333,337,339,340,344,345,346,348,350,351,355,357,377,379,384,386,394,399,401,404,408,417,425,430,442,447,448,452,458,460,494,496,497,502,504,506,508,515,517,518],add_molecul:215,add_speci:215,add_to_nodeset:215,added:[497,518],addforc:[2,3,209],adding:[8,212,236,315],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,205,206,207,209,212,220,223,224,228,229,234,236,237,240,241,245,247,248,249,253,256,270,271,272,273,274,275,276,277,278,290,291,293,294,295,297,305,316,319,320,321,323,347,350,351,355,361,367,370,372,377,379,387,389,392,393,394,398,399,401,403,405,407,408,411,413,414,415,416,417,418,422,423,425,426,427,429,430,438,440,441,442,443,444,445,447,449,450,451,452,455,457,458,460,465,466,475,476,477,478,479,480,481,484,488,491,496,497,498,503,504,505,508,510,517,518,519,521,523,526,527,528],addition:[0,4,6,8,11],additionali:203,addres:9,address:[7,8,11,205,252,518],addtorqu:2,adequ:[262,334,347,376,387,505],adher:28,adhikari:256,adiabat:0,adiam:[205,206],adjac:[39,176,178,237,387,447,477,478,479,510,511],adjiman:446,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,202,205,218,224,228,230,250,253,257,261,266,267,270,271,275,293,297,300,302,303,306,307,308,309,314,316,325,334,338,342,347,349,350,351,353,354,356,376,377,385,387,392,394,414,439,440,465,481,506,524],adjust_radiu:325,adjust_radius_factor:325,admiss:275,adof:[158,218],adopt:[315,517],adp:[2,3,7],adri:[9,312,457,458],adust:172,advanc:[3,250,398,491,502],advantag:[1,6,8,11,17,39,40,41,224,392,416,505,510],advect:[3,6,334],advertis:8,advis:[387,456],afer:3,affect:[1,6,10,14,15,16,40,62,63,75,96,128,153,162,176,182,205,206,211,218,219,221,222,225,226,227,228,230,231,237,243,249,251,253,259,265,267,271,272,273,274,276,277,278,284,290,291,293,295,316,318,332,346,356,369,376,383,384,385,387,388,389,392,417,439,440,447,493,494,496,498,499,501,504,506,515],affin:[15,16,17,230,392,407],affiniti:392,afile:247,aforement:17,afresh:[304,504,523],afshar:412,after:[2,3,5,6,8,11,12,14,20,21,32,39,40,41,44,50,59,60,61,63,65,75,156,157,158,159,160,161,162,165,166,167,168,170,171,178,179,181,182,185,186,191,201,202,203,204,205,206,207,209,210,211,215,216,218,219,224,225,226,227,228,230,234,245,256,257,258,259,260,266,267,268,270,276,277,278,284,290,291,293,295,298,302,306,314,316,317,320,329,331,335,337,338,339,341,342,343,344,345,349,351,353,357,360,361,367,375,382,383,385,386,388,390,391,392,393,394,398,405,407,415,416,417,418,419,425,426,427,438,439,440,442,443,444,445,449,450,451,455,457,458,465,466,475,476,478,479,480,481,484,491,493,495,496,497,498,499,501,502,504,506,508,510,513,514,517],afterrun:504,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,15,16,64,152,158,164,172,202,206,230,237,249,302,360,375,387,439,440,491,493,494,496,498,503,510,512,523,526],against:[11,12,13,66,231,387,457,458],aggreg:[6,12,68,71,73,84,102,119,126,249,266,314,316,332,491,524],aggress:[237,249,510],agilio:[9,13],agre:[3,8,198,385,394,427,458],agreement:[5,7],ahd:424,ahead:353,aidan:[0,5,7,9,13,379],aij:13,aim:6,airebo:[2,3,7,225,226,313],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,250],aktulga:[7,9,309,458],al2o3:465,al2o3_001:[130,318],al3:177,ala:[256,465],alain:9,alat:[297,442],albe:[455,479,481],albeit:315,albert:9,alchem:[95,172],alcohol:349,alcu:[393,398],alcu_eam:455,alderton:411,alejandr:[270,271],alessandro:13,algebra:445,algorithm:[0,1,6,7,8,9,41,63,206,209,215,224,227,230,237,249,256,258,259,284,299,307,316,320,321,341,342,346,349,354,383,384,385,389,392,413,417,440,445,462,464,491,493,510],alia:[9,15],alias:[1,377],aliceblu:206,align:[6,9,12,28,41,75,180,198,224,251,379,496,499,517],alkali:417,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106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:[1,6,9,12,16,207,227,231,232,243,245,247,250,297,302,305,315,322,330,342,349,376,392,481,506,517],applicat:215,appling:228,apply:[95,223,228,232,247,253,254,255,320,330,331,332,333],applyt:3,appopri:[9,16],approach:[6,7,202,215,246,298,299,311,316,341,342,344,346,349,376,398,408,410,413,414,421,425,445,459,461,463,474,485],appropri:[1,2,3,6,8,9,11,12,13,14,16,32,37,42,50,56,57,63,77,96,99,127,128,129,156,157,158,186,191,197,198,201,202,203,206,218,219,222,227,228,230,243,244,247,256,265,267,268,270,272,273,274,275,276,277,278,290,291,293,295,299,302,303,306,311,316,321,334,337,338,339,342,349,351,352,354,355,356,367,377,387,394,398,402,406,407,408,416,422,425,427,434,438,445,456,457,458,476,477,478,479,480,481,484,485,496,497,498,500,501,509,510,513,523,524],approri:248,approxim:[6,9,130,134,177,245,247,256,299,318,320,341,376,381,383,384,385,400,410,417,419,421,439,440,445,447,450,456,459,465,478,482,487,510,517],april:11,aprpopri:491,apu:[439,440],aqua:[205,206],aquamarin:206,ar_thermal:215,ar_ttm:215,ara:13,arbitrari:[6,40,60,127,202,203,205,207,229,230,248,270,299,303,307,317,476,494,507,523],arbitrarili:[11,61,127,152,201,228,270,408,523],arcco:3,arch:[1,9,12,14,16],architect:374,architectur:[15,392,445],archiv:[6,7,9,12,336,405,503],archive:[11,12],arcsin:3,area:[6,41,99,123,127,176,224,230,256,342,349,414,422,454,483,493,506],aren:[127,359,458],arflags:12,arg:[3,11,12,21,40,41,44,55,61,65,75,95,128,166,172,176,178,181,182,186,201,202,203,204,206,209,210,211,212,214,216,218,219,220,221,222,223,224,225,226,229,230,231,236,237,243,245,248,249,250,251,259,262,267,272,273,274,286,292,302,315,316,318,319,323,326,327,329,341,344,351,352,353,354,356,357,361,374,387,392,399,400,401,403,404,405,410,411,413,417,423,425,430,434,438,439,440,441,448,452,460,462,464,475,482,493,494,496,499,501,503,505,507,509,514,515,523,524,527,528],argon:245,argonn:12,args:494,argument:[2,3,6,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,41,42,43,44,45,46,47,48,49,51,53,54,56,61,65,77,95,99,117,123,127,152,153,155,160,165,166,167,172,176,178,179,180,182,184,185,186,187,188,189,190,192,193,195,196,198,202,203,206,209,210,211,212,214,217,218,219,220,221,222,223,224,228,229,230,238,240,241,243,244,245,247,248,252,253,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,301,302,304,308,309,313,316,317,318,319,320,334,346,348,352,354,357,359,360,361,362,363,365,366,367,369,371,374,375,377,378,379,382,387,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,410,411,412,413,415,416,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,436,437,438,439,441,442,443,444,447,448,449,450,451,452,454,455,457,458,459,460,465,466,467,475,476,477,478,479,480,481,482,484,486,487,488,490,491,492,493,494,495,496,497,499,501,504,505,506,507,511,513,514,523,524,527],aris:[12,487],arithmet:[3,6,113,376,403,406,433,447,482,483],arkansa:9,arl:[9,88,89,239,321],armv8:16,army:[88,89,239,321],arnold:376,around:[1,3,4,6,9,12,42,59,60,61,69,74,75,76,77,81,127,129,152,156,173,176,178,180,184,201,205,206,213,214,228,230,231,251,267,270,303,305,307,311,316,326,330,334,351,352,355,375,381,386,465,496,499,506,507,517,523],aroung:3,arrai:3,arrang:152,arrheniu:[317,510],art:[9,491,510],artefact:247,articl:[6,465],articul:[7,9,301],artifact:[96,176,517],artifici:[268,306,469,470,472],arun:13,arxiv:[152,204,286,292,381,466],ascend:[41,206,250,259,316,501],asci:7,ascii:[13,203,318,345,387,415,418,442,496],ash:[439,440],asid:8,aside:[178,442],asin:523,ask:[3,11,518],askari:454,askoos:13,asoci:205,aspect:[6,7,61,230,245,421,459,483,496,506,510],aspect_ratio:318,asper:4,aspher:[0,2,3,4],asphere:4,asq:[439,440],assembl:4,assign:[1,2,3,6,7,11,12,14,16,17,32,38,39,40,41,50,58,59,61,63,65,69,75,76,79,86,98,103,114,116,121,124,125,129,130,152,153,158,173,175,177,178,181,191,201,202,203,204,205,206,207,209,210,211,214,218,221,224,226,227,228,231,233,245,250,253,254,255,256,267,270,272,273,274,275,276,277,278,288,290,291,293,294,295,299,302,303,305,307,313,316,318,337,338,339,340,357,367,377,379,382,386,387,391,392,398,415,418,421,424,425,449,450,458,459,488,493,494,496,497,498,499,500,505,506,511,514,523,524],assignemnt:[6,505],assignment:14,assing:305,assingn:477,assist:[7,268],associ:[3,5,6,8,12,21,36,39,40,44,55,61,69,78,79,86,87,95,97,98,103,109,111,113,114,116,129,142,173,186,197,202,203,205,206,210,211,212,216,228,230,236,243,245,246,252,256,267,270,301,311,315,316,317,318,332,334,358,359,361,370,379,385,387,391,392,405,408,412,413,414,415,417,424,425,427,430,434,449,450,461,463,474,475,477,478,494,497,504,516,517,520,523],associd:70,assum:[2,3,4,6,9,11,12,15,16,17,39,61,70,75,96,106,112,114,155,156,157,158,159,160,161,163,164,165,166,167,168,170,171,176,178,181,206,210,211,216,218,219,221,222,228,230,242,250,252,256,259,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,298,302,303,304,307,316,319,322,330,342,345,346,351,354,357,364,376,377,386,387,392,398,400,402,405,406,414,417,424,425,429,434,439,440,4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,247,254,256,269,270,271,293,294,299,303,306,308,316,321,322,334,337,338,341,342,343,344,351,360,369,371,376,377,384,387,394,399,403,404,407,408,409,411,412,413,417,420,421,423,424,430,434,435,438,442,446,447,449,450,452,465,474,482,505,508,510,517],chemic:[9,40,88,89,130,172,177,202,203,215,216,245,307,312,313,341,377,419,450,457,458,470,478],chemistri:[306,307,309,394,398,417,457,458],chen:346,cheng:407,chenoweth:[457,458],chenoweth_2008:[457,458],chi:[102,167,201,297,307,309,372,418,421,524],chiefli:456,child:8,chip:[7,9,16,17,392,509],chipot:229,chiral:369,chmod:[11,12],cho:442,chocol:[7,206],choic:[3,6,9,12,14,15,17,40,41,54,95,153,156,157,171,182,198,218,224,227,230,231,247,253,256,268,270,299,303,307,316,341,370,377,383,384,387,389,392,425,438,447,453,458,496,505,506,509,510,516,517,522],choos:[1,3,6,7,8,9,12,15,16,17,28,39,54,95,128,168,169,205,225,226,227,228,231,242,253,256,268,270,272,273,274,275,276,277,278,302,303,321,334,338,352,376,377,384,485,491,493,505,511],chose:[479,481],chosen:[2,3,6,12,16,152,178,181,190,198,205,211,216,228,231,242,245,246,254,256,268,270,275,299,302,313,334,338,341,342,347,349,350,356,377,378,384,392,413,417,422,429,432,460,479,491,505,510,511,517],chri:176,christian:[7,9,16],christoph:7,chunk:[0,2,3],chunkid:[69,79,86,98,103,114,116,125,158,173,175,218,331],chute:[4,9,10,248],ciccotti:320,cieplak:[6,184,508],cii:219,cij:219,circl:[42,75,329],circular:[3,6,156,200],circumst:17,circumv:[100,117,311],citat:0,cite:[3,7,8,12,253,465],civ:9,cl1:177,clarendon:[28,411],clarifi:[7,479,481],clariti:359,clark:452,class2:[2,3],classic:[0,3,5,6,7,8,9,243,299,306,311,346,371,417],classifi:[475,484],claus:494,clean:[6,12,14,16,504],cleanli:[495,527],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:500,click:[2,11,21,36,44,55,178,186,197,205,250,361,370,387,405,475,518],client:[250,252],climb:[269,387,510],clinic:[7,13],clo:[167,201,524],clock:[12,491,510,515],clockwis:[184,352],clone:518,close:[3,6,11,12,13,39,41,70,75,153,181,202,226,227,228,247,254,256,270,286,293,316,320,352,355,375,377,380,383,384,387,392,394,398,408,409,428,442,447,449,450,457,461,463,477,481,500,506,517,518,520],closer:[3,10,41,127,176,201,202,224,228,232,343,387],closest:[226,297,316,349,421,459,474,485],cloud:[465,517],clovertown:17,clsuter:76,clump1:[301,316],clump2:[301,316],clump3:[301,316],clump:316,cluster:[2,3,6,7,12,63,65,75],clutter:3,cmap:496,cmatrix:247,cmax:442,cmd:[11,12,299,507],cmdarg:11,cmin:442,cmm:7,cmoput:145,cn1:219,cn2:219,cna:[2,3,7,65,74],cnn:219,cnr:13,cnrs:9,cnt:[425,500],co2:[40,177,317,320,386,419],coars:[7,9,10,28,35,40,54,190,241,301,316,317,334,419,423,450,460,478,505,508],coarser:[377,523],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,360,361,367,405,425,429,447,462,464,467,496,525],coeffcient:496,coeffici:[0,2,3,4],coefficienct:412,coefficient0:415,coefficient1:415,coeffieci:[6,396,428],coeffincientn:415,coexist:[245,417],cohes:[6,418,442],coincid:[134,355,403,439,440,491],colberg:204,cold:[6,163,245,249,388,517],coldest:342,coleman8:9,coleman:[9,130,177,318],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,202,203,206,218,229,259,266,301,311,314,316,357,376,386,388,406,496,503,509,515,528],collid:[235,334,356],colliex:177,collinear:[3,301],collis:[3,256,334,352,356,414,422,488],colllis:334,colloid:[2,3,4,6,7],colombo:39,colon:[207,357,497,515],color1:206,color2:206,color:[3,9,41,202,205,206,224,246,306,311],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,259,267,268,306,316,335,336,346,356,394,420,424,457,458,497,511,513,523],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,14,42,65,75],comamnd:230,comand:227,comannd:392,comb3:[2,3],comb:[2,3,4,7,9,209,307],comb_1:308,comb_2:308,combiant:409,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,202,205,215,221,237,245,250,259,262,270,286,292,299,305,321,338,347,355,358,360,376,377,379,384,392,406,408,409,413,417,418,419,425,437,438,466,476,479,481,482,484,487,499,504,509,517,523,525],come:[0,2,3],comfort:[12,13],comid:331,comit:518,comm:[0,3,11,12,63,77,204,250,252,253,377,387,392,412,447,454,477,478,498],comm_modifi:[2,3,6,39],comm_modift:63,comm_styl:[2,3,41,63],comm_world:11,command:[0,1],comment:[2,4,7,11,12,37,56,184,198,202,240,241,254,316,317,346,386,387,393,415,416,418,419,429,442,449,450,451,458,465,466,476,477,478,479,480,481,484,493,494,496,517,518,523],commerci:7,commit:[9,518],commmand:[3,6,12,61,118,294,428,490,491,493,510,527],common:[0,1],commonli:[3,6,9,12,16,24,59,61,115,117,180,202,205,207,371,423,432,466,479,481,496,499,508],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,205,206,224,225,226,228,229,230,250,252,256,258,259,260,270,298,305,307,308,309,316,321,334,346,357,374,376,388,389,390,392,413,414,453,489,493,494,505,506,523,526,528],communc:376,comp:[7,204,252,253,286,292,320,377,387,417,447,454,459,473,477,478,480],compact:[65,209,405,475],compani:[5,7],compar:[1,3,4,6,8,12,16,39,94,121,130,161,177,186,197,206,234,307,357,359,376,377,385,387,442,465,491,510,511,517,522],comparison:0,compart:381,compass:[7,9,20,21,36,43,44,55,185,186,197,360,361,370,404,475],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,202,207,211,217,218,219,221,222,224,237,298,310,338,341,348,351,354,376,392,426,445,447,477,493,494,523],compens:[6,225,226,314,388,417],compet:345,competit:377,compil:[3,7,8,9,12,13,14,15,16,17,18,176,202,204,205,207,250,345,377,392,445,496,497,501,517,523],compl:16,complain:[11,12,16],complement:442,complementari:[7,408,430],complet:[3,6,9,11,12,14,41,61,75,206,224,229,259,299,302,305,334,345,347,358,359,375,387,392,418,462,464,483,491,496,501,504,508,510,513,517,523],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,256,286,329,355,374,387,417,445,477,478,494,496,499,523],compli:[341,345],complic:[6,7,9,12,13,129,216,245,494],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,227,228,230,231,236,237,243,248,252,253,256,259,261,262,266,267,269,270,271,275,276,277,278,290,291,293,295,296,298,299,300,303,314,316,319,320,322,326,327,330,334,337,338,339,341,348,349,354,355,356,376,379,384,385,386,387,392,412,417,422,439,440,462,464,465,466,496,497,506,514,523,524],componenet:6,componennt:129,composit:[6,216,256,415],compound:[407,417,418,484],compres:[75,125,218],compress:[3,6],compris:[40,355,419,459,483],compton:[130,177],comptu:3,compuat:377,comput:[0,1],computation:[3,6,225,226,346,398],computational:517,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,65],compute_peratom:8,compute_sa:[130,318],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,527],concav:355,concentr:[75,241,317,415,419,450,478],concept:[6,158,168,218,505],conceptu:[3,6,75,166,228,230,387,408,425,442,501],concern:[6,77,95,204,246],concetr:75,concis:[11,345],conclud:12,concret:8,concurr:[15,377,523],conden:[346,479,481],condens:[6,160,346,394,410,415,430,484],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:499,confer:445,confid:[3,510],config:[12,202,493],configfil:229,configur:[1,2,6,12,14,16,37,61,134,180,198,201,202,205,209,228,229,230,231,235,245,252,253,284,299,307,345,374,385,387,394,398,416,442,445,476,479,481,484,491,496,498,499,510,518],confin:[496,510],conflict:[3,12,40,203,447,494,518],conform:[3,6,13,61,227,228,269,315,322,345,369,387,417,508],confus:[3,484],conjuct:[9,412],conjug:[7,8,253,384,417,457,458],conjunct:[6,7,75,94,95,125,161,166,172,178,182,206,210,211,253,256,260,284,302,303,307,308,309,311,316,321,334,342,349,354,376,377,387,399,401,405,408,412,413,417,424,430,447,452,460,482,496,499,503,517,528],connect:[3,6,9,95,163,181,227,250,301,316,320,330,381,387,409,422,457,458,474,481,493,494,496,500,517],conner:394,connor:394,conput:3,consecut:[3,11,12,39,75,178,206,210,211,231,250,251,408,430,434,491,497,499],consequ:[1,6,216,346,429,510],conserv:[3,9,28,209,216,227,234,235,246,249,253,255,256,260,266,268,270,284,286,316,320,321,337,338,342,349,350,354,387,411,412,413,422,436,465,505,510],consid:[6,74,75,82,95,126,129,160,163,164,181,202,203,206,210,211,217,219,224,226,227,231,257,271,298,316,341,342,345,346,349,377,405,417,425,458,459,465,474,491,492,494,497,498,499,501,504,506,514,517,523],consider:[6,8,253,254,337,338,339,392,458,505],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,201,207,212,213,218,230,231,234,236,243,246,253,254,255,267,270,272,273,274,275,276,277,278,279,280,282,283,284,285,288,289,290,291,293,294,295,303,306,311,313,314,315,316,317,337,338,339,340,350,376,377,379,381,386,387,392,394,398,400,406,408,417,421,425,428,439,440,442,445,447,449,450,459,462,464,465,477,478,485,494,496,497,498,499,500,501,508,517,523],consistent_fe_initi:215,consit:316,constant:[0,3,4],constantli:237,constitu:[3,6,259,316,351,355,406,459],constitut:[462,464],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,231,237,245,246,251,259,262,264,286,292,301,302,314,316,320,332,342,349,385,386,417,501,508,517],constraint:[3,5],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,228,270,298,315,317,355,388,392,411,445,447,474,476,477,478,499,500,515,523],constructor:[8,11],consult:458,consum:[1,311,453,523],consumpt:374,contact:[0,2,3,4,5,8,9,12,13,40,42,65],contact_stiff:[461,463],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,224,229,231,236,240,241,247,251,252,253,256,268,284,297,298,301,302,304,305,306,309,313,316,317,318,323,334,341,345,346,355,356,359,375,377,386,387,390,391,393,394,395,398,407,408,411,415,416,417,419,425,426,442,445,449,450,451,455,456,457,458,466,476,477,478,479,480,481,482,484,491,492,493,494,496,497,498,499,501,503,505,508,510,511,513,514,517,518,523,526,528],content:[4,8,9,12,17,458,512,514],context:[3,6,8,12,16,127,128,206,225,226,231,301,313,350,384,487,496,503,512,522,523,524],contibut:74,contigu:493,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,206,209,210,211,216,218,219,220,221,222,224,227,228,229,230,231,237,245,246,247,249,250,251,253,254,255,261,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,300,302,305,306,316,318,322,333,334,336,343,344,346,352,355,359,375,391,392,398,412,414,432,435,457,458,459,462,464,480,491,494,496,498,499,504,510,511,513,514,523,526],continuum:[6,7,9,215,346,462,464],contour_integr:215,contract:[61,228,230,270,303,316],contradictori:3,contrain:320,contraint:284,contrari:[247,254],contrast:[1,6,42,55,66,160,163,203,230,357,462,464,487,527],contrib:346,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,228,245,253,256,259,260,265,271,293,294,301,302,310,313,316,318,320,348,376,385,387,395,412,414,415,417,425,439,440,445,447,457,458,465,508,514,517,518],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,202,203,205,209,215,216,224,228,229,230,249,250,253,254,270,272,273,274,275,276,277,278,303,308,316,317,324,325,337,338,339,346,350,374,376,389,417,421,445,457,458,461,463,476,481,491,493,505,511,512],control_typ:215,controlfil:458,convect:99,conveni:[6,12,28,202,207,222,318,379,466,482,518,523],convent:[3,8,28,189,196,197,203,206,315,330,358,415,417,523],converg:[3,6,41,96,202,203,205,207,212,224,227,228,236,243,275,286,292,306,308,311,315,320,383,384,385,387,407,408,430,465,491,503,510],convers:[3,8,152,205,206,216,219,303,376,408,409,410,417,430,434,438,452,494,510,522],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,202,205,206,219,222,268,302,305,357,360,362,366,369,379,387,393,415,445,479,481,488,494,496,497,498,503,513,517,522,523,526,528],convex:[42,355],convinc:[7,12],cook:9,cooki:7,cool:[7,168,237,249,314],cooordin:[202,203],cooper:[5,7],coord123:125,coord1:[3,125,218],coord2:[3,125,218],coord3:[3,125,218],coord:[2,3,6,7,11,61,65,75,76,80],coordb:465,coordbb:465,coordiat:385,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,224,225,226,227,228,229,230,231,234,236,237,238,243,245,248,249,250,251,252,253,254,267,269,270,272,273,274,276,277,278,293,296,297,298,301,302,303,313,314,316,319,320,322,327,330,331,332,333,334,336,344,345,346,353,354,356,357,379,385,386,387,392,393,394,397,416,465,491,496,497,498,499,501,504,506,510,517,523,524],coordn:[125,218],coords:465,copi:[0,3,4,8,9,11,12,14,16,40,131,205,346,387,405,457,494,518],copper:488,coproccesor:15,coprocessor:[1,7,9,15,16,392,509],coproprocessor:16,copy_arrai:8,copyright:[7,8,301],coral:206,core:[0,1,3,4],core_shel:160,cores:517,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,508],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,205,355,356,379,483,496,518],cornflowerblu:206,cornsilk:206,corp:9,corpor:15,corr:407,correct:[3,6,9,11,12,15,16,61,86,95,96,112,113,118,121,127,160,165,172,184,203,205,230,237,245,247,253,270,271,293,301,303,306,345,351,355,376,387,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,486,487,488,489,496,511,514,517,518],correction_max_iter:215,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,231,236,243,254,264,270,271,309,316,320,330,333,352,355,387,388,392,410,440,445,493,494,496,506,518,522,524],correl:[2,3,6,99,100,152,174,209,218],correpond:[240,241],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,223,226,228,230,237,238,241,243,244,248,253,256,257,266,267,268,270,272,273,274,275,276,277,278,279,280,284,288,290,291,293,295,297,298,299,303,308,309,316,317,319,320,341,351,352,354,355,356,358,360,361,362,363,365,366,369,371,377,382,384,386,387,393,394,396,399,400,401,402,403,404,405,406,407,408,411,412,415,416,417,418,419,420,421,422,423,424,425,428,430,431,432,433,434,435,436,437,438,439,442,443,445,447,448,450,451,452,454,455,457,458,459,460,465,466,467,476,477,478,479,480,481,482,484,486,487,488,491,493,494,496,497,499,509,510,511,513,514,517,523],correspondingli:[439,440,505],corrupt:3,cosin:[2,6,7,21],cosineshift:26,cosmo:[247,252],cossq:2,cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,205,206,218,224,225,226,242,270,308,346,376,377,390,408,430,434,445,447,476,493,505],costheta0:[476,479,481,484],costheta:455,costli:[11,96,247,388],couett:4,coul:[2,3,6,9,35,45,46,76,95,118,127,172,184,210,211,347,377,385],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,202,203,205,206,210,211,218,219,224,230,243,252,305,306,307,311,314,316,319,334,335,341,345,346,347,351,355,357,359,367,373,375,383,385,388,392,394,395,420,424,425,428,457,458,492,493,494,496,498,500,503,504,511,512,517,523,524],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,307,309,347,376,377,385,392,399,401,402,403,404,407,408,409,410,411,417,422,423,425,430,434,438,441,447,452,457,458,460,465,475,481,482,484,487,501,508,514,517,522],coulommb:6,cound:3,count:[1,3,6,8,11,12,15,41,65,71,81,99,125,127,128,166,176,182,184,212,213,216,218,221,223,224,231,236,242,245,251,270,284,302,319,320,337,338,355,377,385,386,387,389,392,420,424,447,514,515,523],counter:[3,352,491,502,504,510],counteract:245,counterbal:[237,249],counterbalanc:28,counterclockwis:184,counterpart:[202,491],counterproduct:17,coupl:[0,3,4],couple:[4,6,11,12],courant:323,cours:[3,8,138,140,172,202,210,211,246,315,330,345,351,353,354,356,357,377,439,467,493,496,509,517,523,526],courtesi:379,cov:465,coval:[6,9,28,417,442,465,517],covari:247,cover:[6,12,75,198,206,215,256,417,483],coverag:75,cpc:252,cpp:[1,3,6,8,9,11,12,13,95,202,210,211,243,320],cpu:[1,3,9,10,12,14,15,16,17,65,75,206,220,234,254,347,374,377,392,405,475,491,509,510,513,514,515,523],cpuremain:514,cpus:12,cr2:177,cr3:177,crack:[4,388],crada:[5,7],crai:[5,7,13,17,202],crash:[3,12,388,517],craympi:392,creat:[0,1,2,3,4,6,7,8,9,11,12,13,14,16,37,39,41,42,56,60,61,64,65,75,87,99,113,114,119,120,123,126,130,146,155,161,162,174,176,178,179,180,181,198,202,203,204,205,206,209,214,215,218,221,222,224,225],create_atom:[2,3,6,7,8,40,41,61,99],create_bond:[2,3],create_box:[2,3,6,21,40,41,44,59,60,61,64,75,99,176,178,179],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:0,creation:[3,5],crimson:206,critchlei:301,criteria:[3,127,179,205,206,225,226,227,265,385,454,483,498,501,523],criterion:[12,41,133,178,181,216,224,227,245,284,308,323,352,357,385,387,407,417,422,465,501,510,511],criterioni:510,critic:[6,48,49,268,341,346,385],crmax:75,crmin:75,cross:[3,12,21,75,97,129,156,176,186,202,203,205,217,226,230,267,269,293,316,326,330,333,342,349,361,379,387,403,412,414,415,423,424,425,430,432,434,455,460,462,464,479,481,488,496,500,506,526],crossov:1,crossterm:496,crozier:[0,7,13],crucial:306,crystal:[3,4,6,13,77,117,297,298,344,379,388,496,500,514,517],crystallin:[6,113,298,379,480,517],crystallis:341,crystallogr:[130,177],crystallograph:[379,514],crystallographi:[130,177,379],cs1:177,cs_chunk:6,cs_im:[40,496],cs_re:[40,496],csanyi:[152,456,466],cscl:442,csequ:6,csh:[11,12,405],cshrc:[11,12],csic:[416,476,479,481,484],csinfo:6,csisi:[416,476,479,481,484],csld:[2,3,209],cst:415,cstherm:6,cstyle:493,csvr:[2,3,6,209],ctcm:[393,415],ctemp_core:234,cterm:322,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:442,cube:[6,176,181,234,355,379,517],cubes:[41,224],cubic:[2,3,37,56,117,198,240,256,297,334,377,379,415],cuda:[1,3,7,9,12,14,16,392,509,523],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:398,cummul:[3,6,222,225,226,227,229,242,247,253,255,334,337,338,339,340,342,349,424,514],cumul:[6,216,218,221,235,245,253,268,270,275,284,316,318,387],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,112,113,119,127,128,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,224,225,226,227,228,229,230,231,235,236,237,243,245,247,250,251,253,259,265,267,270,271,276,277,278,284,286,290,291,292,293,295,301,302,307,308,310,313,314,315,316,317,320,321,322,323,324,325,326,327,329,331,332,333,334,337,338,339,345,346,349,350,351,352,353,354,356,357,359,374,375,376,377,380,381,382,384,385,386,387,392,398,405,407,411,413,415,417,418,422,425,426,429,439,440,442,443,444,447,455,457,458,461,462,463,464,467,479,481,482,485,491,492,493,494,496,497,498,499,500,502,503,504,506,508,510,511,513,514,518,523,524,525,526,527,528],curv:[6,178,245,286,292,298],curvatur:[421,459,488],custom:[0,2,3,6],cut0:494,cut1:505,cut2:505,cut:[1,2,3,6,9,12,14,15,16,17,18,41],cuthi:[297,309],cutinn:[400,439,440],cutlo:[297,309],cutmax:455,cutoff1:[404,411,430,434,438,441,452,460],cutoff2:[399,401,402,404,410,411,430,434,438,441,452,460,482],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,226,227,232,240,241,297,306,307,309,311,313,316,321,334,347,351,355,357,374,376,377,385,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,459,460,465,466,467,468,469,470,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,494,498,501,505,517,523],cutoffa:416,cutoffc:416,cuu3:415,cval:177,cvd:341,cvel:322,cvff:[2,7,361],cwiggl:[3,267,351,354,356,523],cyan:[2,205,206],cycl:[3,245,268,270,271,275],cyclic:[3,184,198],cygwin:12,cylind:[3,4,75,205,218,251,292,302,352,355,381,499],cylinder_d:381,cylindr:[6,251,330,352],cypress:392,cyrot:398,cyrstal:298,d3q15:256,d3q19:256,d_double_double:14,d_e:346,d_flag2:305,d_flag:305,d_name:[124,202,305,336,506],d_single_double:14,d_single_single:14,d_sx:305,d_sy:305,d_sz:305,daan:344,dai:12,daili:12,daivi:293,damag:[2,3,9,65],dammak:311,damp:[3,6,209,214,253,254,255,260,270,271,275,292,303,306,307,311,316,337,338,350,352,353,384,385,387,399,401,403,408,411,417,422,430,438,452,460,475,482,510,517],damp_com:254,damp_drud:254,dampen:[316,517],dampflag:[352,422],dan:16,danger:[3,12,245,357,412,514],dangl:181,daniel:9,darden:[377,411],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:307,dash:[422,513],dat:[6,99,198,215,492],data2xmovi:0,data:[1,2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:0,datafil:[12,13,318],dataset:318,datatyp:3,date:[0,4,6,12,13,201,457,458,523],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,202,219],davenport:441,davi:351,david:[9,18,376,377,479,481],daw:[415,455],dcd:[3,6,7,202,204,205,206,207,299,497,501],dcs:9,ddim:201,deactiv:438,dealt:252,debug:[6,7,11,12,13,16,57,130,134,177,178,299,304,374,376,426,447,485,494,495,503,506,513,523],deby:[2,3,7,210,211,311],decai:[100,408,488],decid:[3,6,12,15,75,267,305,316,347,511,518],decipher:379,deck:305,declar:204,declin:334,decod:205,decompos:[95,466],decomposit:[3,5,7,17,64,215,299,321],decoupl:[6,517],decreas:[3,202,203,212,213,220,227,230,236,237,243,245,253,345,376],decrement:322,deepli:373,deeppink:206,deepskyblu:206,def:[12,13,494],defaul:63,defect:[6,74,176,445],defgrad:2,defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,235,236,239,241,243,244,245,248,251,252,253,254,255,256,265,267,269,270,271,272,273,274,275,276,277,278,280,281,282,285,288,289,290,291,293,294,295,297,298,299,301,302,303,305,307,309,314,316,317,318,319,320,323,327,331,332,334,336,337,338,339,340,342,343,344,346,348,349,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,369,370,371,372,374,376,377,379,382,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,401,402,403,404,405,406,408,409,411,412,413,414,416,417,419,420,421,422,423,424,425,426,428,430,431,432,433,434,435,436,437,438,439,440,441,445,446,447,448,449,450,451,452,454,455,457,458,459,460,461,462,463,464,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,493,494,496,497,499,500,501,502,505,506,507,508,510,511,513,514,517,519,520,521,522,523,524,525],definit:[2,3,6,8,12,13,82,85,127,152,206,218,219,220,221,222,230,239,251,275,318,336,348,351,354,356,358,370,374,386,395,398,406,413,417,428,455,462,464,466,483,494,496,498,505,507,522,523],defint:514,deform:[2,3,6,7,8,40,42,59,61,63,65,85,122,134,138,139,153],deg2theta:177,deg:517,degener:[3,301],degrad:[8,17,298,377,505],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,227,234,245,247,248,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,315,316,320,337,338,339,344,360,362,366,369,371,385,411,415,424,506,514,517,524],degrees:198,degress:[158,218],del:510,delai:[3,6,12,388,414,514],deleg:425,delet:[2,3,7,8,12,54,59,62,65,176,181,182,209,218,219,221,222,225,227,242,245,270,318,337,338,357,359,375,386,388,391,447,474,496,497,498,499,507,508,513,518,519,521,523,524],delete_atom:[2,3,7,178],delete_bond:[2,3,43,45,46,47,48,49,50,51,53,54,55,56,68,73,126,179],delete_el:215,deli:201,delimit:[317,494,523],dellago:[6,237],deloc:[271,417,465],delr:442,delt_lo:510,delta:[2,21],delta_1:398,delta_3:398,delta_7:398,delta_conf:3,delta_ij:[442,455],delta_pi:398,delta_r:455,delta_sigma:398,deltah_f:241,delx:201,delz:201,demand:311,demo:11,demon:296,demonstr:[306,442],den:302,dendrim:424,dendtrit:381,denniston:[9,256,258,259,260,298],denomin:[7,183],denot:[130,234,237,254,298,309,311,408,423,425,458,462,464],dens:[75,227,417],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,210,211,215,218,224,230,243,256,259,263,264,298,302,303,305,307,346,351,379,382,386,393,394,398,415,442,443,444,449,450,455,459,465,469,471,472,473,496,505,506,514,522],density_continuity:464,density_summation:464,dent:381,depart:[0,7],departur:[268,306],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,223,224,226,228,230,236,238,241,244,247,248,249,251,253,254,256,258,259,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,297,308,309,311,313,316,317,319,320,321,327,334,337,338,339,341,343,345,346,348,351,354,355,356,357,359,360,361,362,363,365,366,369,371,377,379,385,386,388,389,390,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,415,416,417,418,419,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,442,443,445,446,448,449,450,451,452,454,455,457,458,459,460,465,466,467,475,476,477,479,480,481,482,484,486,487,488,491,493,496,498,499,502,506,508,510,513,514,516,523,524],dependend:6,depflags:12,dephas:[491,510],depos:231,deposit:[2,3,4,112,180,209,216],deprec:[3,307,457],deprect:218,depth:[51,156,205,346,419,421,459],dequidt:9,der:[95,118,406,407,438,457,458,487],deriv:[6,7,8,9,37,56,65,95,152,172,198,219,228,230,237,245,253,267,270,272,273,274,275,276,277,278,297,303,307,311,343,344,346,351,352,355,384,386,394,398,406,411,417,418,423,432,436,437,442,445,457,458,475,477,478,487,517],derjagin:487,derlet:297,descend:206,descent:[7,384],descib:[40,205,307],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,224,227,228,229,230,231,233,234,240,241,246,247,250,251,252,253,254,255,256,258,259,260,265,269,270,271,275,283,294,297,299,304,305,306,307,308,309,316,317,322,330,334,335,336,337,338,339,340,341,342,343,344,349,351,352,354,359,376,377,379,383,384,385,386,387,391,394,395,397,399,400,401,403,404,405,406,407,408,411,415,417,418,419,421,422,423,425,428,430,431,432,433,434,435,436,437,438,439,440,441,442,445,446,449,450,454,455,456,457,458,459,460,465,466,467,474,475,476,477,478,479,480,481,482,484,486,487,488,489,491,493,494,496,497,498,499,500,506,509,510,513,518,523,524,526],descript:[2,3,6,8,9,11,12,13,17],descriptor:[152,202,426],deserno:377,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,215,227,233,234,270,271,297,298,318,341,346,395,396,397,400,403,408,410,417,438,439,440,443,444,455,458,477],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,201,218,222,228,230,243,245,246,253,254,255,259,270,293,301,302,303,304,307,311,316,319,320,334,337,338,339,340,345,352,367,373,376,377,379,383,385,386,387,412,415,424,439,440,476,479,481,492,493,494,496,500,505,510,511,513,514,515,523,524,526],desk:7,desktop:[4,6,7,10,12,205],despit:517,destabil:398,destre:369,destroi:[9,11,39,225,226],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,112,114,116,118,120,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,227,228,229,230,231,237,243,245,246,247,248,250,251,253,255,256,260,267,268,269,270,271,272,273,274,275,276,277,278,282,284,290,291,293,294,295,298,301,302,303,305,306,308,309,310,316,320,321,334,337,338,339,340,341,342,344,345,346,347,348,349,350,357,359,361,370,376,377,380,385,386,388,389,392,393,394,395,397,398,400,402,403,404,405,406,407,408,411,412,417,418,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,440,441,442,446,447,449,450,454,457,458,459,465,466,467,475,483,486,487,489,494,496,497,498,499,501,502,505,506,508,511,514,515,518,523,524,528],detect:[2,3,12,42,63,65,94,100,244,302,345,387,407,424,429,491,493,496,507,510,523],determin:[1,3,6,8,9,12,14,39,40,42,51,59,60,61,63,64,71,75,95,112,118,120,123,129,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,228,230,231,234,236,241,245,248,249,251,253,254,259,265,267,268,270,276,277,278,290,291,293,295,297,299,302,303,306,313,314,315,316,317,318,319,323,325,327,334,337,338,339,341,347,348,351,352,353,354,355,356,357,370,376,377,379,386,388,389,392,394,395,402,407,411,414,415,419,420,422,425,426,434,442,445,447,450,458,459,465,474,477,478,482,487,493,496,497,499,501,503,506,510,512,513,515,522,523,524],determinist:321,detil:119,devan:[9,460],devanathan:481,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,250,275,301,306,307,310,394,398,417,444,445,465,484,498],devemi:9,deviat:[268,275,297,420],deviator:9,devic:[1,3,12,14,16,250,392],device_typ:392,devin:[308,407],devis:444,dfactor:205,dff:517,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,377],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,310,445],dhi:[61,201,230,302],dhug:[268,306],dhugoniot:[268,306],dia:442,diagnost:[2,5],diagon:[3,6,91,129,152,153,154,228,270,303,316,349,462,464],diagonalstyl:466,diagram:[41,130,177,197,224,299],diallo:424,diam:[205,206,302,386],diamet:[3,6,40,42,124,178,202,203,205,206,210,211,253,302,305,316,334,336,350,352,386,406,421,422,432,459,483,487,496,497,506],diamond:[379,417,442],diamter:[40,302],dick:6,dicsuss:267,dictat:[216,268],did:[3,12,385,412,414,415,422,447,479,481,504],didn:3,die:17,diel:2,dielectr:2,diff:[3,6,12,174,348,376],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,224,225,226,227,228,229,230,234,237,240,244,245,246,247,248,249,250,253,254,256,267,270,271,272,273,274,276,277,278,280,282,285,288,289,290,291,295,297,299,301,303,306,307,308,311,314,316,320,322,330,332,334,337,338,339,342,343,344,346,349,350,351,352,355,359,360,370,373,375,376,377,379,380,383,384,386,387,389,390,391,392,393,394,398,402,403,405,406,407,412,413,415,417,419,421,422,423,425,428,430,431,433,434,441,442,443,444,446,447,448,449,450,451,455,457,458,459,460,461,462,464,465,466,467,475,476,477,478,479,481,483,484,487,490,491,493,494,496,498,499,500,501,504,505,506,508,510,511,513,514,515,517,522,523,524,526],differenti:[1,3,6,28,198,317,376,408,455,480],difficult:[228,299,392,424,505],difficulti:[100,117,320,457],diffract:[7,9,130,177,318],diffus:[0,4],diffuse:[4,6],digit:[2,3,206,359,445,523],dih_table1:198,dih_table2:198,dihedr:[0,2,3,7],dihedral_coeff:[2,3,184,185],dihedral_cosine_shift_exp:26,dihedral_styl:0,dihedralcoeff:[3,199],dihedraltyp:226,dihydrid:417,dij:320,dilat:[2,3,61,63,65,82],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,201,230,251,352,379,442,499,522,523,524],dimdim:523,dimems:298,dimens:[1,2,3,6,7,12,41,59,60,61,63,65,75,99,125,129,153,158,165,166,167,178,180],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,269,298,346,379,383,387,455,496,506],dimensionless:[115,133,134,136,139,141,143,148,152,346,377,466,487],dimensions:318,diment:3,dimentionless:147,dimer:[6,316,442],dimgrai:206,dimstr:[41,224],dinola:[303,337],dintel_offload_noaffinity:15,dipol:[0,2,3,4],dipolar:[4,28,40,202,203,336,517],dir1:507,dir2:507,dir:[1,3,4,8,10,11,12,268,297,306,333,455,457,458,494,507,523],dirac:152,direc:455,direct:[2,3,6,7,12,13,28,59,75,117,130,152,176,177,178,184,201,202,205,209,212,213,214,230,231],directli:[3,6,8,9,11,12,95,124,129,152,154,202,203,204,205,212,236,247,251,256,298,317,318,338,350,352,353,354,355,379,384,392,393,394,399,401,402,408,411,415,417,430,434,447,452,460,474,494,506,507,508,514,523],directori:[0,1,2,3],disabl:[3,12,15,346,429,494,509,523],disadvantag:[6,224],disallow:[202,230,270],disappear:498,discard:[2,3,41,75,220,224,347,355,493,498,499],discontinu:[198,385,436],discourag:442,discov:[13,347],discret:[6,8,40,42,205,206,253,256,292],discuss:[0,1,2,3],disk:[6,92,93,100,171,200,231,245,302,494],disloc:[74,445],disord:[39,74,445],disp:[0,2,3],dispar:459,disperion:[411,434],dispers:[3,6,7,9,176,298,376,377,402,411,434,439,447,458,477,484],displac:[2,3,6,7,12,42,61,65],displace_atom:[2,3,7,113],displace_box:61,displacemet:499,displai:[11,13,21,36,44,55,186,197,202,205,361,370,405,475],dispters:3,disregard:445,dissip:[6,9,40,88,89,239,246,253,298,321,343,344,400,412,413,422,439,440,475],dissolut:225,dist:[6,73,99,119,128,202,299,315,414,474,491,524],distanc:[2,3,6,7,8,9,12,19,20,39,43,45,46,47,48,49,51,53,54,55,56,57,58,60,61,63,65,66,69,73,75,76,77,78,79,80,81,86,87,94,97,98,100,103,113,114,115,116,117,119,125,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,201,202,203,205,206,214,218,225,226,227,228,230,231,232,235,237,245,251,256,267,268,269,270,275,284,297,298,302,306,307,314,315,316,320,322,326,330,331,332,333,334,341,342,344,345,346,349,351,352,353,354,355,356,360],distinct:[6,234,313,376,459],distinguish:[6,94,152,259,417,495,523],distort:[176,393],distrbut:393,distribut:[0,2,4,5,6],distro:[122,405,454,455],ditto:[8,12,14,15,16,17,42,126,226,316,488,494],div:8,divd:128,diverg:[3,12,39,316,344,394,498,517,526],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,197,206,218,219,221,224,230,297,342,349,354,376,385,387,418,458,465,484,505,513,523],divis:[6,256,398,428,438,493,514,523],dl_poly:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,345,496,497,501],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,202],dlen:506,dlmp_intel_offload:[9,15],dlo:[61,201,230,302],dlopen:6,dlvo:[7,406,487],dm_lb:256,dmax:[334,383],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,21,36,40,42,55,59,61,65,69,71,79,86,95,98,103,112,114,115,116,118,120,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,231,245,253,254,265,270,271,276,277,278,282,290,291,293,294,295,302,305,316,330,334,337,338,339,348,352,355,357,359,361,370,375,385,386,387,392,393,394,397,405,407,408,415,416,418,424,425,427,428,442,443,444,447,451,454,455,456,466,475,476,479,481,483,484,494,496,497,498,499,501,504,505,506,513,514,518,523,524,526,527],docuement:459,dodd:42,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,223,224,226,227,228,230,234,236,237,240,241,242,245,246,249,251,253,254,256,259,266,270,271,272,273,274,276,277,278,290,291,292,293,294,295,303,304,305,309,311,314,316,334,337,339,341,342,346,349,350,351,354,355,356,357,362,363,364,366,367,369,375,376,377,378,379,386,387,388,393,394,395,396,397,398,400,402,403,404,406,407,408,409,411,412,414,415,416,417,419,420,421,422,423,425,426,427,428,429,432,433,435,436,437,439,440,442,443,444,445,447,449,450,455,456,457,458,459,461,462,463,464,465,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,489,491,492,493,494,496,497,498,499,500,503,504,506,507,508,509,510,513,514,517,518,523,528],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,330,386,388,392,394,407,416,427,457,458,476,479,480,481,484,496,498],dof:[3,8,123,156,157,158,171,218,316,524],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[386,496],doi:[6,229,297],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,201,204,205,206,209,216,224,228,230,231,249,252,256,270,271,299,311,316,321,346,351,352,376,377,387,392,414,447,491,493,496,500,513],domin:[1,417,510],don:[0,8,9,12,13,127,181,212,236,254,355,442,465,494,496,518],donadio:338,done:[1,3,6,7,8,12,14,15,16,17,37,39,41,56,61,64,75,172,175,178,181,198,202,205,206,215,216,218,220,221,222,224,225,226,227,228,230,231,240,241,243,245,250,251,253,254,261,270,276,277,278,290,291,293,295,296,298,299,300,302,305,313,316,318,320,334,337,338,339,341,343,344,357,359,375,376,377,385,387,388,391,392,394,402,415,425,426,427,434,440,441,442,447,449,450,457,474,477,478,483,491,492,493,494,497,500,501,504,514,515,517,518,523,524],donor:424,dot:[153,174,212,236,248,269],doti:[398,455],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,230,243,304,355,359,375,377,391,392,398,418,423,445,457,458,492,496,500,504,509,523,524],dover:215,down:[3,6,7,8,11,39,75,228,245,253,334,350,417,447,465,495,515],downhil:[383,384],download:[5,7,8,9,11,12,13,16,250,426,456],downsid:6,downward:313,dozen:[8,9,12,118,209,457,458],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[2,3,6,7],dpde:263,dpdtheta:[40,88,89,413],dpdtheta_i:[239,240,241],dproduct:395,dr_ewald:[130,318],drag:[2,6,99,209],dragforc:256,drai:[268,306],drain:[249,350,385],dramat:[9,61,201,225,226,227,228,230,270,334,337,338,377,447,465,493],drautz:398,draw:205,drawback:305,drawn:[42,202,205,206,246,491],drayleigh:[268,306],dreid:[2,3,4,6,9],dreiding:0,drfourth:115,drho:[124,393,415,449,450],drift:[6,113,115,237,246,247,249,253,254,266,314,334,505,513,517],drive:[11,12,213,228,230,248,270,297,303,316,353,387],driven:[6,190],driver:[6,12,14,209,243,250],drop:[3,206,412],droplet:425,drsquar:115,drude:[0,2],drudes:[254,517],dry:242,dsecriptor:426,dsf:[2,3],dsmc:[2,3,9],dstyle:302,dt_collis:256,dt_lb:256,dt_md:256,dt_srd:334,dtilt:[61,230],dtneb:510,dtqm:306,dtype:[126,226],dual:[15,16,334,392],dudarev:177,due:[1,3,6,9,12,15,16,18,40,54,57,59,60,63,69,74,75,78,79,86,87,94,96,97,98,103,112,113,114,115,116,121,127,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,223,225,226,227,228,229,230,231,236,238,242,243,246,247,250,251,253,254,255,256,259,260,261,266,267,268,269,270,275,284,297,300,302,314,315,316,319,321,330,331,333,334,335,337,338,339,340,341,343,344,346,350,351,353,354,355,357,376,377,383,385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or:3,eros:442,erose_form:442,erot:[2,3,6,9,65],errata:[479,481],erratum:351,erron:3,error:[0,1,2],erta:422,ervel:[124,203,496],escap:[231,517],especi:[8,15,166,178,209,216,224,245,306,311,314,315,392,493],espresso:[9,310],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,219,298,350,377,394,408,430,481,501,514],essential:[8,275],essex:28,establish:[95,249],estim:[1,3,6,10,12,37,41,56,99,153,215,224,235,268,334,341,376,377,383,447,458,477,478,510,514],estimat:3,esu:522,esub:442,eta:[6,256,270,306,307,309,350,416,418,421,455,480,484,522],eta_dot:270,eta_ij:455,eta_ji:418,etag:[40,496],etail:514,etap:270,etap_dot:270,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,225,226,230,231,243,245,246,253,270,302,313,318,346,347,355,359,375,376,385,386,387,388,390,415,416,425,438,440,445,453,457,458,476,479,481,484,491,494,496,497,498,503,505,506,510,511,512,513,514,515,517,522,523,526,528],ethernet:17,etol:[385,387,491,510],etot0:306,etot:[6,104,106,107,121,153,164,206,234,254,268,306,513,514],eu2:177,eu3:177,euler:[385,387],eulerian:215,euqat:468,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,230,236,246,248,249,251,252,253,254,298,304,307,319,323,327,337,338,339,348,351,354,356,357,359,383,385,445,447,449,450,455,461,463,465,477,478,491,492,494,498,499,501,503,504,505,506,510,512,514,523,524],evaluat:[376,377,523],evalut:[359,494],evan:[166,293],evanseck:[6,19,184,403,508],evapor:[2,3,9,59,112,209,216],evaul:[8,385],evdwl:[118,154,457,458,514],even:[3,6,8,12,14,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,224,225,226,228,230,231,234,237,251,254,268,270,271,298,302,311,313,316,318,329,334,342,346,349,351,355,357,368,376,383,385,387,392,397,417,418,422,425,428,447,459,484,485,489,496,497,499,501,502,503,505,506,508,511,513,514,515,517,528],evenli:[3,41,57,153,198,224,256,428,485],event:[2,3,6,8,65],eventu:[3,6,12,14,180,510],eventual:307,ever:[9,54,56,252,334],everaer:[406,421,459,475],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,235,237,242,243,245,247,249,250,251,256,257,266,270,271,275,286,292,296,297,298,302,303,304,305,306,307,308,309,311,313,314,316,317,318,320,322,331,334,336,337,338,339,340,341,342,345,346,347,348,349,357,359,375,377,387,388,389,392,412,414,425,438,457,458,465,471,490,491,492,496,498,500,501,503,504,505,510,511,512,514,515,518,523,528],everyth:[8,118,518],everywher:[127,432],eviri:417,evolut:[237,247,256,299,491],evolv:[256,299,347],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,347,376,377,385,399,401,402,408,411,417,430,434,452,460,475,477,482],ewald_disp:411,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,224,227,246,247,253,254,255,302,311,312,334,346,361,376,405,498,503,510,523,526,528],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,198,210,211,221,224,230,235,240,246,253,254,255,271,283,284,294,298,305,306,334,339,340,353,392,405,412,415,422,425,439,447,449,450,477,478,498,499,506,510,523],exager:517,examin:[6,8,16,227,298],examp:[494,523],exampl:[0,1,2,3],exce:[3,6,15,16,17,41,60,75,180,217,218,221,222,224,228,230,235,242,270,298,313,318,324,325,334,385,392,496,523],exceed:[3,41,61,224,230,270,334,458,504],excel:417,except:[1,2,5,6,8,10,11,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,223,224,228,230,238,244,245,248,251,253,255,270,271,272,273,274,275,276,277,278,279,280,283,284,288,290,291,293,294,295,299,308,309,316,319,320,330,334,340,346,354,357,358,359,360,361,362,363,365,366,369,370,371,376,377,379,382,386,387,388,390,391,392,393,394,396,399,400,401,402,403,404,405,406,407,408,410,411,412,415,416,417,418,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,440,443,448,451,452,454,457,458,459,460,467,475,476,477,479,480,481,482,484,486,487,488,491,493,494,496,498,499,501,504,505,506,507,508,510,514,517,522,523,524,527],exception:494,excess:[220,417],exchang:[2,3,6,8,63,64,209,215,216,237,245,249,253,308,316,342,346,349,376,392,417,511],exchange:376,excit:417,excite:417,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,202,218,225,226,257,266,301,314,316,341,352,357,385,386,388,400,422,425,428,439,440,447,474,508],exclude:388,exclus:[1,3,12,15,95,184,407,445,447,505,515],excurs:[270,491],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,205,250,310,359,375,378,391,492,494,504,507,510,523],exempl:465,exemplari:246,exemplifi:417,exert:[6,251,254,286,311,353,354,355,377],exhaust:[215,391,523],exhibit:[100,237,249,270,384,417,505],exist:[3,6,7,8,11,12,13,15,36,55,57,61,71,74,134,178,179,197,204,205,206,209,214,223,226,228,231,245,301,302,304,305,357,358,360,362,363,364,366,370,380,386,413,425,457,474,485,492,494,496,497,498,507,508,509,518,523,524,526],exit:[2,3,11,12,41,59,202,224,375,391,494,495,504,513,515,523],exlanatori:3,exp6:2,exp:2,expand:[2,3,44],expans:[12,152,202,507,523],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,198,224,236,245,247,267,297,303,305,306,311,316,357,377,388,405,442,445,447,491,494,496,498,501,505,510,523],expens:[6,75,206,297,301,316,346,357,376,377,388,392,494],experi:[6,13,14,223,231,250,259,269,303,315,316,383,387,412,447,505,510],experienc:[6,12,258,259],experiment:[16,245,376,392,510],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,15,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,198,202,203,205,206,209,218,219,222,224,226,228,230,270,286,297,305,316,330,357,359,375,376,379,386,387,391,397,415,428,465,467,483,494,497,498,501,503,506,517,518,523,528],explan:[3,6,61,124,129,152,202,203,218,269,297,425,490,493,494,496,505],explanatori:[3,8,128,202,203,217,218,221,316,386,493,523],explantori:[3,312],explic:446,explicit:[6,9,11,21,44,81,95,124,127,172,186,210,211,230,317,324,325,361,376,382,394,395,398,403,405,415,417,429,439,482,490,493,497,500,518],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,230,238,244,246,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,305,306,308,309,316,319,320,339,340,346,354,360,362,363,365,366,369,371,386,392,393,394,396,399,400,401,402,403,404,405,406,407,408,409,411,412,414,415,416,418,419,420,421,422,423,424,425,429,430,431,432,433,434,435,436,437,438,439,443,445,447,448,449,450,451,452,454,458,459,460,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,484,486,487,488,496,498,499,505,506,508,509,515,517,518],explictli:[15,509],exploit:[14,16,299],explor:[130,177],expon:[3,307,309,317,415,419,421,424,438,446,460],exponenti:[95,419,455,476,484,488,510,523],expos:11,exposit:[215,412,414],express:[6,152,164,178,210,211,228,267,297,307,317,346,352,359,398,415,417,432,442,465,466,475,523],expression:359,expressiont:398,extend:[0,3,6,7],extens:[3,6,9,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,222,223,229,232,236,237,243,244,245,247,248,249,251,253,255,268,270,275,284,297,298,314,315,316,319,322,327,330,331,333,337,338,339,340,341,343,344,346,348,351,355,356,421,442,445,458,459,466,513,514,522],extensiv:[65,209,514],extent:[1,3,41,42,45,59,75,176,180,202,214,224,251,353,356,376,379,394,461,463,477,478,493,496,499],exterior:[3,6,176,355],extern:[2,3,9,94,95,176,205,209,223,228,236],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,206,221,224,226,270,304,305,306,316,334,385,386,389,390,411,422,425,428,442,447,493,494,496,499,508,517,523],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,210,211,309,387,408,418,442,466,494,501,513],extract_atom:11,extract_comput:[11,494],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,205,220,228,230,270,344,417,480,517],extrema:438,extreme:417,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,348],f_a:[479,480,481],f_ave:128,f_c:480,f_f:481,f_fix_id:306,f_foo:523,f_harm:344,f_i:[28,455],f_id:[6,75,128,131,202,203,209,217,218,219,220,221,222,265,336,348,514,523],f_ij:455,f_indent:222,f_int:343,f_j:28,f_jj:99,f_k:455,f_langevin:346,f_max:[306,311],f_msst:268,f_r:[254,479,480,481],f_sigma:398,f_solid:344,f_ss:6,face:[3,6,59,61,75,166,176,180,214,351,353,354,355,356,379,421,442,459,496,499],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,247,302,334,344,422,457,465,508],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,201,202,205,206,210,211,219,224,228,230,231,237,245,250,253,255,256,268,270,271,275,299,303,307,315,317,320,323,325,334,338,342,349,350,351,355,366,377,379,386,392,394,395,398,399,401,403,408,409,410,412,413,417,422,425,429,430,442,445,447,449,450,451,452,458,460,467,476,482,493,496,499,500,505,508,510,511,514,517,522,523],factori:[3,494],factoriz:376,fail:[3,9,11,12,61,182,228,231,376,385,387,410,458,494],failur:[133,462,495,523],fairli:[11,447,505,510,518],faken:77,falcon:250,fall:[3,6,206,221,302,494,523],fals:[94,357,465,523],fame:8,famili:[484,493],familiar:[0,11,518],fan:455,far:[3,6,12,16,59,61,63,94,202,203,206,207,224,225,226,228,231,270,297,315,316,334,351,362,366,383,387,388,483,494,496,501,514],farago:253,farrel:[479,481],farther:202,fashion:[6,8,41,75,178,206,209,210,211,216,224,226,231,245,247,251,267,268,270,272,273,274,275,276,277,278,287,290,291,293,294,295,305,306,308,316,322,326,333,336,344,346,350,351,352,354,356,387,425,439,499,508,523,527],fasolino:427,fast:[6,7,9,12,13,16,39,202,203,281,306,347,376,377,400,439,440,445,475,477,478,498,503,505,514,524,528],faster:[1,6,9,11,12,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,223,224,230,238,244,248,252,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,303,307,308,309,316,319,320,334,341,343,346,350,354,360,362,363,365,366,369,371,376,377,389,390,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,411,412,415,416,418,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,443,448,451,452,454,458,459,460,467,475,476,477,479,480,481,482,484,486,487,488,491,499,505,509,517],fastest:[1,6,16,166,346,347,392,493],fatal:[3,513],fault:[74,458],faulti:12,fava:421,favor:227,favorit:7,fbmc:341,fcc:[2,3,6,7,66,74,77,99,117,209],fcm:[287,523],fcold:237,fdirect:234,fdotr:426,fdt:[2,9,239,240,241,317,321],fdti:95,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[0,3,5,6],fecr:415,feedback:[7,250],feel:[7,250,251,259,297,355,357,387,447],felling:444,felt:355,femtosecond:522,fene:[2,3,6,7,10,44],fennel:[408,430],fep:[0,2],ferguson:[6,184,508],fermi:[1,9,10,12,14,164,392,481],fermion:417,fernando:441,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,207,217,218,219,221,222,237,254,270,302,305,307,320,348,376,385,386,387,394,465,493,496,501,505,507,515,526],fewer:[1,3,11,14,15,63,259,505],fewest:3,fextern:243,feynman:299,fff:494,ffield:[407,418,457,458,465],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,96,120,121,153,298,376,377,505],fft_inc:[12,377],fft_lib:12,fft_path:12,fftbench:[376,515],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:237,ficiti:474,fictiti:[6,212,213,236,243,247,299,315,408,430,434,474],field1:[497,501],field2:497,field:[0,2,3,5],fifth:[6,330,419,451],figshar:297,figur:[1,3,8,12,306,493,494,518],fij:411,file0:297,file1:[11,13,241,297,345,359,386,501,503,507],file2:[11,13,241,345,359,386,501,503,507],file:[0,1,2,3,4],file_from:204,filen:386,filenam:[3,12,13,37,41,56,198,202,203,205,206,207,215,218,219,220,221,222,224,229,240,241,297,301,304,307,308,309,312,313,316,317,318,345,346,373,374,375,386,387,393,394,398,408,415,416,418,419,427,442,443,444,449,450,451,455,456,457,458,465,466,476,477,478,479,480,481,484,492,493,494,497,498,503,507,514,523,526,527,528],filennam:503,filep:[3,202,203,206,498,503,528],filepo:313,fill:[7,9,178,205,302,346,379,388,398,445,458,499,518],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,410],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,198,207,216,227,228,240,241,242,245,269,297,302,303,311,315,383,385,387,388,408,425,430,434,442,449,450,465,475,477,478,517,518,523],find_custom:8,fine:[15,16,182,212,236,344,388,392,518,523],finer:[152,178,523],finest:376,finger:[178,201,267,499],finish:[6,11,41,224,359,373,375,376,389,391,392,483,501,523,524],finit:[0,3,4],finni:[7,415,475],finverse:234,fiorin:[9,229],fire:[2,3,209],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,224,227,230,240,241,245,246,251,256,267,268,269,270,297,299,304,305,306,308,313,316,320,322,330,331,332,334,335,336,343,344,345,346,348,352,357,359,360,367,379,385,386,387,388,391,392,393,394,397,398,399,401,403,405,407,408,415,417,418,419,422,423,425,426,427,428,429,430,434,439,440,442,444,445,447,449,450,451,455,457,458,465,466,474,476,477,478,479,480,481,484,488,491,492,493,494,496,497,498,501,503,505,508,509,510,513,514,517,518,523,524,525,526,528],fischer:[6,9,18,19,184,403,508],fit:[3,6,9,12,37,56,198,240,315,334,394,398,427,442,447,449,450,470,477,478,480,504,518,523],five:[77,164,306,386,398,443,496,510],fix:[0,1],fix_deposit:3,fix_flux:215,fix_heat:237,fix_id:[3,228,268,270,272,273,274,275,276,277,278,303,306],fix_manifoldforc:518,fix_modifi:[2,3,6,8,160,163,209],fix_nh:8,fix_nv:518,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:320,fix_reax_bond:457,fix_saed_vtk:318,fix_setforc:8,fix_shak:320,fix_srd:3,fixedpoint:[228,270],fixextern:243,fixid:215,fji:411,flag1:[233,390],flag2:[233,390],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,199,202,203,205,206,207,222,227,229,233,250,253,257,259,266,267,298,305,316,330,333,334,341,345,354,357,372,374,377,386,390,391,392,394,424,429,442,445,474,489,491,493,494,496,497,498,500,501,502,506,518,523],flag_buck:402,flag_coul:[402,411,434],flag_lj:[411,434],flagfld:[400,439,440],flaghi:[3,400,439,440],flaglog:[400,439,440],flagn:233,flagvf:[400,439,440],flat:[6,346,351,352,356],flavor:[2,7,12],fld:[351,439,440],flen:395,flex_press:395,flexibl:[3,6,8,179,205,218,229,247,271,342,349,417,480,514],flip:[3,6,230,270,353,354],floor:523,flop:12,floralwhit:206,flow:[4,5],fluctuat:[6,66,95,228,245,246,253,256,270,275,297,298,303,321,344,346,369,413],fluid:[2,6,7,9,10,40,69,79,86,96,103,116,127,128,158,173,175,228,230,248],fluid_veloc:260,flush:[3,206,513],flux:[2,3,6,65],flv:205,fly:[7,9,12,41,205,209,215,220,231,234,316,320,347,398,445,514,517],fmackai:9,fmag:232,fmass:299,fmax:[385,514],fmomentum:234,fmsec:[2,206,253,254,267,270,303,316,337,338,505,516,522,524],fname:375,fno:[9,15],fnorm:[385,514],fnpt:234,fnve:237,fnvt:234,foce:425,fock:395,focu:320,fogarti:[9,309,458],foil:[152,297,466],fold:[332,505],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,224,229,230,231,234,235,239,240,241,243,245,246,247,250,252,253,254,256,259,268,270,275,276,277,278,290,291,293,295,298,299,301,304,305,306,307,309,311,313,315,316,317,318,320,336,337,338,339,342,343,344,345,346,348,349,357,358,362,363,364,365,366,369,371,374,379,382,385,386,387,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,450,451,452,454,455,456,457,458,459,460,462,464,465,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,489,491,493,494,496,497,499,501,503,504,505,508,510,511,512,517,518,523,524,527],foo:[4,8,11,12,202,205,243,317,494,507,523],foo_species:317,foot:6,footprint:[12,392],fopenmp:[9,15,17],forc:[0,1,2,3,5],force_uvm:16,forceatom:259,forcefield:[315,424],forcegroup:256,forcezero:383,ford:411,forestgreen:206,forev:75,forget:[254,517],forgiv:270,fork:[12,202],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,206,209,210,211,226,246,247,253,255,259,267,293,298,309,311,315,316,317,346,351,355,360,361,364,369,382,384,386,387,394,395,398,405,413,415,417,420,424,425,429,441,442,444,445,449,450,451,452,455,457,458,459,465,466,467,475,477,479,480,481,487,490,493,494,496,501,506,513,517,523],formal:[6,82,85,99,246,247,253,270,299,334,342,465],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,198,202,203,204,205,206,207,218,221,222,224,226,240,241,298,301,305,307,309,312,316,317,318,329,345,346,357,358,361,382,386,387,393,394,398,405,415,418,419,429,442,444,449,450,456,457,458,460,466,477,478,484,485,493,494,496,497,498,501,512,513,514,523,525,526],formation:241,former:[6,12,15,39,41,206,224,346,350,398,400,502,508,523],formerli:[7,13],formul:[1,6,9,40,66,153,212,236,253,270,293,307,309,315,320,345,376,394,398,415,417,421,442,454],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,222,223,230,236,248,249,251,253,254,267,297,298,304,313,319,327,332,334,337,338,339,348,351,354,356,357,359,360,361,363,370,379,386,394,395,397,398,403,404,405,406,411,412,415,416,421,422,423,424,426,429,430,432,433,434,436,437,439,440,442,446,447,448,459,460,467,475,476,477,479,480,481,484,486,487,492,496,499,506,513,514,522,523,524],forth:[1,6,11,12,13,14,391,494,499,503],fortran:[3,6,9,11,12,13,243,415,425,442,457,458],fortun:8,forward:[3,8,95,375,387,392],foster:[398,454,455],foul:181,found:[3,6,9,12,77,172,202,227,229,237,245,250,256,262,298,341,347,359,375,388,405,408,411,491,497,498,513],four:[6,11,54,87,113,114,152,174,268,346,369,386,387,445,491],fourier:[2,6,12],fourth:[6,115,315,330,341,403,419,451,465],fox:[6,130,184,473,508],fphi:[37,56,477,478],fpic:12,fplo:[37,56,477,478],fprime:[477,478],fqdn:252,fqq:411,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,201,205,206,216,225,226,227,228,268,302,306,313,314,334,339,340,379,387,392,398,400,419,422,439,440,501,506],fragment:[42,250,313],fraig:42,frame:[91,152,206,215,268,306,353,421],framer:[205,206],framework:[5,247,393,466],franc:9,frattl:237,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,210,211,297,334,343,344,345,346,384,387,395,417,438,445,448,455,487,493],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,227,234,245,247,253,254,259,270,271,275,276,277,278,290,291,293,295,299,301,316,320,337,338,339,344,385,411,514,517,524],freeli:[0,6,7,12,156,157,171,176,205],freez:[2,3,6,209,214],frenkel:[6,237,245,344],freq:214,frequenc:[3,6,15,39,113,206,220,284,298,299,306,311,374,412,417,458,465,491,505,510,523,527],frequent:[3,66,70,74,76,77,81,96,100,117,152,206,225,226,237,242,342,349,447,482,503,515],fri:[268,306],friction:[4,5,6,9,10,42,209,247,253,306,311,316,346,350,352,422,506],friedrich:323,from:[0,1,2,3,5],fron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334,346,352,353,377,379,417,496,500,522],infinitesim:6,inflect:[409,432,475],influenc:[3,9,41,85,160,267,302,376,377,447,479,480,481],inform:[0,1,2,3,6,7,8,9,11,12,13,14,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,242,243,244,245,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,269,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,300,301,302,303,304,305,307,308,309,310,311,312,313,314,315,316,318,319,320,323,330,331,332,334,335,337,338,339,340,341,342,343,345,348,349,350,351,353,354,355,356,358,374,376,377,380,384,385,386,387,388,390,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,411,412,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,452,454,455,456,457,458,459,460,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,486,487,488,489,493,494,496,497,498,500,501,503,508,510,511,513,515,523,525,526,527,528],informat:[8,12,497],infrequ:[6,270,412,491,510,515],infti:[409,439,440],ingtegr:398,inher:[376,385,447],inherit:[6,482],inhomogen:[17,346,447],inidividu:385,init:[3,8,314,465],init_fil:346,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,179,180,198,201,202,203,205,206,207,210,211,214,215,219,224,226,227,228,230,238,240,241,245,246,250,251,252,253,254,256,261,266,267,268,269,270,275,284,286,298,299,300,305,306,311,314,315,316,319,321,331,333,334,336,341,343,344,345,346,347,348,351,352,353,354,356,357,359,376,380,384,385,387,394,395,411,412,414,445,449,450,456,457,458,465,477,478,491,493,494,496,498,499,501,503,504,506,510,511,514,517,523,524,526,528],initial:[2,3,6,87,113,180,523],initial_integr:8,initial_integrate_respa:8,initialis:456,initialt:346,inlclud:11,inlin:494,inner2:[403,423],inner:[3,8,15,57,202,251,359,375,383,384,385,387,391,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,411,412,414,415,416,417,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,454,456,457,458,459,460,465,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,483,484,485,486,487,488,489,505,510,523],inner_distance_cutoff:424,innergroup:259,innermost:[37,56,75,390,477,478,505],innernod:259,innner:436,inordin:347,inorgan:[6,484],inp:[229,359,466,484],input1:[68,71,73,84,102,119,124,125,126,128,129,131,336],input2:[68,71,73,84,102,119,124,125,126,128,129,131,336],input:[0,1],input_doubl:3,inquir:323,insensit:12,insert:[3,5,7,8,9,12,61,178,209,231,245,251,302,376,466,474,494,500,517],insertion:[3,231,245,302],insid:[2,3,6,8,11,75,129,141,147,178,202,203,206,217,231,232,237,242,245,251,256,259,302,316,334,351,353,354,355,356,357,374,379,494,495,496,498,499,506,523],inside:[256,432,494,510],insight:[6,13],instabl:[256,411,464],instal:[1,3,6,8,9,11,12,14,15,16,176,202,204,205,207,377,387,402,403,426,430,434,438,445,491,497,498,503,511,518,528],install:[0,8],instanc:[6,9,11,210,229,247,353,420,425,447,455,494,517],instantan:[6,65,227,228,246,247,270,275,298,303,306,311,313,316,341,502,514],instanti:[6,11,12,215,425,493],instead:[1,3,6,8,11,12,13,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,198,202,203,211,218,221,222,224,228,229,245,253,256,259,260,298,304,305,314,316,336,354,374,376,377,380,388,392,401,402,415,429,431,438,442,445,448,458,475,482,491,499,503,510,512,517,523],institut:[9,250,301],instruct:[3,4,6,8,9,10,11,12,13,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,198,200,205,212,223,230,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,308,309,316,319,320,354,360,362,363,365,366,369,371,377,392,393,394,396,399,400,401,402,403,404,406,407,408,411,412,415,416,418,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,443,448,451,452,454,458,459,460,467,476,477,479,480,481,482,484,486,487,488,499,505,517],instruction:11,insuffici:[3,6,12],insult:270,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,198,202,203,205,206,212,225,226,231,236,238,242,243,245,248,253,266,304,305,314,316,334,346,351,355,356,357,359,375,386,388,392,406,421,425,453,459,477,489,493,494,496,497,501,504,505,513,514,523,524],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,198,201,202,205,206,216,218,225,226,227,231,233,243,245,246,247,250,253,254,255,256,298,301,302,305,306,311,316,334,336,338,341,345,346,365,376,379,400,412,413,414,428,442,457,458,462,464,466,491,493,494,495,496,504,505,506,510,513,523,524],integer:[3,496],integr:[2,3,5],integral:[299,449,450],integrate_ulsph:324,intel:[1,2,3,7],intel_cpu:[12,15],intel_phi:[12,15],intend:[3,6,8,12,13,35,220,246,456,496],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,209,218,219,221,222,224,225,226,227,235,242,249,259,268,270,275,313,316,318,334,342,346,348,349,513,514,522],intensiv:[65,209,514],intepol:523,inter:[17,42,63,64,158,181,182,202,227,253,255,269,308,316,376,387,398,506,517,523,526,528],interact:[1,3,6,7,8,9,10,11,12,14,15,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,202,203,209,210,211,225,226,227,244,245,250,251,253,255,259,284,297,299,301,302,307,309,315,316,317,324,325,334,335,341,346,350,351,352,355,356,361,362,363,364,366,368,370,376,377,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,452,453,454,455,458,459,460,462,464,465,466,467,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,491,494,496,498,500,501,505,506,508,513,514,517,526],interatom:[3,4,7,9,10,178,202,269,343,344,393,398,415,417,426,442,445,465,480,523],intercept:130,interchang:6,interconnect:17,interconvert:417,intereract:39,interesect:355,interest:[1,5,7,8,9,11,13,75,177,299,341,344,377,416,440,457,458,494,523],interf:[392,518],interfac:[0,3],interfer:[12,270,394],interg:[6,517],intergr:505,interi:440,interior:[3,6,41,355,499],interlac:442,interleav:[6,178,504],intermedi:[6,12,61,205,269,297,369,387,494,495,504,508],intermix:491,intermolecular:[154,394],intern:[0,2,3,5,6,9,11,15,19,20,23,27,31,34,35,39,40,42,65,88,89,95,109,111,129],internal:[3,205,211,302,523],internal_element_set:215,internal_quadratur:215,internat:[130,177,215],internet:252,interpenetr:442,interpentr:[469,470,472],interpol:[6,14,37,56,110,198,205,206,215,240,241,256,297,376,377,387,398,447,449,450,458,471,477,478,479],interpret:[2,6,11,205,221,422,467,491,494,510,523],interrupt:306,intersect:[3,6,130,206,355,357,499],intersert:355,interspers:385,interstiti:[176,445],intertia:[3,103],interv:[3,6,99,204,219,253,270,306,311,312,325,465,471,491,510,523],intestieti:130,intial:[6,392,394],intiial:[41,501],intiti:[3,333],intra:316,intra_energi:245,intramolecular:[28,154,245],introduc:[6,9,100,117,205,237,270,306,311,316,369,376,393,408,417,430,434,438,476,510,523],introduct:0,intuit:379,inv:[130,177,318],invalid:[3,12,75,97,181,284,387,439,440,498],invari:[117,145,150,152],invent:320,invers:[3,6,51,130,177,206],inverse:517,invert:[1,6,182,298],invis:355,invoc:[176,227,392,462,464,494],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,230,231,232,233,235,236,237,238,242,243,244,245,246,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,264,266,267,269,270,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,300,301,302,303,304,305,307,308,309,310,311,312,313,314,316,318,319,320,322,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,360,362,363,365,366,369,371,375,376,377,378,379,385,387,392,393,394,396,399,400,401,402,403,404,406,407,408,411,412,415,416,418,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,443,447,448,451,452,454,458,459,460,462,464,466,467,476,477,479,480,481,482,484,485,486,487,488,490,493,494,495,497,499,501,504,505,507,508,510,513,514,517,523,524],invokd:3,invoke:[3,12,16],involv:[3,6,7,8,12,65,119,126,127,128,158,182,209,216,225,245,256,301,304,309,334,376,384,385,387,397,414,421,428,476,479,481,492,493,499,501,505,510,511],ioff:[386,496],ion:[6,7,9,160,296,330,346,377,398,409,418,420,442,445,465,475,481,488,496,517],ionic:[6,9,399,401,409,417,418,452,465,517],ioniz:[407,417],ionocoval:9,iparam:[3,226],ipi:[2,13],ipp:0,ir3:177,ir4:177,irregular:[6,41,60,224,228,230,270,316],irrelev:451,irrespect:[439,440],irrevers:[234,317],is_act:[3,523],is_avail:[3,523],is_defin:[3,523],isbn:487,isele:[376,377],isenthalp:[9,270,271,272,273,274],ismail:[376,377,402,434],isn:[3,8,11,12,237,249],iso:[3,228,234,254,270,271,272,273,274,275,276,277,278,303,311,316,517],isobar:[9,270,271,276,277,278,321,413],isodem:417,isoenerget:[9,321,413],isoenthalp:[321,413],isol:[3,181,357],isomorph:299,isotherm:[9,245,270,271,276,277,278,303,321,413],isotop:305,isotrop:[6,100,253,303,376,377,400,421,439,440],isovolum:318,isralewitz:322,issu:[1,3,6,9,11,12,13,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,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177,pr4:177,practic:[3,12,228,270,271,298,305,484,493,518],prb:[479,481],prd:[2,3,4,6,9,94,230,387],pre:[3,6],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec:465,prece:464,preced:[2,6,61,184,203,217,218,219,220,221,222,252,313,317,318,359,379,387,392,398,424,510,513,514,523],preceed:[11,12,75,166,219,351,494,523],precipit:176,precis:[1,3,9,12,13,14,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,43,45,46,47,48,49,51,53,54,56,113,123,155,165,178,184,185,187,188,189,190,192,193,195,196,198,202,206,212,218,222,223,228,230,237,238,244,248,253,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,307,308,309,316,319,320,354,360,362,363,365,366,369,371,376,377,385,392,393,394,396,399,400,401,402,403,404,406,407,408,411,412,415,416,418,420,421,422,423,424,430,431,432,433,434,435,436,437,438,439,443,445,448,451,452,454,457,458,459,460,465,467,476,477,479,480,481,482,484,486,487,488,498,499,505,506,509,514,517,522,523,524],precv:493,predefin:[196,206,357,417],predict:[1,6,10,12,284,316,392],preexponenti:510,prefactor:[23,24,27,31,34,35,172,186,197,210,211,219,351,362,366,369,385,406,420,451,459,460,467,487],prefer:[7,8,12,249,315,347,394,518],prefix:[11,12,205,229,298,317,490,493],preliminari:[37,56,198,240,241,449,450,477,478],prematur:385,prepar:[8,9,307,310,334,507,517],prepend:457,preprint:[152,286,292,381,466],preprocessor:250,prerecord:229,prescrib:[6,8,156,157,158,171,209,210,215,218,231,267,287,347],presenc:[202,225,226,256,259,439,440,445,487,526],present:[1,3,9,12,17,176,198,204,205,231,246,247,252,256,257,259,260,311,329,352,355,358,407,417,429,438,445,458,459,465,493,517],preserv:[3,61,228,230,270,320,334,356,497],press:[2,3,6,9,28,95,106,107,121,153,164,209,228,234,245,247,254,265,268,270,272,273,274,275,276,277,278],pressdown:223,pressur:[1,2,3,6,7,8,9,59,65],pressure_with_eviri:417,presum:[77,167,209,210,211,230,387,425,499],prevent:[2,3,6,40,132,231,244,302,334,345,369,376,383,385,387,392,412,425,453,469,470,472,474,494,498,504,506,517,523],previou:[0,2,3,5,6,8,11],previouli:231,previous:[3,9,11,61,63,75,94,112,128,131,167,178,180,182,201,202,203,204,206,214,216,217,218,219,221,222,230,231,245,251,265,267,302,314,316,319,320,346,348,351,352,353,354,356,357,378,422,475,491,494,498,499,509,511,513,514,519,520,521,523,524],prevoiu:352,price:[6,411],primari:[0,6,346],primarili:[5,7,9,16,154],prime:[234,254,423,445,479,481,493],primit:[3,6,354,355,379],princip:[3,129,250,465],principl:[6,9,11,250,271,307,417,426,445,476,493,518],prinicp:[42,316,386],print:[0,1,2,3,6,7,8,11,12,15,16,17,18,41,99,106,107,128,152,202,203,205,206,207,209,218,219,220,221,222,227,228,231,250,253,256,265,268,270,272,273,274,275,276,277,278,286,287,290,291,292,293,295,297,301,302,303],printabl:2,printflag:426,printfluid:256,prior:[176,200,321,378,527],priori:505,prism:[3,6,166,180,499],priveleg:3,privileg:[11,12,250],prob:[225,226],probab:467,probabl:[3,8,12,40,75,168,181,182,216,224,225,226,227,231,245,254,270,302,351,357,385,447,449,450,477,491,510,517],probe:523,problem:[0,1,2],problemat:245,proc:[1,3,8,11,12,14,124,202,203,375,493],proce:[41,54,182,224,235,387,445,503,511,514],procedur:[6,12,39,41,206,216,224,245,253,254,255,270,272,273,274,275,276,277,278,290,291,293,294,295,298,337,338,339,340,343,344,385,387,394,400,497,517],proceed:[12,445],procesor:[41,493],process:[1,3,4],processor:[1,2,3,4,6,7,8,9,11,12,13,14,16,17,39,40,41,42,60,61,63,64,65,68,71,73,75,84,102,119,124,126,127,129,166,176,178,180,181,182,201,202,203,205,206,209,215,218,224,225,226,227,228,230,243,246,247,253,254,256,270,299,305,308,311,316,320,321,334,346,357,373,374,375,376,380,387,389,390,391,392,412,414,453,465,490,491],processsor:[41,224,493],procp1:[202,203],procsessor:515,procssor:505,produc:[1,3,4,6,7,12,13,14,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,42,43,45,46,47,48,49,51,53,54,56,65,68,71,73,75,84,102,119,121,123,124,125,126,128,129,131,153,155,165,176,184,185,187,188,189,190,192,193,195,196,198,202,203,206,209,212,217,218,219,221,222,223,224,227,230,238,243,244,246,247,248,253,254,255,265,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,302,306,307,308,309,311,316,318,319,320,335,336,346,347,348,351,354,359,360,362,363,365,366,369,371,377,385,387,390,392,393,394,396,399,400,401,402,403,404,406,407,408,411,412,415,416,417,418,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,443,448,451,452,454,455,458,459,460,467,476,477,478,479,480,481,482,484,486,487,488,491,493,498,499,501,502,505,510,511,514,523,524],product:[6,15,16,17,152,176,230,293,307,317,347,392,395,417,419,450,458,478,493,523],proessor:392,prof:301,profi:167,profil:[2,3,6,65,156,157,158,161],program:[3,4,6,7,9,11,12,13,16,154,202,205,206,207,209,229,243,250,256,310,415,494,495,507,523],programm:[13,16],progress:[1,41,224,250,268,306,384,385,387,514,517],prohibit:506,project:[6,7,13,384,475,518],promis:7,promot:398,prompt:[8,11,12,250,507],proni:[3,246,247],pronounc:249,proofread:8,prop:[6,305],propag:[4,9,214,270,3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1],rapidli:[3,8,12,75,227,253,268,270,316,337,338,350,408,412],rapp:[307,308,309],rappe_and_goddard:308,rare:6,rasmol:[6,7],rasmussen:421,raster3d:[6,7],rate:[2,6,12,136],rather:[2,6,9,12,40,41,64,123,161,205,224,230,246,247,316,338,346,350,352,353,354,357,417,449,450,457,477,478,497,501,506,508,513,523],ratio:[6,61,95,111,152,216,224,230,253,255,334,342,349,350,376,390,421,422,459,469,483,493,496,506,510],rational:[347,508],rattl:[2,3,9,209,237,262],rattle:[3,9,209,237,247,286,292,320],rattle_debug:320,ravelo:[275,432],rayleigh:[268,306],rb1:177,rbb:465,rbg:206,rcb:[3,41,224],rcm:[97,98],rcmx:[97,98],rcmy:[97,98],rcold:237,rcut:63,rcutfac:[152,466],rd1:387,rdc:16,rdf:[2,3,65],rdn:387,rdt:387,rdx:4,reach:[6,12,41,131,220,224,226,228,254,275,326,334,341,359,375,391,409,515,517,523],reacquaint:518,react:6,reactant:[317,417],reaction:[9,241,317,322,332,345,356,387,417,419,450,478],reactiv:[9,313,394],read:[2,3,6,7,8,9,11,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,58,61,126,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,201,202,203,205,206,207,208,209,215,216,227,228,230,231,240,241,245,247,250,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,298,299,301,302,304,305,309,316,317,320,322,326,329,333,336,344,345,346,352,358,360,361,362,363,364,365,366,368,369,370,371,372,373,375,382,386,387,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,452,454,455,456,457,458,459,460,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,491,493,496,497,498,500,501,502,503,504,506,507,508,510,523,524,525,526,528],read_data:[2,3,6,7,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,64,69,75,78,79,86,87,90,97,98,103,113,114,116,126,173,176,178,179,180,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,202,205,226,227,230,267,299,305,315,317,345,360,361,362,363,364,365,366,368,369,370,371,372,382,386,387,390,391,392,395,396,397,399,400,401,402,403,404,405,406,408,409,411,412,413,414,417,420,421,423,424,425,428,430,431,432,433,434,435,436,437,438,439,440,441,446,448,452,454,455,457,458,459,460,465,467,474,475,483,486,487,489,493],read_dump:[2,3,202,387,496],read_restart:[2,3,6,8,9,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,39,40,41,43,44,45,46,47,48,49,51,53,54,55,59,60,61,64,178,184,185,186,187,188,189,190,192,193,195,196,197,209,215,216,228,229,230,231,245,256,267,268,270,272,273,274,275,276,277,278,290,291,293,294,295,299,305,316,322,333,336,346,352,360,361,362,363,364,365,366,369,370,371,382,387,395,396,397,399,400,401,402,403,404,405,406,408,409,411,412,413,414,417,420,421,422,423,425,428,430,431,432,433,434,435,436,437,438,439,440,441,446,448,452,454,459,460,467,474,475,483,486,487,489,493,496,497],read_restart_set:8,readabl:[203,205,386,503,528],reader:[3,13,497],readi:[11,12,179,181,182,250,506,517,526,527,528],readme:[1,4,6,8,9,10,11,12,13,176,202,203,207,310,426,445,457,458,494],real:[3,6,7,11,26,29,30,61,75,99,100,117,152,167,178,187,201,206,214,230,231,234,250,251,254,267,299,306,311,314,350,351,353,354,356,365,376,377,379,383,389,408,445,447,457,458,481,496,499,505,513,516,522,524],realist:[3,231,500],realiz:[75,209,494],realli:[1,3,8,12,123,134,153,206,251,388,425,508,518],realloc:3,realtim:250,reamin:[351,355],rearrang:[203,387],reason:[3,6,7,11,12,18,39,159,170,178,218,253,303,316,343,344,347,357,386,387,392,405,409,417,418,420,440,447,483,485,500,505,524],reax:[0,2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,209,307,309,312,313,425,457,458,475,508],rebal:[41,224],rebalanc:[41,224],rebo:[2,7,9,313],rebuild:[11,12,14,15,245,388,412,514],rebuilt:[3,12,202,203,204,205,207,388,392],recalcul:[75,95,334],receiv:[3,223,250,252,297,493],recent:[2,3,11,12,209,218,221,222,224,225,226,249,266],reciproc:[6,12,130,176,177,298,376,399,401,402,408,411,417,430,434,452,460,510],recog:12,recoginz:3,recogn:[3,12,15,77,180,225,226,270,317,386,415,442,457,494,496,503,504,517],recomend:6,recommend:[7,12,15,205,206,237,306,344,376,417,425,439,440,445,458,459,462,464,465,505,515,518],recompil:[1,3,9,12,207,320],recomput:[112,140,182,235,322,414,508],reconstruct:[3,229,465],record:[207,229,322],recov:[228,237,270],recreat:358,rectangl:[41,224,379],rectangular:[7,41,64,180,224,245,379,496,498,500],rectilinear:[130,177,203],rector:53,recurs:[41,224,398,483],recust:41,recv:493,red:[2,205,206,227,299],redefin:[3,498,504,523],redirect:12,redo:12,reduc:[1,2,3,6,12,16,17,18,26,41,65,75,96,120,121,123,124,125,126],reduct:[17,18,128,130,177,268,306,376],redund:418,ree:470,reed:[268,306],rees:[7,9,13],ref:[343,344,384],refactor:6,refer:[2,3,6,7,8,9,11,12,14,28,65,71,75,85,91,94,95,112,113,114,124,126,128,131,156,157,158,171,178,201,202,203,204,209,215,217,218,219,221,222,227,228,230,231,237,244,268,270,271,275,297,299,301,302,304,305,306,316,320,322,341,348,353,359,360,371,376,377,384,388,393,400,414,421,428,442,444,445,459,472,473,479,481,491,492,494,498,501,504,505,506,509,510,514],referenc:[3,6,12,65,71,75,125,131,202,203,209,219,245,305,348,377,408,424,451,459,494,514,523],reflect:[2,3,6,75,130,152,177,197,205,209,225,226,231,259,268,296,298,316,351,353],refman:9,reformat:7,refresh:215,reg:499,regard:[6,61,267,320,321,326,454,458],regardless:[14,75,178,181,201,221,230,253,270,272,273,274,276,277,278,303,316,327,334,392,493,499,506],regim:[6,342,349,409,505],region:[0,2,3,6,7],region_spher:8,region_styl:355,regist:[8,127,154,329],regoin:6,regress:523,regspher:178,regstrip:357,regul:6,regular:[1,3,41,64,96,176,180,202,205,216,224,245,305,346,377,409,428,493,496,498,500],reigon:523,reinhardt:[343,344],reject:[178,227,457,511],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,206,209,216,224,230,231,234,237,245,251,254,266,267,293,297,302,311,313,314,322,330,334,336,341,342,346,353,357,376,377,385,417,421,422,439,440,442,459,487,497,505,510,514,517,524],relat:[1,6,8,9,10,12],relationship:[6,240,307,359,376,465,487,517,523],relax:[2,3,4,6,7,209],releas:[0,5,7,8,13,225],relect:[3,447],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,206,210,211,214,215,216,217,218,219,220,221,222,224,225,226,230,231,235,237,238,242,244,245,246,249,250,256,257,258,260,261,262,263,264,266,267,269,279,280,281,282,283,284,285,286,287,288,289,292,296,300,301,302,304,305,310,312,313,314,318,320,327,332,334,335,336,341,342,345,346,347,348,349,350,351,352,353,354,356,357,376,381,385,395,396,400,406,408,409,411,412,414,417,420,421,422,423,424,429,431,432,433,435,436,437,439,440,447,448,449,450,454,459,467,474,477,478,486,487,488,493,509,524],reli:[3,12,308,417,458,488,496,506],reloc:12,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,202,210,211,216,218,219,228,230,253,254,261,270,271,276,277,278,290,291,293,295,300,301,325,334,337,338,339,345,346,357,359,367,370,386,398,417,425,438,445,447,475,491,496,497,501,506,508,510,514,517,518,523,524],remaina:398,remaind:[9,178,202,231,302,334,347,481,496],remap:[3,6,12,61,63,75,161,178,201,230,251,267,293,376,496,497,498],remedi:[6,517],rememb:[2,518],remot:518,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,203,209,218,225,242,253,254,259,262,266,268,270,276,277,278,290,291,293,295,301,307,316,317,318,320,334,337,338,339,341,357,376,387,411,440,445,496,499,507,508,518,523,524],remove_bia:8,remove_bias_al:8,remove_molecul:215,remove_sourc:215,remove_speci:215,ren:177,renam:[12,358,507,518],render:[12,13,202,205,206],rendon:[270,271],reneighbor:[3,8,12,39,59,75,224,245,334,347,357,412,513,514],renssela:301,renumb:75,reorder:[3,12,39,493],rep:511,repeat:[2,6,205,206,227,228,245,326,379,398,479,481,483,491,510],repeatedli:2,repel:251,repes:202,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,202,203,205,206,207,218,219,221,222,224,227,231,253,275,304,305,311,313,394,408,432,449,450,477,497,498,503,504,514,523,524,526,528],replic:[2,3,7,379,493,496],replica:[0,2,3,4],replica_fil:12,report:[0,1],repositori:[7,9,12,426,456,457,458],reprens:346,repres:[1,3,6,8,9,12,14,40,41,42,61,70,75,98,124,127,129,190,198,202,203,205,218,219,220,221,222,228,234,241,246,248,253,256,270,299,301,303,311,316,317,318,322,330,331,346,348,355,377,387,393,398,421,428,438,439,440,442,443,444,452,455,457,458,482,483,491,493,496,506,508,511,517,523,526],represent:[3,6,8,9,59,61,146,180,202,246,247,299,346,398,417,421,445,459,496,499,517],reprocess:501,reproduc:[3,270,352,408,415,422],repul:442,repuls:[6,7,35,40,45,46,119,251,307,351,352,355,394,398,406,408,412,417,419,422,424,438,442,446,465,474,481,484,487,488,506],reqir:[307,309],request:[3,6,8,12,41,113,181,198,202,250,256,314,321,334,336,374,376,447,457,458,491,501,506,510,518,523,524,526],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,76,81,100,117,127,152,202,205,447,497],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,209,216,219,221,222,237,245,247,249,253,254,266,270,275,293,301,303,311,316,334,337,338],research:[5,7,88,89,239,256,260,321,445,491,510],resembl:[311,518],resepct:6,reserv:[12,250,517],reservoir:[99,237,245,249,253,346],reset:[2,3,6,8,11,12,63,69,75,78,79,86,87,97,98,103,113,114,116,173,182,209,210,211,228,230],reset_atomic_reference_posit:215,reset_dt:8,reset_target:8,reset_tim:215,reset_timestep:[2,6,99,497,501],resid:13,residu:250,residue1:388,resist:[6,250],resolut:[220,465,477,478],resolv:[228,299,334,440,518],resort:3,resourc:[7,393,415],respa:[3,15,212,213,223,232,235,236,248,250,251,265,270,297,308,315,319,322,330,331,332,333,350,351,355,390,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,411,412,414,415,416,417,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,44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,95,127,186,210,211,316,361,382,405,424,490,498,503,526,528],wildcard:[3,12,172,182,202,203,205,206,313,405,474,503,506,527,528],wildli:[270,303],win:392,window:[3,4,12,13,75,202,205,207,218,219,220,221,222,250,318,339,340,405,497,518],wipe:[209,425,475,519,521],wire:315,wirnsberg:[6,237],wirt:206,wisconsin:13,wise:[3,12,412,476,505],wish:[2,3,5,6,7,8,11,12,16,40,42,59,60,61,75,128,153,158,179,180,182,184,202,203,206,210,217,218,219,222,226,230,231,242,245,251,256,260,302,305,316,320,334,335,351,352,376,379,387,392,401,424,425,442,447,449,450,457,477,478,494,496,497,498,504,508,514,523,524,528],within:[1,2,3,6,8,9,11,12,13,14,15,16,28,39,40,41,42,55,61,63,65,68,73,74,75,76,77,81,84,100,102,117,119,123,126,127,128,129,131,134,152,169,178,181,204,205,206,210,211,216,217,218,221,222,224,225,226,227,231,233,240,241,242,245,251,253,297,301,302,303,305,307,316,317,318,320,323,325,329,330,335,346,349,351,355,357,359,375,379,385,386,387,388,389,392,397,399,401,408,413,414,415,416,417,419,420,425,426,429,430,442,445,450,452,453,454,459,460,475,476,478,479,480,481,482,484,489,491,493,494,496,504,505,508,510,517,522,523],without:[1,2,3,4,6,7,8,9,11,12,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,61,95,123,155,160,165,179,184,185,187,188,189,190,192,193,195,196,198,202,205,206,207,209,212,218,220,221,222,223,228,230,238,240,241,244,246,248,250,253,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,294,295,302,305,307,308,309,310,314,316,317,318,319,320,326,334,350,354,358,360,362,363,365,366,369,371,375,376,377,387,388,392,393,394,396,399,400,401,402,403,404,405,406,407,408,411,412,415,416,417,418,419,420,421,422,423,424,425,430,431,432,433,434,435,436,437,438,439,443,445,447,448,449,450,451,452,454,458,459,460,467,475,476,477,478,479,480,481,482,484,486,487,488,494,496,499,504,505,511,514,517,518,522,523],wolf:[2,3,7,76,127],wolff:[447,477,478],won:[3,314,440],wong:[215,398],word:[2,3,6,8,12,28,65,206,209,216,217,218,219,222,229,251,281,287,304,309,315,348,359,375,406,447,492,494,496,523,524],work:[1,3,6,7,8,9,11,12,15,17,39,54,61,62,96,128,129,130,156,157,159,160,161,165,166,167,168,170,171,176,177,202,205,207,210,211,218,227,243,245,252,253,254,256,260,267,270,276,277,278,286,290,291,293,294,295,303,305,313,315,318,320,337,338,339,344,375,376,388,392,405,407,410,412,425,439,440,442,445,447,465,491,493,494,497,498,500,504,505,507,510,523],workaround:[76,127,316,447,524],worker:[12,457,458,484],workflow:518,workhors:8,workstat:494,world:[3,12,152,375,387,391,490,493,494,511,523],worlei:412,worri:16,worsen:17,worst:355,worth:[218,219,221,222,306,318],would:[1,3,4,5,6,7,8,11,12,21,28,36,41,42,44,55,74,75,76,97,99,127,129,153,158,166,178,179,180,181,182,184,186,197,202,203,205,206,207,209,210,211,213,216,218,224,227,229,230,234,235,237,242,245,248,249,250,254,267,270,271,284,297,299,303,305,307,311,314,334,341,345,353,354,357,359,360,361,362,363,364,366,367,370,376,379,382,384,385,387,388,391,392,393,394,398,405,406,407,408,412,413,414,415,416,418,425,426,427,428,442,443,444,445,451,455,457,458,462,464,466,474,476,479,480,481,484,491,494,496,499,500,501,503,504,505,506,507,511,513,514,517,518,523,524,527,528],wrap:[1,3,6,9,11,12,59,61,129,178,180,201,202,203,204,206,207,217,229,230,231,250,256,267,316,330,334,351,353,355,376,377,387,494,496,497,499,504],wrapper:[0,6,7],wrigger:322,wright:385,writabl:3,write:3,write_atom_weight:215,write_coeff:2,write_data:[2,3,8,12,13,305,496,525],write_dump:[2,3,204],write_freq:458,write_head:8,write_restart:[2,3,8,9,13,209,215,256,498,503,525,526],writen:318,written:[3,5,6,7,8,9,12,13,16,57,68,73,126,152,176,202,203,204,205,206,207,209,210,211,212,213,214,215,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,234,235,236,237,238,242,243,244,246,247,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,264,266,269,279,280,281,282,283,284,285,286,287,288,289,292,296,297,298,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,318,319,320,330,331,332,334,335,337,338,339,340,341,342,343,345,346,348,349,350,351,353,354,355,356,358,374,379,388,415,425,441,445,485,487,491,492,494,497,498,502,503,510,511,512,513],wrong:[3,11,228,270,296,351,355,356,388,458,498,503],wrote:[3,9,498],wt1:447,wt2:447,wt3:447,wurtzit:379,www:[0,2,3,5,6,7,8,10,11,12,13,14,393,415,439,456,457,458,522],x86:[12,445],x_ij:455,x_ijkl:360,x_kjli:360,x_ljik:360,xave:6,xavx:15,xcm:[8,316,523],xdr:[12,202],xeon:[1,7,9,10,12,15,16,17,392,509],xflag:[165,166,257,259,266,316,341],xhi:[2,6,59,61,180,202,230,345,351,354,356,496,499,514,523],xhi_bound:[6,202],xhi_new:496,xhost:[9,15],xi_ij:455,xiaowang:[13,418,479,481],xiij:297,xk7:9,xlat:[178,230,251,514],xlo:[2,6,11,59,61,180,202,230,251,345,351,354,356,496,499,514,523],xlo_bound:[6,202],xlo_new:496,xmax:[6,214,235,284,523],xmgrace:0,xmin:523,xml:[203,207,456],xml_label:456,xmovi:[0,4,6,7],xmu:[352,422],xorig:75,xplane:352,xplor:202,xpo:178,xrd:[2,9,130],xsph:9,xsu:[3,202,203,336,497],xt3:202,xt4:[17,202],xt5:[17,202],xtc:[3,6,7,12,202,204,205,206,207],xtcdump:206,xvf:12,xwall:[353,354,356],xxx:12,xyz:[3,6,7,9,13,42,69,75,116,119,166,173,178,202,204,205,206,207,228,259,270,271,275,303,313,314,316,330,333,352,354,356,378,386,493,497,524,527],xzhou:[13,418],xzy:493,yang:[445,455],yate:445,yb2:177,yb3:177,ybox:230,ycm:316,year:[5,7],yeh:376,yellow:[205,206],yellowgreen:206,yet:[3,7,16,39,42,205,210,313,351,377,384,385,392,404,406,407,417,487,494,496,497,518,523,525,526,527],yflag:[165,166,257,259,266,316,341],yhi:[6,61,180,202,230,345,351,354,356,496,499,514],yhi_bound:[6,202],yield:[6,99,121,128,153,161,166,206,219,228,234,270,293,307,317,342,348,349,352,357,376,397,412,422,447,454,514,523],yip:343,ylat:[178,230,251,514],ylo:[6,61,180,202,230,345,351,354,356,496,499,514],ylo_bound:[6,202],ymax:[214,523],ymin:523,yorig:75,york:[299,377],yoshida:[270,316],you:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,32,34,37,39,40,41,42,43,45,46,47,48,49,50,51,53,54,56,59,60,61,63,65,67,69,71,72,75,76,77,78,79,81,83,86,87,88,89,95,96,97,98,99,100,101,103,112,113,114,116,117,118,120,121,123,125,127,128,129,152,153,155,156,157,158,161,165,166,171,172,173,174,175,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,202,203,205,206,207,209,210,211,212,213,216,217,218,219,221,222,223,224,225,226,227,228,230,231,234,236,237,238,240,242,243,244,245,246,247,248,249,250,251,253,254,255,265,267,270,272,273,274,275,276,277,278,279,280,284,287,288,290,291,293,294,295,298,299,301,302,303,305,307,308,309,311,314,315,316,319,320,322,330,331,333,334,335,337,338,339,340,342,343,344,345,346,348,349,350,351,352,354,355,356,357,359,360,362,363,365,366,367,369,371,375,376,377,379,382,384,385,386,387,388,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,411,412,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,465,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,484,486,487,488,490,491,492,493,494,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,513,514,515,517,518,522,523,524,525,526,528],young:[422,461,463],your:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,43,45,46,47,48,49,51,53,54,56,61,63,118,123,127,155,156,157,161,165,171,176,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,198,201,202,203,204,205,212,215,219,221,222,223,225,226,227,228,230,231,238,244,245,248,250,253,267,270,272,273,274,275,276,277,278,279,280,288,290,291,293,295,302,305,308,309,314,316,319,320,322,336,342,346,348,349,351,352,354,355,356,357,360,362,363,365,366,369,371,377,379,386,387,388,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,411,412,414,415,416,418,420,421,422,423,424,425,426,427,430,431,432,433,434,435,436,437,438,439,442,443,444,445,447,448,451,452,454,455,457,458,459,460,467,474,476,477,478,479,480,481,482,484,486,487,488,490,493,494,496,498,499,500,503,504,505,506,507,508,509,513,514],yourself:[6,8,12,13,228,386,518],yplane:352,ypo:178,ysu:[3,202,203,336,497],yuan:9,yukawa:[2,3,7,9,406,475],yukawa_1_1:485,yxz:493,yzx:493,z_i:[417,481,488],z_j:[481,488],z_meam:442,zachari:13,zannoni:421,zbl:[2,3,442,466,475],zblcut:481,zblcutinn:466,zblcutout:466,zblexpscal:481,zblz:466,zcm:316,zcylind:352,zepeda:216,zero:[2,3,4,6,9,11,12,25,26,33,36],zeta:[3,256,307,418],zfactor:205,zflag:[165,166,257,259,266,316,341],zhang:[316,342,422],zhi:[3,6,180,202,214,345,351,354,356,496,499,514],zhi_bound:[6,202],zhou:[13,398,418,455,479,481],zhu:473,ziegenhain:13,ziegler:[301,442,475,481,488],zimmerman2004:215,zimmerman2010:215,zimmerman:[9,74,215,398],zlat:[230,251,514],zlib:[9,202],zlim:465,zlo:[3,6,180,202,214,345,351,353,354,356,496,499,514],zlo_bound:[6,202],zmax:[214,256,523],zmin:[256,523],zn2:177,zone:[130,318],zoom:[3,202,205,206],zorig:75,zplane:352,zr4:177,zrest:333,zsu:[3,202,203,336,497],zwall:351,zwall_veloc:256,zxy:493,zybin:458,zyx:493},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.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":225,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,225,226,228,229,230,231,235,242,245,246,251,253,254,255,256,257,259,265,268,270,271,275,293,294,298,299,302,303,304,305,306,308,311,313,314,316,318,334,336,341,342,343,344,347,349,351,353,357,370,374,376,377,379,380,383,384,386,388,389,390,392,395,398,400,417,439,440,445,447,457,458,474,475,491,492,493,496,497,499,501,503,504,505,508,510,512,513,514,515,516,522,524,526,527],"function":523,"long":[220,399,401,402,403,404,408,410,411,430,434,438,452,460,482],"new":8,"static":12,acceler:1,account:518,ackland:66,acknowledg:7,adapt:[210,211],addforc:212,adding:518,addition:[12,13,518],addtorqu:213,adiabat:6,adjust_dt:323,adp:393,after:518,airebo:394,alloi:415,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:214,arrai:6,aspher:[6,90,156,272,276,280,281,290],asphere:9,atc:[9,215],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,214,216,217,305,523],atom_modifi:39,atom_styl:40,attract:5,aveforc:223,awpmd:[9,395],axel:518,balanc:[41,224],barostat:6,basal:70,bcc:297,beck:396,berendsen:[303,337],between:6,binary2txt:13,bodi:[6,8,42,71,157,273,277,282,291,397],body:9,bond:[8,13,72,73,225,226,227,312],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:398,born:[399,410],boundari:[7,59],box:[6,60,228],branch:518,brownian:400,buck:[401,402,410,441],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:518,change_box:61,charmm:[6,19,184,403,438],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,218,331],citat:7,class2:[9,20,43,185,360,404],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,351,406,487],colvar:[13,229],colvars:9,com:[78,79,159],comb3:407,comb:[308,407],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,519,520,521,522,523,524,525,526,527,528],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,523],compute_modifi:112,condit:7,conduct:[6,342],constant:[6,523],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[219,220],cosin:[22,23,24,25,26,27,187],cossq:362,coul:[399,401,402,403,404,408,409,410,423,430,434,438,452,460],coupl:6,creat:226,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:338,csvr:338,cubic:432,custom:[8,202,203],cut:[49,395,401,404,408,411,417,420,430,431,438,446,452,482],cvff:363,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[408,430],defgrad:139,deform:[161,162,230],delete_atom:181,delete_bond:182,delta:23,deposit:231,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,519,520,521,522,523,524,525,526,527,528],diagnost:7,diel:409,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:85,dimens:200,dipol:[6,28,86,411],dipole:9,direct:234,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:201,distanc:364,distribut:[7,12],document:0,dpd:[9,88,89,412,413],drag:232,dreid:424,dreiding:6,drude:[6,9,163,233,234,254,517],dsf:[408,430],dsmc:414,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:307,eam:[13,415],echo:208,edip:416,eff:[9,13,106,107,162,164,169,255,271,283,294,340,417],efield:236,ehex:237,eim:418,elastic:6,emac:13,energi:[135,413],enforce2d:238,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:242,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,509,510,511,512,513,514,515,516,519,520,521,522,523,524,525,526,527,528],exp6:419,exp:[26,187],expand:[46,433],extend:[8,11],extern:243,fcc:297,fdt:413,featur:[7,8,518,523],fene:[45,46],fep:[9,13,95,211],field:[6,7],file:6,finit:6,fire:307,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239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\ No newline at end of file diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index acb051aff9..f09489467d 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -963,7 +963,7 @@ package"_Section_start.html#start_3. "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx"_pair_multi_lucy_rx.html, "quip"_pair_quip.html, -"reax/c"_pair_reax_c.html, +"reax/c (k)"_pair_reax_c.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/triangulated/surface"_pair_smd_triangulated_surface.html,