diff --git a/doc/html/Manual.html b/doc/html/Manual.html index cf1eb5cf4..f8779937e 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -1,426 +1,426 @@ LAMMPS Documentation — LAMMPS documentation

LAMMPS Documentation

13 Jul 2016 version

15 Jul 2016 version

Version info:

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page).

If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of LAMMPS.
If you browse the HTML doc pages included in your tarball, they describe the version you have.
The PDF file on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don’t want it to be part of every patch.
There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS.

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at http://lammps.sandia.gov has more information about the code and its uses.

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation.

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands.

PDF file of the entire manual, generated by htmldoc

Indices and tables

\ No newline at end of file diff --git a/doc/html/_sources/Manual.txt b/doc/html/_sources/Manual.txt index 6de6ddbb4..369dcccbb 100644 --- a/doc/html/_sources/Manual.txt +++ b/doc/html/_sources/Manual.txt @@ -1,105 +1,105 @@ .. raw:: html

LAMMPS Documentation ==================== -13 Jul 2016 version +15 Jul 2016 version ------------------- Version info: ------------- The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on `this page of the WWW site `_. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page). * If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of LAMMPS. * If you browse the HTML doc pages included in your tarball, they describe the version you have. * The `PDF file `_ on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of every patch. * There is also a `Developer.pdf `_ file in the doc directory, which describes the internal structure and algorithms of LAMMPS. LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary developers of LAMMPS are `Steve Plimpton `_, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The `LAMMPS WWW Site `_ at http://lammps.sandia.gov has more information about the code and its uses. .. _bug: http://lammps.sandia.gov/bug.html .. _sjp: http://www.sandia.gov/~sjplimp ---------- The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation. Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page ` at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands. `PDF file `_ of the entire manual, generated by `htmldoc `_ .. toctree:: :maxdepth: 2 :numbered: Section_intro Section_start Section_commands Section_packages Section_accelerate Section_howto Section_example Section_perf Section_tools Section_modify Section_python Section_errors Section_history Indices and tables ================== * :ref:`genindex` * :ref:`search` .. raw:: html .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/pair_brownian.txt b/doc/html/_sources/pair_brownian.txt index 79ad76338..19216ec42 100644 --- a/doc/html/_sources/pair_brownian.txt +++ b/doc/html/_sources/pair_brownian.txt @@ -1,159 +1,159 @@ .. index:: pair_style brownian pair_style brownian command =========================== pair_style brownian/omp command =============================== pair_style brownian/poly command ================================ pair_style brownian/poly/omp command ==================================== Syntax """""" .. parsed-literal:: pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF * style = *brownian* or *brownian/poly* * mu = dynamic viscosity (dynamic viscosity units) * flaglog = 0/1 log terms in the lubrication approximation on/off * flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects * cutinner = inner cutoff distance (distance units) * cutoff = outer cutoff for interactions (distance units) * t_target = target temp of the system (temperature units) * seed = seed for the random number generator (positive integer) * flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions * flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms Examples """""""" .. parsed-literal:: pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) pair_coeff 1 1 2.05 2.8 pair_coeff * * Description """"""""""" -Styles *brownian* and *brownain/poly* compute Brownian forces and +Styles *brownian* and *brownian/poly* compute Brownian forces and torques on finite-size spherical particles. The former requires monodisperse spherical particles; the latter allows for polydisperse spherical particles. These pair styles are designed to be used with either the :doc:`pair_style lubricate ` or :doc:`pair_style lubricateU ` commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters *mu*\ , *flaglog*\ , *flagfld*\ , *cutinner*\ , and *cutoff* should be specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles. The *t_target* setting is used to specify the target temperature of the system. The random number *seed* is used to generate random numbers for the thermostatting procedure. The *flagHI* and *flagVF* settings are optional. Neither should be used, or both must be defined. ---------- The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: * cutinner (distance units) * cutoff (distance units) The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair_style command are used. Otherwise both must be specified. ---------- 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:`this section ` 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:`this section ` of the manual for more instructions on how to use the accelerated styles effectively. ---------- **Mixing, shift, table, tail correction, restart, rRESPA info**\ : For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair_modify" command for details. This pair style does not support the :doc:`pair_modify ` shift option for the energy of the pair interaction. The :doc:`pair_modify ` table option is not relevant for this pair style. This pair style does not support the :doc:`pair_modify ` tail option for adding long-range tail corrections to energy and pressure. This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. 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. ---------- Restrictions """""""""""" These styles are part of the COLLOID package. They are only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. Only spherical monodisperse particles are allowed for pair_style brownian. Only spherical particles are allowed for pair_style brownian/poly. Related commands """""""""""""""" :doc:`pair_coeff `, :doc:`pair_style lubricate `, :doc:`pair_style lubricateU ` Default """"""" The default settings for the optional args are flagHI = 1 and flagVF = 1. .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html index f9c30b7b1..0f4bca68e 100644 --- a/doc/html/pair_brownian.html +++ b/doc/html/pair_brownian.html @@ -1,308 +1,308 @@ pair_style brownian command — LAMMPS documentation

pair_style brownian command

pair_style brownian/omp command

pair_style brownian/poly command

pair_style brownian/poly/omp command

Syntax

pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
 

style = brownian or brownian/poly
mu = dynamic viscosity (dynamic viscosity units)
flaglog = 0/1 log terms in the lubrication approximation on/off
flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects
cutinner = inner cutoff distance (distance units)
cutoff = outer cutoff for interactions (distance units)
t_target = target temp of the system (temperature units)
seed = seed for the random number generator (positive integer)
flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions
flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms

Examples

pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
 pair_coeff 1 1 2.05 2.8
 pair_coeff * *
 

Description

Styles brownian and brownain/poly compute Brownian forces and +

Styles brownian and brownian/poly compute Brownian forces and torques on finite-size spherical particles. The former requires monodisperse spherical particles; the latter allows for polydisperse spherical particles.

These pair styles are designed to be used with either the pair_style lubricate or pair_style lubricateU commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters mu, flaglog, flagfld, cutinner, and cutoff should be specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles.

The t_target setting is used to specify the target temperature of the system. The random number seed is used to generate random numbers for the thermostatting procedure.

The flagHI and flagVF settings are optional. Neither should be used, or both must be defined.

The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart commands, or by mixing as described below:

cutinner (distance units)
cutoff (distance units)

The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair_style command are used. Otherwise both must be specified.

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 this section 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 this section of the manual for more instructions on how to use the accelerated styles effectively.

Mixing, shift, table, tail correction, restart, rRESPA info:

For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is geometric. See the “pair_modify” command for details.

This pair style does not support the pair_modify shift option for the energy of the pair interaction.

The pair_modify table option is not relevant for this pair style.

This pair style does not support the pair_modify tail option for adding long-range tail corrections to energy and pressure.

This pair style writes its information to binary restart files, so pair_style and pair_coeff commands do not need to be specified in an input 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.

Restrictions

These styles are part of the COLLOID package. They are only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

Only spherical monodisperse particles are allowed for pair_style brownian.

Only spherical particles are allowed for pair_style brownian/poly.

Default

The default settings for the optional args are flagHI = 1 and flagVF = 1.

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ed:[498,519],addforc:[],adding:[],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,235,237,238,241,242,246,248,249,250,254,257,271,272,273,274,275,276,277,278,279,291,292,294,295,296,298,306,317,320,321,322,324,348,351,352,356,362,368,371,373,378,380,388,390,393,394,395,399,400,402,404,406,408,409,412,414,415,416,417,418,419,423,424,426,427,428,430,431,439,441,442,443,444,445,446,448,450,451,452,453,456,458,459,461,466,467,476,477,478,479,480,481,482,485,489,492,497,498,499,504,505,506,509,511,518,519,520,522,524,527,528,529],addition:[],additionali:204,addres:9,address:[7,8,11,206,253,519],addtorqu:[],adequ:[263,335,348,377,388,506],adher:28,adhikari:257,adiabat:[],adiam:[206,207],adjac:[39,176,178,238,388,448,478,479,480,511,512],adjiman:447,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,251,254,258,262,267,268,271,272,276,294,298,301,303,304,307,308,309,310,315,317,318,326,335,339,343,348,350,351,352,354,355,357,377,378,386,388,393,395,415,440,441,466,482,507,525],adjust_radiu:326,adjust_radius_factor:326,admiss:276,adof:[158,219],adopt:[316,518],adp:[],adri:[9,313,458,459],adust:172,advanc:[3,15,251,399,492,503],advantag:[1,6,8,11,17,39,40,41,225,393,417,506,511],advect:[3,6,335],advertis:8,advis:[318,388,457,516],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,231,232,238,244,250,252,254,260,266,268,272,273,274,275,277,278,279,285,291,292,294,296,317,319,333,347,357,370,377,384,385,386,388,389,390,393,418,440,441,448,494,495,497,499,500,502,505,507,516],affin:[15,16,17,231,393,408],affiniti:393,afile:248,aforement:17,afresh:[305,505,524],afshar:413,after:[],afterrun:505,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,231,238,250,303,361,376,388,440,441,492,494,495,497,499,504,511,513,524,527],against:[11,12,13,66,232,388,458,459],aggreg:[6,12,68,71,73,84,102,119,126,250,267,315,317,333,492,525],aggress:[238,250,511],agilio:[9,13],agre:[3,8,199,386,395,428,459],agreement:[5,7],ahd:425,ahead:354,aidan:[0,5,7,9,13,380],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,251],aktulga:[7,9,310,459],al2o3:466,al2o3_001:[130,319],al3:177,ala:[257,466],alain:9,alat:[298,443],albe:[456,480,482],albeit:316,albert:9,alchem:[95,172],alcohol:350,alcu:[394,399],alcu_eam:456,alderton:412,alejandr:[271,272],alessandro:13,algebra:446,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,231,238,250,257,259,260,285,300,308,317,321,322,342,343,347,350,355,384,385,386,390,393,414,418,441,446,463,465,492,494,511],alia:[9,15],alias:[1,378],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,252,380,497,500,518],alkali:418,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,263,264,266,267,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,330,331,332,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,366,371,373,375,376,377,378,379,380,383,386,387,388,389,390,392,393,394,395,396,398,399,400,402,403,404,405,406,408,409,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,507,508,509,510,511,512,514,515,516,518,519,523,524,525,527,528,529],allen:[28,95,412,422],allentildeslei:95,allign:3,allindex:359,alloc:[3,5,6,8,9,11,12,62,244,349,387,389,393,454,459,497,505],allocat:3,alloi:[],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,236,237,244,246,247,248,249,251,252,254,257,260,261,266,268,271,272,298,302,303,304,305,306,307,309,311,316,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97,98,108,113,114,115,125,127,129,130,158,159,160,163,166,170,173,175,178,206,207,210,211,212,214,219,222,229,231,232,233,235,246,247,252,254,255,260,267,271,277,278,279,291,292,294,296,303,308,314,315,317,319,323,331,332,333,335,337,338,339,340,342,343,345,352,356,361,380,382,387,398,417,418,422,423,429,440,441,443,444,445,458,459,477,480,481,482,484,485,500,507,518,524],centimet:523,centr:238,central:[3,63,74,80,81,100,117,127,134,152,176,260,298,321,333,365,387,446,452,458,459,485,497],centro:[],centroid:[3,300,484,507],cerda:377,ceriotti2:248,ceriotti:[13,248,253],certain:[1,2,3,6,8,12,16,39,75,124,128,131,182,203,204,206,218,219,220,222,223,228,244,245,317,320,336,349,360,368,376,389,426,448,459,483,499,503,518,524],certainli:252,cerutti:378,cfg:[3,6,7,9,13,203,205,206,207,208],cfile:459,cfl:[140,324],cfor:323,cg_type:461,ch2:321,ch2lmp:[],ch3:321,ch5md:205,chain3:389,chain:[],challeng:[6,323],chalopin:312,champaign:[251,377,378,440],chan:446,chandler:[394,416],chandrasekhar:[6,431],chang:[],change_box:[],changeabl:203,channel:[4,213],chapter:[300,378],charact:[2,3,6,12,37,41,56,65,199,203,204,206,207,208,210,225,241,242,306,314,318,360,387,392,418,420,430,450,451,456,458,459,466,478,479,494,495,499,504,505,524,527,528,529],character:[6,70,74,117,127,152,467,492,511],characterist:[255,335,344],charg:[1,3,4,5,6,7,9,11,14,40,86,95,96,124,130,177,178,203,204,208,210,211,212,217,232,237,246,306,308,309,310,314,337,350,377,378,387,400,402,408,409,411,412,416,418,419,426,431,435,439,453,458,459,466,476,482,483,485,486,488,489,497,498,502,507,509,518,523,524],charmm2lammp:13,charmm:[],chartreus:207,cheap:335,cheaper:[236,422,460],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,199,200,217,225,226,227,232,243,246,252,253,303,316,321,335,343,345,350,358,360,373,376,386,387,388,389,390,393,415,427,430,448,459,490,492,494,495,497,505,511,514,515,516,524],checkf:199,checkout:519,checkqeq:459,checku:199,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,221,230,235,238,247,248,255,257,270,271,272,294,295,300,304,307,309,317,322,323,335,338,339,342,343,344,345,352,361,370,372,377,378,385,388,395,400,404,405,408,409,410,412,413,414,418,421,422,424,425,431,435,436,439,443,447,448,450,451,453,466,475,483,506,509,511,518],chemic:[9,40,88,89,130,172,177,203,204,216,217,246,308,313,314,342,378,420,451,458,459,471,479],chemistri:[307,308,310,395,399,418,458,459],chen:347,cheng:408,chenoweth:[458,459],chenoweth_2008:[458,459],chi:[102,167,202,298,308,310,373,419,422,525],chiefli:457,child:8,chip:[7,9,16,17,393,510],chipot:230,chiral:370,chmod:[11,12],cho:443,chocol:[7,207],choic:[3,6,9,12,14,15,17,40,41,54,95,153,156,157,171,182,197,199,219,225,228,231,232,248,254,257,269,271,300,304,308,317,342,353,371,378,384,385,388,390,393,426,439,448,454,459,497,506,507,510,511,517,518,523],choos:[1,3,6,7,8,9,12,16,17,28,39,54,95,128,168,169,206,226,227,228,229,232,243,254,257,269,271,273,274,275,276,277,278,279,303,304,322,335,339,353,377,378,385,486,492,494,506,512],chose:[480,482],chosen:[2,3,6,12,16,152,178,181,190,199,206,212,217,229,232,243,246,247,255,257,269,271,276,300,303,314,335,339,342,343,348,350,351,357,378,379,385,393,414,418,423,430,433,461,480,492,506,511,512,518],chri:176,christian:[7,9,16],christoph:7,chunk:[],chunkid:[69,79,86,98,103,114,116,125,158,173,175,219,332],chute:[4,9,10,249],ciccotti:321,cieplak:[6,184,509],cii:220,cij:220,circl:[42,75,330],circular:[3,6,156,201],circumst:17,circumv:[100,117,312],citat:[],cite:[3,7,8,12,254,466],civ:9,cl1:177,clarendon:[28,412],clarifi:[7,480,482],clariti:360,clark:453,class2:[],classic:[0,3,5,6,7,8,9,15,244,300,307,312,347,372,418],classifi:[476,485],claus:495,clean:[6,12,14,16,505],cleanli:[496,515,528],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:501,click:[2,11,21,36,44,55,178,186,198,206,251,362,371,388,406,476,519],client:[251,253],climb:[270,388,511],clinic:[7,13],clo:[167,202,525],clock:[12,492,511,516],clockwis:[184,353],clone:519,close:[3,6,11,12,13,39,41,70,75,153,181,203,227,228,229,248,255,257,271,287,294,317,321,353,356,376,378,381,384,385,388,393,395,399,409,410,429,443,448,450,451,458,462,464,478,482,501,507,518,519,521],closer:[3,10,41,127,176,202,203,225,229,233,344,388],closest:[227,298,317,350,422,460,475,486],cloud:[466,518],clovertown:17,clsuter:76,clump1:[302,317],clump2:[302,317],clump3:[302,317],clump:317,cluster:[],clutter:3,cmap:497,cmatrix:248,cmax:443,cmd:[11,12,300,508],cmdarg:11,cmin:443,cmm:[],cmoput:145,cn1:220,cn2:220,cna:[],cnn:220,cnr:13,cnrs:9,cnt:[426,501],co2:[40,177,318,321,387,420],coars:[7,9,10,28,35,40,54,190,242,302,317,318,335,420,424,451,461,479,506,509],coarser:[378,524],coarsest:152,code:[],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,197,361,362,368,406,426,430,448,463,465,468,497,526],coeffcient:497,coeffici:[],coefficienct:413,coefficient0:416,coefficient1:416,coeffieci:[6,397,429],coeffincientn:416,coexist:[246,418],cohes:[6,419,443],coincid:[134,356,404,440,441,492],colberg:205,cold:[6,163,246,250,389,518],coldest:343,coleman8:9,coleman:[9,130,177,319],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,260,267,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[236,335,357],colliex:177,collinear:[3,302],collis:[3,257,335,353,357,415,423,489],colllis:335,colloid:[],colombo:39,colon:[208,358,498,516],color1:207,color2:207,color:[3,9,41,203,206,207,225,247,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,260,268,269,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:231,comand:228,comannd:393,comb3:[],comb:[],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,238,246,251,260,263,271,287,293,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,205,251,253,254,378,388,393,413,448,455,478,479,499],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,184,199,203,241,242,255,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,295,429,491,492,494,511,528],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,231,251,253,257,259,260,261,271,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,205,253,254,287,293,321,378,388,418,448,455,460,474,478,479,481],compact:[65,210,406,476],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,235,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:[],compart:382,compass:[7,9,20,21,36,43,44,55,185,186,198,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,238,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,226,227,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,208,251,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,207,225,230,260,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,257,287,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,217,246,495],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,237,238,244,249,253,254,257,260,262,263,267,268,270,271,272,276,277,278,279,291,292,294,296,297,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,217,257,416],compound:[408,418,419,485],compres:[75,125,219],compress:[],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[],computation:[3,6,226,227,347,399],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:[75,242,318,416,420,451,479],concept:[6,158,168,219,506],conceptu:[3,6,75,166,229,231,388,409,426,443,502],concern:[6,77,95,205,247],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[],conducit:6,conduct:[],cone:500,confer:[15,446],confid:[3,511],config:[12,203,494],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,231,232,236,246,253,254,285,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,515,519],confin:[497,511],confirm:516,conflict:[3,12,40,204,448,495,519],conform:[3,6,13,61,228,229,270,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,254,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,254,257,261,285,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,228,251,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,207,211,212,232,251,252,409,431,435,492,498,500],consequ:[1,6,217,347,430,511],conserv:[3,9,28,210,217,228,235,236,247,250,254,256,257,261,267,269,271,285,287,317,318,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,232,258,272,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,254,255,338,339,340,393,459,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,235,237,244,247,254,255,256,268,271,273,274,275,276,277,278,279,280,281,283,284,285,286,289,290,291,292,294,295,296,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:216,consit:317,constant:[],constantli:238,constitu:[3,6,260,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,232,238,246,247,252,260,263,265,287,293,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,271,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:[15,459],consum:[1,312,454,524],consumpt:375,contact:[],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,232,237,241,242,248,252,253,254,257,269,285,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,15,16,127,128,207,226,227,232,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,238,246,247,248,250,251,252,254,255,256,262,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,216,347,463,465],contour_integr:216,contract:[61,229,231,271,304,317],contradictori:3,contrain:321,contraint:285,contrari:[248,255],contrast:[1,6,42,55,66,160,163,204,231,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,246,254,257,260,261,266,272,294,295,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230,231,250,251,254,255,271,273,274,275,276,277,278,279,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:216,controlfil:459,convect:99,conveni:[6,12,28,203,208,223,319,380,467,483,516,519,524],convent:[3,8,28,189,196,198,204,207,316,331,359,416,418,524],converg:[3,6,41,96,203,204,206,208,213,225,228,229,237,244,276,287,293,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511,516],convers:[3,8,152,206,207,217,220,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,269,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,238,250,315],cooordin:[203,204],cooper:[5,7],coord123:125,coord1:[3,125,219],coord2:[3,125,219],coord3:[3,125,219],coord:[],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,231,232,235,237,238,239,244,246,249,250,251,252,253,254,255,268,270,271,273,274,275,277,278,279,294,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,219],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,206,347,388,406,458,495,519],copper:489,coproccesor:[],coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:207,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:[3,6,40,124,206,356,357,380,484,497,519],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,231,238,246,248,254,271,272,294,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,232,237,244,255,265,271,272,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[],correpond:[241,242],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,238,239,242,244,245,249,254,257,258,267,268,269,271,273,274,275,276,277,278,279,280,281,285,289,291,292,294,296,298,299,300,304,309,310,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[],cosineshift:26,cosmo:[248,253],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,243,271,309,318,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,15,96,248,389],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,244,253,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,232,237,243,246,252,271,285,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:246,counterbal:[238,250],counterbalanc:28,counterclockwis:184,counterpart:[203,492],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:324,cours:[3,8,15,138,140,172,203,211,212,247,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:248,cover:[6,12,75,199,207,216,257,418,484],coverag:75,cpc:253,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,244,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,235,255,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuinfo:15,cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,389,518],craympi:393,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:216,create_faceset:216,create_group:205,create_nodeset:216,createatom:[],creation:[],crimson:207,critchlei:302,criteria:[3,127,179,206,207,226,227,228,266,386,455,484,499,502,524],criterion:[12,41,133,178,181,217,225,228,246,285,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,269,342,347,386],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,231,268,270,294,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,15,77,117,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,15,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[],cst:416,cstherm:6,cstyle:494,csvr:[],ctcm:[394,416],ctemp_core:235,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,235,356,380,518],cubes:[41,225],cubic:[],cuda:[1,3,7,9,12,14,16,393,510,524],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:399,cummul:[3,6,223,226,227,228,230,243,248,254,256,335,338,339,340,341,343,350,425,515],cumul:[6,217,219,222,236,246,254,269,271,276,285,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,236,237,238,244,246,248,251,252,254,260,266,268,271,272,277,278,279,285,287,291,292,293,294,296,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,246,287,293,299],curvatur:[422,460,489],custom:[],cut0:495,cut1:506,cut2:506,cut:[],cuthi:[298,310],cutinn:[401,440,441],cutlo:[298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,233,241,242,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[],cwiggl:[3,268,352,355,357,524],cyan:[2,206,207],cycl:[3,246,269,271,272,276],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,252,293,303,353,356,382,500],cylinder_d:382,cylindr:[6,252,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:257,d3q19:257,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,203,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:294,damag:[],dammak:312,damp:[3,6,210,215,254,255,256,261,271,272,276,293,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:255,damp_drud:255,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,246,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:207,darkcyan:207,darken:206,darkgoldenrod:207,darkgrai:207,darkgreen:207,darkkhaki:207,darkmagenta:207,darkolivegreen:207,darkorang:207,darkorchid:207,darkr:207,darksalmon:207,darkseagreen:207,darkslateblu:207,darkslategrai:207,darkturquois:207,darkviolet:207,dasgupta:308,dash:[423,514],dat:[6,99,199,216,493],data2xmovi:[],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:[0,4,6,12,13,202,458,459,524],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,203,220],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dcd:[3,6,7,203,205,206,207,208,300,498,502],dcs:9,ddim:202,deactiv:439,dealt:253,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[],decai:[100,409,489],decid:[3,6,12,15,75,268,306,317,348,512,519],decipher:380,deck:306,declar:205,declin:335,decod:206,decompos:[95,467],decomposit:[3,5,7,17,64,216,300,322],decoupl:[6,518],decreas:[3,15,203,204,213,214,221,228,231,237,238,244,246,254,346,377],decrement:323,dedic:[15,393],deepli:374,deeppink:207,deepskyblu:207,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,235,236,237,240,242,244,245,246,249,252,253,254,255,256,257,266,268,270,271,272,273,274,275,276,277,278,279,281,282,283,286,289,290,291,292,294,295,296,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,240,252,276,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,235,246,248,249,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:199,degress:[158,219],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,243,246,271,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[],delete_bond:[],delete_el:216,deli:202,delimit:[318,495,524],dellago:[6,238],deloc:[272,418,466],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:242,delx:202,delz:202,demand:312,demo:11,demon:297,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,257,259,260,261,299],denomin:[7,183],denot:[130,235,238,255,299,310,312,409,424,426,459,463,465],dens:[75,228,318,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,231,244,257,260,264,265,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[269,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,231,237,239,242,245,248,249,250,252,254,255,257,259,260,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,298,309,310,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:232,deposit:[],deprec:[3,308,458],deprect:219,depth:[51,156,206,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,238,246,254,268,271,273,274,275,276,277,278,279,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:298,descend:207,descent:[7,385],descib:[40,206,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,234,235,241,242,247,248,251,252,253,254,255,256,257,259,260,261,266,270,271,272,276,284,295,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[],descriptor:[152,203,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,234,235,271,272,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,244,246,247,254,255,256,260,271,294,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,206],despit:518,destabil:399,destre:370,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,238,244,246,247,248,249,251,252,254,256,257,261,268,269,270,271,272,273,274,275,276,277,278,279,283,285,291,292,294,295,296,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,245,303,346,388,408,425,430,492,494,497,508,511,524],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,123,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,231,232,235,237,242,246,249,250,252,254,255,260,266,268,269,271,277,278,279,291,292,294,296,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,251,276,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[269,276,298,421],deviator:9,devic:[1,3,12,14,16,251,393],device_typ:393,devin:[309,408],devis:445,dfactor:206,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,202,231,303],dhug:[269,307],dhugoniot:[269,307],dia:443,diag:318,diagnost:[],diagon:[3,6,91,129,152,153,154,229,271,304,317,350,463,465],diagonalstyl:467,diagram:[41,130,177,198,225,300],diallo:425,diam:[206,207,303,387],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,254,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:268,dictat:[217,269],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,15,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,235,238,241,245,246,247,248,249,250,251,254,255,257,268,271,272,273,274,275,277,278,279,281,283,286,289,290,291,292,296,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,199,318,377,409,456,481],difficult:[229,300,393,425,506,516],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[],diffuse:[4,6],digit:[2,3,207,360,446,524],dih_table1:199,dih_table2:199,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,200],dihedraltyp:227,dihydrid:418,dij:321,dilat:[],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,231,252,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,270,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:207,dimstr:[41,225],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,203,204,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,269,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[],directli:[3,6,8,9,11,12,95,124,129,152,154,203,204,205,206,213,237,248,252,257,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directori:[],disabl:[3,12,15,347,393,430,495,510,524],disadvantag:[6,225],disallow:[203,231,271],disappear:499,discard:[2,3,41,75,221,225,348,356,494,499,500],discontinu:[199,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,206,207,254,257,293],discuss:[],disk:[6,92,93,100,171,201,232,246,303,495],disloc:[74,446],disord:[39,74,446],disp:[],dispar:460,disperion:[412,435],dispers:[3,6,7,9,176,299,377,378,403,412,435,440,448,459,478,485],displac:[],displace_atom:[],displace_box:61,displacemet:500,displai:[11,13,21,36,44,55,186,198,203,206,362,371,406,476],dispters:3,disregard:446,dissip:[6,9,40,88,89,240,247,254,299,322,344,345,401,413,414,423,440,441,476],dissolut:226,dist:[6,73,99,119,128,203,300,316,415,475,492,525],distanc:[],distinct:[6,235,314,377,460],distinguish:[6,94,152,260,418,496,524],distort:[176,394],distrbut:394,distribut:[],distro:[122,406,455,456],ditto:[8,12,14,16,17,42,126,227,317,489,495],div:[8,15],divd:128,diverg:[3,12,39,317,345,395,499,518,527],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,231,298,343,350,355,377,386,388,419,459,466,485,506,514,524],divis:[6,197,257,399,429,439,494,515,524],dl_poly:[6,7],dlambda:172,dlammps_async_imd:251,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,346,497,498,502],dlammps_jpeg:[3,12,206],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,206],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,203],dlen:507,dlmp_intel_offload:[9,15],dlo:[61,202,231,303],dlopen:6,dlvo:[7,407,488],dm_lb:257,dmax:[335,384],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,86,95,98,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,232,246,254,255,266,271,272,277,278,279,283,291,292,294,295,296,303,306,317,331,335,338,339,340,349,353,356,358,360,362,371,376,386,387,388,393,394,395,398,406,408,409,416,417,419,425,426,428,429,443,444,445,448,452,455,456,457,467,476,477,480,482,484,485,495,497,498,499,500,502,505,506,507,514,515,519,524,525,527,528],docuement:460,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,235,237,238,241,242,243,246,247,250,252,254,255,257,260,267,271,272,273,274,275,277,278,279,291,292,293,294,295,296,304,305,306,310,312,315,317,335,338,340,342,343,347,350,351,352,355,356,357,358,363,364,365,367,368,370,376,377,378,379,380,387,388,389,394,395,396,397,398,399,401,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,426,427,428,429,430,433,434,436,437,438,440,441,443,444,445,446,448,450,451,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,493,494,495,497,498,499,500,501,504,505,507,508,509,510,511,514,515,518,519,524,529],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,331,387,389,393,395,408,417,428,458,459,477,480,481,482,485,497,499],dof:[3,8,123,156,157,158,171,219,317,525],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[387,497],doi:[6,230,298],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,231,232,250,253,257,271,272,300,312,317,322,347,352,353,377,378,388,393,415,448,492,494,497,501,514],domin:[1,418,511],don:[0,8,9,12,13,15,127,181,213,237,255,356,443,466,495,497,519],donadio:339,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,241,242,244,246,251,252,254,255,262,271,277,278,279,291,292,294,296,297,299,300,301,303,306,314,317,319,321,335,338,339,340,342,344,345,358,360,376,377,378,386,388,389,392,393,395,403,416,426,427,428,435,441,442,443,448,450,451,458,475,478,479,484,492,493,494,495,498,501,502,505,515,516,518,519,524,525],donor:425,dot:[153,174,213,237,249,270],doti:[399,456],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,231,244,305,356,360,376,378,392,393,399,419,424,446,458,459,493,497,501,505,510,524,525],dover:216,down:[3,6,7,8,11,39,75,229,246,254,335,351,418,448,466,496,516],downhil:[384,385],download:[5,7,8,9,11,12,13,16,251,427,457],downsid:6,downward:314,dozen:[8,9,12,118,210,458,459],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[],dpde:264,dpdtheta:[40,88,89,414],dpdtheta_i:[240,241,242],dproduct:396,dr_ewald:[130,319],drag:[],dragforc:257,drai:[206,269,307],drain:[250,351,386],dramat:[9,61,202,226,227,228,229,231,271,335,338,339,378,448,466,494],drautz:399,draw:206,drawback:306,drawn:[42,203,206,207,247,492],drayleigh:[269,307],dreid:[],dreiding:[],drfourth:115,drho:[124,394,416,450,451],drift:[6,113,115,238,247,248,250,254,255,267,315,335,506,514,518],drive:[11,12,214,229,231,249,271,298,304,317,354,388],driven:[6,190],driver:[6,12,14,210,244,251],drop:[3,207,413],droplet:426,drsquar:115,drude:[],drudes:[255,518],dry:243,dsecriptor:427,dsf:[],dsmc:[],dstyle:303,dt_collis:257,dt_lb:257,dt_md:257,dt_srd:335,dtilt:[61,231],dtneb:511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,518],especi:[8,15,166,178,210,217,225,246,307,312,315,316,393,494,516],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,299,351,378,395,409,431,482,502,515],essential:[8,276],essex:28,establish:[95,250],estim:[1,3,6,10,12,37,41,56,99,153,216,225,236,269,318,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,257,271,307,308,310,351,417,419,422,456,481,485,523],eta_dot:271,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:271,etap_dot:271,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,231,232,244,246,247,254,271,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,207,235,255,269,307,514,515],eu2:177,eu3:177,euler:[318,386,388],eulerian:216,euqat:469,europhi:257,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,237,247,249,250,252,253,254,255,299,305,308,318,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,294],evanseck:[6,19,184,404,509],evapor:[],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,231,232,235,238,252,255,269,271,272,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,199,225,257,429,486],event:[],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,253,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,238,243,244,246,248,250,251,252,257,258,267,271,272,276,287,293,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[238,248,257,300,492],evolv:[257,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,247,248,254,255,256,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,231,236,241,247,254,255,256,272,284,285,295,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,228,299,318],examp:[495,524],exampl:[],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,231,236,243,271,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,225,231,271,335,459,505],excel:418,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,231,239,245,246,249,252,254,256,271,272,273,274,275,276,277,278,279,280,281,284,285,289,291,292,294,295,296,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[221,418],exchang:[2,3,6,8,63,64,210,216,217,238,246,250,254,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,258,267,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[271,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,251,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:247,exemplifi:418,exert:[6,252,255,287,312,354,355,356,378],exhaust:[216,392,524],exhibit:[100,238,250,271,385,418,506],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,232,246,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,203,225,376,392,495,496,505,514,515,516,524],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,152,197,203,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,237,246,248,268,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,207,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,224,232,251,260,270,304,316,317,384,388,413,448,506,511],experienc:[6,12,15,259,260],experiment:[16,246,377,393,511],expert:12,expertis:7,expir:[515,516],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,231,271,287,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,203,204,219,270,298,426,491,494,495,497,506],explanatori:[3,8,128,203,204,218,219,222,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,231,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,231,239,245,247,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,306,307,309,310,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,459,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,318,420,456,477,485,489,511,524],expos:11,exposit:[216,413,415],express:[6,152,164,178,211,212,229,268,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,233,237,238,244,245,246,248,249,250,252,254,256,269,271,276,285,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,210,515],extent:[1,3,41,42,45,59,75,176,180,203,215,225,252,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,271,305,306,307,317,335,386,387,390,391,393,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,231,271,345,418,481,518],extrema:439,extreme:418,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,266,337,349,515,524],f_ij:456,f_indent:223,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:269,f_r:[255,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,215,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,248,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,231,232,238,246,251,254,256,257,269,271,272,276,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,229,232,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:251,fall:[3,6,207,222,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,232,271,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:254,farrel:[480,482],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,232,246,248,252,268,269,271,273,274,275,276,277,278,279,288,291,292,294,295,296,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,15,16,39,203,204,282,307,318,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,231,239,245,249,253,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,304,308,309,310,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:228,favorit:7,fbmc:342,fcc:[],fcm:[288,524],fcold:238,fdirect:235,fdotr:427,fdt:[],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[],fecr:416,feedback:[7,251],feel:[7,251,252,260,298,356,358,388,448],fehlberg:318,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:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,238,255,271,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,260,506],fewest:3,fextern:244,feynman:300,fff:495,ffield:[408,419,458,459,466],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:238,ficiti:475,fictiti:[6,213,214,237,244,248,300,316,409,431,435,475],field1:[498,502],field2:498,field:[],fifth:[6,331,420,452],figshar:298,figur:[1,3,8,12,15,307,494,495,519],fij:412,file0:298,file1:[11,13,242,298,346,360,387,502,504,508],file2:[11,13,242,346,360,387,502,504,508],file:[],file_from:205,filen:387,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,241,242,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,203,204,207,499,504,529],filepo:314,fill:[7,9,178,206,303,347,380,389,399,446,459,500,519],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,241,242,243,246,270,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,213,237,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,202,268,500],finish:[6,11,41,225,360,374,376,377,390,392,393,484,502,524,525],finit:[],finni:[7,416,476],finverse:235,fiorin:[9,230],fire:[],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,241,242,246,247,252,257,268,269,270,271,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,199,241,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[],fix_deposit:3,fix_flux:216,fix_heat:238,fix_id:[3,229,269,271,273,274,275,276,277,278,279,304,307],fix_manifoldforc:519,fix_modifi:[],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[229,271],fixextern:244,fixid:[206,216],fji:412,flag1:[234,391],flag2:[234,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,234,251,254,258,260,267,268,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:234,flagvf:[401,440,441],flat:[6,15,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,206,219,230,248,272,343,350,418,481,515],flip:[3,6,231,271,354,355],floor:524,flop:12,floralwhit:207,flow:[],fluctuat:[6,66,95,229,246,247,254,257,271,276,298,299,304,322,345,347,370,414],fluid:[],fluid_veloc:261,flush:[3,207,514],flux:[],flv:206,fly:[7,9,12,41,206,210,216,221,232,235,317,321,348,399,446,515,518],fmackai:9,fmag:233,fmass:300,fmax:[386,515],fmomentum:235,fmsec:[2,207,254,255,268,271,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:235,fnve:238,fnvt:235,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,298,467],fold:[15,333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,235,236,240,241,242,244,246,247,248,251,253,254,255,257,260,269,271,276,277,278,279,291,292,294,296,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,203,206,244,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,17],forc:[],force_uvm:16,forceatom:260,forcefield:[316,425],forcegroup:257,forcezero:384,ford:412,forestgreen:207,forev:75,forget:[255,518],forgiv:271,fork:[],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,207,210,211,212,227,247,248,254,256,260,268,294,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,247,248,254,271,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,241,242,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:242,former:[6,12,39,41,207,225,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,213,237,254,271,294,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,237,249,250,252,254,255,268,298,299,305,314,320,328,333,335,338,339,340,349,352,353,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,244,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,203,228,230,238,246,251,257,263,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,269,347,370,387,388,446,492],fourier:[],fourth:[6,15,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:253,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,202,206,207,217,226,227,228,229,269,303,307,314,315,318,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,251,314],fraig:42,frame:[91,152,207,216,269,307,354,422],framer:[206,207],framework:[5,248,394,467],franc:9,frattl:238,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,211,212,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,219,228,235,246,248,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,206],freez:[],frenkel:[6,238,246,345],freq:215,frequenc:[3,6,15,39,113,207,221,285,299,300,307,312,318,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,207,226,227,238,243,343,350,448,483,504,516],fri:[269,307],friction:[4,5,6,9,10,42,210,248,254,307,312,317,347,351,353,423,507],friedrich:324,from:[],front:[269,307,354],frontend:[206,311],frozen:[6,123,182,245,247,255,389,421],fs2:[6,99],fscale:251,fstr:524,fstring:495,fstyle:353,ftol:[386,388,492,511],fuchsia:207,fuction:409,fudg:321,fugac:246,fugacity_coeff:246,fulfil:6,full:[1,2,3,6,9,12,15,16,37,39,40,99,206,220,221,230,238,257,298,318,377,378,393,399,416,418,419,422,459,4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5,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,203,252,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:260,innermost:[37,56,75,391,478,479,506],innernod:260,innner:437,inordin:348,inorgan:[6,485],inp:[230,360,467,485],input1:[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:[3,5,7,8,9,12,61,178,210,232,246,252,303,377,467,475,495,501,518],insertion:[3,232,246,303],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,232,233,238,243,246,252,257,260,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[257,433,495,511],insight:[6,13],instabl:[257,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[],instanc:[6,9,11,211,230,248,354,421,426,448,456,495,518],instantan:[6,65,228,229,247,248,271,276,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,216,426,494],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,246,254,257,260,261,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,459,476,483,492,500,504,511,513,518,524],institut:[9,251,302],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:271,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,232,237,239,243,244,246,249,254,267,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,232,234,244,246,247,248,251,254,255,256,257,299,302,303,306,307,312,317,318,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[],integral:[300,450,451],integrate_ulsph:[],intel:[],intel_coprocessor:15,intel_cpu:12,intel_cpu_intelmpi:15,intel_cpu_mpich:15,intel_cpu_openpmi:15,intel_phi:12,intend:[3,6,8,12,13,35,221,247,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,236,243,250,260,269,271,276,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,210,515],intepol:524,inter:[17,42,63,64,158,181,182,203,228,254,256,270,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,245,246,251,252,254,256,260,285,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,203,270,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[],interfer:[12,271,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,206,270,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],intern:[],internal:[3,206,212,303,524],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:253,interpenetr:443,interpentr:[470,471,473],interpol:[6,14,37,56,110,199,206,207,216,241,242,257,298,377,378,388,399,448,450,451,459,472,478,479,480],interpret:[2,6,11,197,206,222,423,468,492,495,511,524],interrupt:307,intersect:[3,6,130,207,356,358,500],intersert:356,interspers:386,interstiti:[176,446],intertia:[3,103],interv:[3,6,99,205,220,254,271,307,312,313,326,466,472,492,511,524],intestieti:130,intial:[6,393,395],intiial:[41,502],intiti:[3,334],intra:317,intra_energi:246,intramolecular:[28,154,246],introduc:[6,9,100,117,206,238,271,307,312,317,370,377,394,409,418,431,435,439,477,511,524],introduct:[],intuit:380,inv:[130,177,319],invalid:[3,12,75,97,181,285,388,440,441,499],invari:[117,145,150,152],invent:321,invers:[],inverse:518,invert:[1,6,182,299],invis:356,invoc:[176,228,393,463,465,495],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,243,244,245,246,247,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,268,270,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,317,319,320,321,323,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,361,363,364,366,367,370,372,376,377,378,379,380,386,388,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,427,431,432,433,434,435,436,437,438,439,440,441,444,448,449,452,453,455,459,460,461,463,465,467,468,477,478,480,481,482,483,485,486,487,488,489,491,494,495,496,498,500,502,505,506,508,509,511,514,515,518,524,525],invokd:3,invoke:[3,12,16],involv:[3,6,7,8,12,65,119,126,127,128,158,182,210,217,226,246,257,302,305,310,335,377,385,386,388,398,415,422,429,477,480,482,493,494,500,502,506,511,512],ioff:[387,497],ion:[6,7,9,160,297,331,347,378,399,410,419,421,443,446,466,476,482,489,497,518],ionic:[6,9,400,402,410,418,419,453,466,518],ioniz:[408,418],ionocoval:9,iparam:[3,227],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,41,60,225,229,231,271,317],irrelev:452,irrespect:[440,441],irrevers:[235,318],is_act:[3,524],is_avail:[3,524],is_defin:[3,524],isbn:488,isele:[377,378],isenthalp:[9,271,272,273,274,275],ismail:[377,378,403,435],isn:[3,8,11,12,238,250],iso:[3,229,235,255,271,272,273,274,275,276,277,278,279,304,312,317,518],isobar:[9,271,272,277,278,279,322,414],isodem:418,isoenerget:[9,322,414],isoenthalp:[322,414],isol:[3,181,358,423],isomorph:300,isotherm:[9,246,271,272,277,278,279,304,322,414],isotop:306,isotrop:[6,100,254,304,377,378,401,422,440,441],isovolum:319,isralewitz:323,issu:[1,3,6,9,11,12,13,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,61,75,77,87,113,123,155,165,184,185,187,188,189,190,192,193,195,196,199,206,213,224,228,229,231,232,237,238,239,245,246,249,254,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,300,304,306,309,310,317,320,321,334,338,339,340,345,355,357,360,361,363,364,366,367,370,372,378,387,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,475,477,478,480,481,482,483,485,487,488,489,497,499,500,506,509,514,515,516,524,525],issue:216,ital:[458,459],itali:13,item:[6,7,8,41,203,207,225],iter:[3,6,12,39,41,65,205,213,214,224,225,229,235,237,244,252,287,293,299,308,309,317,321,332,342,358,360,376,384,385,386,388,392,466,492,502,506,511,515,516,524],iterat:[12,386],ith:[75,128,131,218,219,220,221,222,223,337,349,515,524],itself:[2,3,6,7,8,9,11,12,13,17,42,61,99,118,169,203,205,206,207,208,220,221,230,235,255,270,311,317,347,358,360,387,388,409,419,422,426,427,450,451,478,479,495,501,504,505,509,524,529],itset:507,ityp:[3,57,126,127,178,215,227,310,486],itype1:127,itype2:127,itypen:127,ivector:8,ivori:207,ixcm:317,ixi:[42,317,387],ixx:[42,103,317,387,524],ixy:[103,387,524],ixz:[42,103,317,387,524],iycm:317,iyi:[42,103,317,387,524],iyz:[42,103,317,387,524],izcm:317,izrailev:323,izumi:481,izz:[42,103,317,387,524],j0jt:99,j20:220,j_m:152,jackson:447,jacobi:3,jacobsen:385,jacs:[6,184,509],jagreat:13,jame:[9,18],janssen:298,januari:443,jaramillo:[7,9,13,418],jarzynski:323,jatempl:9,jcc:9,jcp:352,jec:13,jeff:13,jeffer:15,jello:271,jensen:[254,377],jeremi:[9,445],jerom:9,jewett:13,jiang:[255,518],jiao:[9,13],jiht:[7,9],jik:399,jim:7,jku:[7,9],jmake:1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,415,509],reconstruct:[3,230,466],record:[208,230,323],recov:[229,238,271],recreat:359,rectangl:[41,225,380],rectangular:[7,41,64,180,225,246,380,497,499,501],rectilinear:[130,177,204],rector:53,recurs:[41,225,399,484],recust:41,recv:494,red:[2,206,207,228,300],redefin:[3,499,505,524],redirect:12,redo:12,reduc:[],reduct:[17,18,128,130,177,269,307,377],redund:419,ree:471,reed:[269,307],rees:[7,9,13],ref:[344,345,385],refactor:6,refer:[],referenc:[3,6,12,65,71,75,125,131,203,204,210,220,246,306,349,378,409,425,452,460,495,515,524],reflect:[],refman:9,reformat:7,refresh:216,reg:500,regard:[6,61,268,321,322,327,455,459],regardless:[14,75,178,181,202,222,231,254,271,273,274,275,277,278,279,304,317,328,335,393,494,500,507],regim:[6,343,350,410,506],region:[],region_spher:8,region_styl:356,regist:[8,127,154,330],regoin:6,regress:524,regspher:178,regstrip:358,regul:6,regular:[1,3,41,64,96,176,180,203,206,217,225,246,306,347,378,410,429,494,497,499,501],reigon:524,reinder:15,reinhardt:[344,345],reject:[178,228,458,512],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,207,210,217,225,231,232,235,238,246,252,255,267,268,294,298,303,312,314,315,318,323,331,335,337,342,343,347,354,358,377,378,386,418,422,423,440,441,443,460,488,498,506,511,515,518,525],relat:[],relationship:[6,241,308,360,377,466,488,518,524],relax:[],releas:[0,5,7,8,13,226],relect:[3,448],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,207,211,212,215,216,217,218,219,220,221,222,223,225,226,227,231,232,236,238,239,243,245,246,247,250,251,257,258,259,261,262,263,264,265,267,268,270,280,281,282,283,284,285,286,287,288,289,290,293,297,301,302,303,305,306,311,313,314,315,319,321,328,333,335,336,337,342,343,346,347,348,349,350,351,352,353,354,355,357,358,377,382,386,396,397,401,407,409,410,412,413,415,418,421,422,423,424,425,430,432,433,434,436,437,438,440,441,448,449,450,451,455,460,468,475,478,479,487,488,489,494,510,525],reli:[3,12,309,418,459,489,497,507],reloc:12,reltol:318,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,231,254,255,262,271,272,277,278,279,291,292,294,296,301,302,326,335,338,339,340,346,347,358,360,368,371,387,399,418,426,439,446,448,476,492,497,498,502,507,509,511,515,516,518,519,524,525],remaina:399,remaind:[9,178,203,232,303,335,348,482,497],remap:[3,6,12,61,63,75,161,178,202,231,252,268,294,377,497,498,499],remedi:[6,518],rememb:[2,519],remot:519,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,243,254,255,260,263,267,269,271,277,278,279,291,292,294,296,302,308,317,318,319,321,335,338,339,340,342,358,377,388,412,441,446,497,500,508,509,519,524,525],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,359,508,519],render:[12,13,203,206,207],rendon:[271,272],reneighbor:[3,8,12,39,59,75,225,246,335,348,358,413,514,515],renssela:302,renumb:75,reorder:[3,12,39,494],rep:512,repeat:[2,6,206,207,228,229,246,318,327,380,399,480,482,484,492,511],repeatedli:2,repel:252,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,232,254,276,305,306,312,314,353,393,395,409,423,433,450,451,478,498,499,504,505,515,524,525,527,529],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:347,repres:[1,3,6,8,9,12,14,40,41,42,61,70,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,235,242,247,249,254,257,271,300,302,304,312,317,318,319,323,331,332,347,349,356,378,388,394,399,422,429,439,440,441,443,444,445,453,456,458,459,483,484,492,494,497,507,509,512,518,524,527],represent:[3,6,8,9,59,61,146,180,203,247,248,300,347,399,418,422,446,460,497,500,518],reprocess:502,reproduc:[3,15,271,353,409,416,423],repul:443,repuls:[6,7,35,40,45,46,119,252,308,352,353,356,395,399,407,409,413,418,420,423,425,439,443,447,466,475,482,485,488,489,507],reqir:[308,310],request:[3,6,8,12,41,113,181,199,203,251,257,315,322,335,337,375,377,448,458,459,492,502,507,511,516,519,524,525,527],requir:[],rerun:[],rescal:[],research:[5,7,88,89,240,257,261,322,446,492,511],resembl:[312,519],resepct:6,reserv:[12,251,518],reservoir:[99,238,246,250,254,347],reset:[],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[],resid:13,residu:251,residue1:389,resist:[6,251],resolut:[221,466,478,479],resolv:[229,300,335,441,519],resort:3,resourc:[7,394,416],respa:[3,15,213,214,224,233,236,237,249,251,252,266,271,298,309,316,320,323,331,332,333,334,351,352,356,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,505,506,516,517,524],respecifi:446,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,231,238,239,245,249,252,254,255,257,271,273,274,275,276,277,278,279,280,281,287,289,291,292,294,296,308,309,310,317,319,321,323,331,334,347,352,355,361,363,364,366,367,370,372,375,377,378,383,386,387,392,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,452,453,455,459,460,461,465,466,467,468,477,478,480,481,482,483,485,487,488,489,494,498,507,510,516,518,524,526,527,529],respon:9,respond:[6,7,161,231,418,455],respons:[6,7,269,343,350],resquar:[],rest:[6,8,12,38,58,200,306,310,316,373,399,441,443,490,514,515,518],restart1:300,restart2:300,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,113,178,211,212,266,306,323,331,332,337,359,514,515],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,230,269,316,334,430],restratin:316,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,199,202,203,204,206,207,210,213,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,235,238,239,241,245,246,247,249,254,255,257,261,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,295,296,299,300,308,309,310,314,315,317,318,320,321,335,343,344,345,347,348,349,352,353,355,357,360,361,363,364,366,367,370,372,377,378,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,443,444,446,448,449,450,451,452,453,455,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,497,499,500,502,506,507,508,509,511,523,524,525],resum:524,retain:[2,226,227,395,399,446,494],retart:[32,50,191,368],retir:[3,458],retreiv:8,retriev:[6,8,244,444,445,524],reus:[3,509],rev:[6,13,66,74,100,117,121,152,153,166,217,248,254,256,269,271,272,276,294,299,309,312,317,323,335,339,342,344,345,350,385,399,407,408,409,412,416,417,418,422,423,428,433,440,441,442,443,445,450,451,456,460,467,477,480,481,482,485,492],revers:[2,6,8,95,189,228,252,271,297,298,308,327,343,344,350,388,439,506,518],review:[152,308,323,342,446,457,467,492,511,518,519],rewind:376,rewrap:203,rewrit:[5,12],rewritten:18,rezwanur:455,rfac0:[152,467],rfactor:335,rfile:317,rg0:333,rgb:207,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[450,451,478,479],rho0:[443,463,465,473,474],rho0_meam:443,rho:[],rho_0:[473,474],rho_alpha_beta:416,rho_bkgd:443,rho_colloid:352,rho_e:347,rho_fin:346,rho_i:[444,445],rho_initi:346,rho_ref_meam:443,rho_wal:352,rhodo:[9,10],rhodopsin:[1,10,15],rhohi:303,rholo:303,rhosum:[],rhot:238,rhs:318,ribier:385,richard:9,richardson:317,richi:[9,18],rick:[308,309,408,466],rick_and_stuart:309,ridg:[9,18],right:[3,6,11,12,41,154,178,196,198,202,204,225,228,252,257,268,297,298,318,360,380,409,497,500,507,519,524],rightmost:[41,225],rigid:[],rigidid:129,rigidifi:317,rii:[97,98],rij:[100,117,226,227,298,413,414,450,451,475],rin:[425,436,437],ring:[],rino:[77,485],rinv:377,rirj:[353,423],risi:[152,467],risk:[8,316,506],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rk4:318,rkf45:318,rlo:[450,451,478,479],rmask:[3,524],rmass:[3,306],rmax:[75,179,226],rmdir:508,rmin0:[152,467],rmin:[75,179,227,433],rms:[318,377,378],rmsd:346,rnemd:6,robert:9,robin:207,robust:[384,385,386,459],rock:443,rockett:456,rod:317,rodata:12,rodnei:312,roi:7,role:[6,342],roll:12,ronchetti:117,room:[59,61],root:[11,95,97,98,205,342,346,416,504],rosati:39,rose:443,ross:443,rosski:300,rosybrown:207,rot:[6,99,300,316,342,525],rotat:[],rotate:327,rotation:117,rotaton:500,rough:[6,178,206,357],roughli:[7,10,12,41,161,206,221,246,254,255,263,270,271,285,304,317,335,338,339,342,378,388,393,462,464,499,506],round:[1,3,12,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,42,43,45,46,47,48,49,51,53,54,56,75,123,155,165,184,185,187,188,189,190,192,193,195,196,199,207,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,429,431,432,433,434,435,436,437,438,439,440,444,449,450,451,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,499,500,506,523,524],rous:247,rout:[95,425,439],routin:[5,6,8,11,14,15,37,39,56,96,182,257,446,457,478,479,510],roux:[6,235,255,483,518],row:[6,68,69,71,73,79,84,86,98,102,103,114,116,119,125,126,127,129,131,158,166,173,175,176,177,219,220,222,223,260,317,347,349,357,418],royalblu:207,rozero:443,rperp:[268,327],rpi:302,rpm:12,rrespa:[1,3,5,7,8,15,211,212,268,271,389,394,395,396,397,398,400,401,402,403,404,405,407,408,4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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","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":226,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,231,232,236,243,246,247,252,254,255,256,257,258,260,266,269,271,272,276,294,295,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[221,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,adding:519,addition:[12,13,519],addtorqu:214,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:215,arrai:6,aspher:[6,90,156,273,277,281,282,291],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:224,awpmd:[9,396],axel:519,balanc:[41,225],barostat:6,basal:70,bcc:298,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,274,278,283,292,398],body:9,bond:[8,13,72,73,226,227,228,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,229],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:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,230],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,custom:[8,203,204],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,43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ed:[498,519],addforc:[],adding:[],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,235,237,238,241,242,246,248,249,250,254,257,271,272,273,274,275,276,277,278,279,291,292,294,295,296,298,306,317,320,321,322,324,348,351,352,356,362,368,371,373,378,380,388,390,393,394,395,399,400,402,404,406,408,409,412,414,415,416,417,418,419,423,424,426,427,428,430,431,439,441,442,443,444,445,446,448,450,451,452,453,456,458,459,461,466,467,476,477,478,479,480,481,482,485,489,492,497,498,499,504,505,506,509,511,518,519,520,522,524,527,528,529],addition:[],additionali:204,addres:9,address:[7,8,11,206,253,519],addtorqu:[],adequ:[263,335,348,377,388,506],adher:28,adhikari:257,adiabat:[],adiam:[206,207],adjac:[39,176,178,238,388,448,478,479,480,511,512],adjiman:447,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,251,254,258,262,267,268,271,272,276,294,298,301,303,304,307,308,309,310,315,317,318,326,335,339,343,348,350,351,352,354,355,357,377,378,386,388,393,395,415,440,441,466,482,507,525],adjust_radiu:326,adjust_radius_factor:326,admiss:276,adof:[158,219],adopt:[316,518],adp:[],adri:[9,313,458,459],adust:172,advanc:[3,15,251,399,492,503],advantag:[1,6,8,11,17,39,40,41,225,393,417,506,511],advect:[3,6,335],advertis:8,advis:[318,388,457,516],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,231,232,238,244,250,252,254,260,266,268,272,273,274,275,277,278,279,285,291,292,294,296,317,319,333,347,357,370,377,384,385,386,388,389,390,393,418,440,441,448,494,495,497,499,500,502,505,507,516],affin:[15,16,17,231,393,408],affiniti:393,afile:248,aforement:17,afresh:[305,505,524],afshar:413,after:[],afterrun:505,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,231,238,250,303,361,376,388,440,441,492,494,495,497,499,504,511,513,524,527],against:[11,12,13,66,232,388,458,459],aggreg:[6,12,68,71,73,84,102,119,126,250,267,315,317,333,492,525],aggress:[238,250,511],agilio:[9,13],agre:[3,8,199,386,395,428,459],agreement:[5,7],ahd:425,ahead:354,aidan:[0,5,7,9,13,380],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,251],aktulga:[7,9,310,459],al2o3:466,al2o3_001:[130,319],al3:177,ala:[257,466],alain:9,alat:[298,443],albe:[456,480,482],albeit:316,albert:9,alchem:[95,172],alcohol:350,alcu:[394,399],alcu_eam:456,alderton:412,alejandr:[271,272],alessandro:13,algebra:446,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,231,238,250,257,259,260,285,300,308,317,321,322,342,343,347,350,355,384,385,386,390,393,414,418,441,446,463,465,492,494,511],alia:[9,15],alias:[1,378],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,252,380,497,500,518],alkali:418,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,263,264,266,267,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,330,331,332,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,366,371,373,375,376,377,378,379,380,383,386,387,388,389,390,392,393,394,395,396,398,399,400,402,403,404,405,406,408,409,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,507,508,509,510,511,512,514,515,516,518,519,523,524,525,527,528,529],allen:[28,95,412,422],allentildeslei:95,allign:3,allindex:359,alloc:[3,5,6,8,9,11,12,62,244,349,387,389,393,454,459,497,505],allocat:3,alloi:[],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,236,237,244,246,247,248,249,251,252,254,257,260,261,266,268,271,272,298,302,303,304,305,306,307,309,311,316,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9,518],coldest:343,coleman8:9,coleman:[9,130,177,319],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,260,267,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[236,335,357],colliex:177,collinear:[3,302],collis:[3,257,335,353,357,415,423,489],colllis:335,colloid:[],colombo:39,colon:[208,358,498,516],color1:207,color2:207,color:[3,9,41,203,206,207,225,247,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,260,268,269,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:231,comand:228,comannd:393,comb3:[],comb:[],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,238,246,251,260,263,271,287,293,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,205,251,253,254,378,388,393,413,448,455,478,479,499],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,37,56,184,199,203,241,242,255,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,295,429,491,492,494,511,528],common:[],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,231,251,253,257,259,260,261,271,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,205,253,254,287,293,321,378,388,418,448,455,460,474,478,479,481],compact:[65,210,406,476],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,235,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:[],compart:382,compass:[7,9,20,21,36,43,44,55,185,186,198,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,238,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,226,227,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,208,251,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,207,225,230,260,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,257,287,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,217,246,495],complier:12,compon:[3,6,8,12,63,65,69,70,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,237,238,244,249,253,254,257,260,262,263,267,268,270,271,272,276,277,278,279,291,292,294,296,297,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,217,257,416],compound:[408,418,419,485],compres:[75,125,219],compress:[],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[],computation:[3,6,226,227,347,399],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:[75,242,318,416,420,451,479],concept:[6,158,168,219,506],conceptu:[3,6,75,166,229,231,388,409,426,443,502],concern:[6,77,95,205,247],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[],conducit:6,conduct:[],cone:500,confer:[15,446],confid:[3,511],config:[12,203,494],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,231,232,236,246,253,254,285,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,515,519],confin:[497,511],confirm:516,conflict:[3,12,40,204,448,495,519],conform:[3,6,13,61,228,229,270,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,254,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,254,257,261,285,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,228,251,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,207,211,212,232,251,252,409,431,435,492,498,500],consequ:[1,6,217,347,430,511],conserv:[3,9,28,210,217,228,235,236,247,250,254,256,257,261,267,269,271,285,287,317,318,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,232,258,272,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,254,255,338,339,340,393,459,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,235,237,244,247,254,255,256,268,271,273,274,275,276,277,278,279,280,281,283,284,285,286,289,290,291,292,294,295,296,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:216,consit:317,constant:[],constantli:238,constitu:[3,6,260,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,232,238,246,247,252,260,263,265,287,293,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,271,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:[15,459],consum:[1,312,454,524],consumpt:375,contact:[],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,232,237,241,242,248,252,253,254,257,269,285,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,15,16,127,128,207,226,227,232,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,238,246,247,248,250,251,252,254,255,256,262,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,216,347,463,465],contour_integr:216,contract:[61,229,231,271,304,317],contradictori:3,contrain:321,contraint:285,contrari:[248,255],contrast:[1,6,42,55,66,160,163,204,231,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,246,254,257,260,261,266,272,294,295,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230,231,250,251,254,255,271,273,274,275,276,277,278,279,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:216,controlfil:459,convect:99,conveni:[6,12,28,203,208,223,319,380,467,483,516,519,524],convent:[3,8,28,189,196,198,204,207,316,331,359,416,418,524],converg:[3,6,41,96,203,204,206,208,213,225,228,229,237,244,276,287,293,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511,516],convers:[3,8,152,206,207,217,220,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,269,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,238,250,315],cooordin:[203,204],cooper:[5,7],coord123:125,coord1:[3,125,219],coord2:[3,125,219],coord3:[3,125,219],coord:[],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,231,232,235,237,238,239,244,246,249,250,251,252,253,254,255,268,270,271,273,274,275,277,278,279,294,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,219],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,206,347,388,406,458,495,519],copper:489,coproccesor:[],coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:207,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:[3,6,40,124,206,356,357,380,484,497,519],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,231,238,246,248,254,271,272,294,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,232,237,244,255,265,271,272,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[],correpond:[241,242],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,238,239,242,244,245,249,254,257,258,267,268,269,271,273,274,275,276,277,278,279,280,281,285,289,291,292,294,296,298,299,300,304,309,310,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[],cosineshift:26,cosmo:[248,253],cossq:[],cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,243,271,309,318,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,15,96,248,389],couett:4,coul:[],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,244,253,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,232,237,243,246,252,271,285,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:246,counterbal:[238,250],counterbalanc:28,counterclockwis:184,counterpart:[203,492],counterproduct:17,coupl:[],couple:[4,6,11,12],courant:324,cours:[3,8,15,138,140,172,203,211,212,247,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:248,cover:[6,12,75,199,207,216,257,418,484],coverag:75,cpc:253,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,244,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,235,255,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuinfo:15,cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,389,518],craympi:393,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:216,create_faceset:216,create_group:205,create_nodeset:216,createatom:[],creation:[],crimson:207,critchlei:302,criteria:[3,127,179,206,207,226,227,228,266,386,455,484,499,502,524],criterion:[12,41,133,178,181,217,225,228,246,285,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,269,342,347,386],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,231,268,270,294,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,15,77,117,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,15,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[],cst:416,cstherm:6,cstyle:494,csvr:[],ctcm:[394,416],ctemp_core:235,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,235,356,380,518],cubes:[41,225],cubic:[],cuda:[1,3,7,9,12,14,16,393,510,524],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:399,cummul:[3,6,223,226,227,228,230,243,248,254,256,335,338,339,340,341,343,350,425,515],cumul:[6,217,219,222,236,246,254,269,271,276,285,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,236,237,238,244,246,248,251,252,254,260,266,268,271,272,277,278,279,285,287,291,292,293,294,296,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,246,287,293,299],curvatur:[422,460,489],custom:[],cut0:495,cut1:506,cut2:506,cut:[],cuthi:[298,310],cutinn:[401,440,441],cutlo:[298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,233,241,242,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[],cwiggl:[3,268,352,355,357,524],cyan:[2,206,207],cycl:[3,246,269,271,272,276],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,252,293,303,353,356,382,500],cylinder_d:382,cylindr:[6,252,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:257,d3q19:257,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,203,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:294,damag:[],dammak:312,damp:[3,6,210,215,254,255,256,261,271,272,276,293,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:255,damp_drud:255,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,246,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:207,darkcyan:207,darken:206,darkgoldenrod:207,darkgrai:207,darkgreen:207,darkkhaki:207,darkmagenta:207,darkolivegreen:207,darkorang:207,darkorchid:207,darkr:207,darksalmon:207,darkseagreen:207,darkslateblu:207,darkslategrai:207,darkturquois:207,darkviolet:207,dasgupta:308,dash:[423,514],dat:[6,99,199,216,493],data2xmovi:[],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:[0,4,6,12,13,202,458,459,524],datom1:126,datom2:126,datom3:126,datom4:126,datum:[3,6,42,68,71,73,84,102,119,126,203,220],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dcd:[3,6,7,203,205,206,207,208,300,498,502],dcs:9,ddim:202,deactiv:439,dealt:253,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[],decai:[100,409,489],decid:[3,6,12,15,75,268,306,317,348,512,519],decipher:380,deck:306,declar:205,declin:335,decod:206,decompos:[95,467],decomposit:[3,5,7,17,64,216,300,322],decoupl:[6,518],decreas:[3,15,203,204,213,214,221,228,231,237,238,244,246,254,346,377],decrement:323,dedic:[15,393],deepli:374,deeppink:207,deepskyblu:207,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:[],defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,235,236,237,240,242,244,245,246,249,252,253,254,255,256,257,266,268,270,271,272,273,274,275,276,277,278,279,281,282,283,286,289,290,291,292,294,295,296,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,240,252,276,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,235,246,248,249,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:199,degress:[158,219],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,243,246,271,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[],delete_bond:[],delete_el:216,deli:202,delimit:[318,495,524],dellago:[6,238],deloc:[272,418,466],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:242,delx:202,delz:202,demand:312,demo:11,demon:297,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,257,259,260,261,299],denomin:[7,183],denot:[130,235,238,255,299,310,312,409,424,426,459,463,465],dens:[75,228,318,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,231,244,257,260,264,265,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[269,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,231,237,239,242,245,248,249,250,252,254,255,257,259,260,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,298,309,310,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:232,deposit:[],deprec:[3,308,458],deprect:219,depth:[51,156,206,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,238,246,254,268,271,273,274,275,276,277,278,279,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:298,descend:207,descent:[7,385],descib:[40,206,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,234,235,241,242,247,248,251,252,253,254,255,256,257,259,260,261,266,270,271,272,276,284,295,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[],descriptor:[152,203,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,234,235,271,272,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,244,246,247,254,255,256,260,271,294,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,206],despit:518,destabil:399,destre:370,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,238,244,246,247,248,249,251,252,254,256,257,261,268,269,270,271,272,273,274,275,276,277,278,279,283,285,291,292,294,295,296,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,245,303,346,388,408,425,430,492,494,497,508,511,524],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,123,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,231,232,235,237,242,246,249,250,252,254,255,260,266,268,269,271,277,278,279,291,292,294,296,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,251,276,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[269,276,298,421],deviator:9,devic:[1,3,12,14,16,251,393],device_typ:393,devin:[309,408],devis:445,dfactor:206,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,202,231,303],dhug:[269,307],dhugoniot:[269,307],dia:443,diag:318,diagnost:[],diagon:[3,6,91,129,152,153,154,229,271,304,317,350,463,465],diagonalstyl:467,diagram:[41,130,177,198,225,300],diallo:425,diam:[206,207,303,387],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,254,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:268,dictat:[217,269],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:[],dielectr:[],diff:[3,6,12,15,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,235,238,241,245,246,247,248,249,250,251,254,255,257,268,271,272,273,274,275,277,278,279,281,283,286,289,290,291,292,296,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,199,318,377,409,456,481],difficult:[229,300,393,425,506,516],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[],diffuse:[4,6],digit:[2,3,207,360,446,524],dih_table1:199,dih_table2:199,dihedr:[],dihedral_coeff:[],dihedral_cosine_shift_exp:26,dihedral_styl:[],dihedralcoeff:[3,200],dihedraltyp:227,dihydrid:418,dij:321,dilat:[],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,231,252,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,270,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:207,dimstr:[41,225],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[],dipolar:[4,28,40,203,204,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,269,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[],directli:[3,6,8,9,11,12,95,124,129,152,154,203,204,205,206,213,237,248,252,257,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directori:[],disabl:[3,12,15,347,393,430,495,510,524],disadvantag:[6,225],disallow:[203,231,271],disappear:499,discard:[2,3,41,75,221,225,348,356,494,499,500],discontinu:[199,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,206,207,254,257,293],discuss:[],disk:[6,92,93,100,171,201,232,246,303,495],disloc:[74,446],disord:[39,74,446],disp:[],dispar:460,disperion:[412,435],dispers:[3,6,7,9,176,299,377,378,403,412,435,440,448,459,478,485],displac:[],displace_atom:[],displace_box:61,displacemet:500,displai:[11,13,21,36,44,55,186,198,203,206,362,371,406,476],dispters:3,disregard:446,dissip:[6,9,40,88,89,240,247,254,299,322,344,345,401,413,414,423,440,441,476],dissolut:226,dist:[6,73,99,119,128,203,300,316,415,475,492,525],distanc:[],distinct:[6,235,314,377,460],distinguish:[6,94,152,260,418,496,524],distort:[176,394],distrbut:394,distribut:[],distro:[122,406,455,456],ditto:[8,12,14,16,17,42,126,227,317,489,495],div:[8,15],divd:128,diverg:[3,12,39,317,345,395,499,518,527],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,231,298,343,350,355,377,386,388,419,459,466,485,506,514,524],divis:[6,197,257,399,429,439,494,515,524],dl_poly:[6,7],dlambda:172,dlammps_async_imd:251,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,346,497,498,502],dlammps_jpeg:[3,12,206],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,206],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,203],dlen:507,dlmp_intel_offload:[9,15],dlo:[61,202,231,303],dlopen:6,dlvo:[7,407,488],dm_lb:257,dmax:[335,384],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,86,95,98,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,232,246,254,255,266,271,272,277,278,279,283,291,292,294,295,296,303,306,317,331,335,338,339,340,349,353,356,358,360,362,371,376,386,387,388,393,394,395,398,406,408,409,416,417,419,425,426,428,429,443,444,445,448,452,455,456,457,467,476,477,480,482,484,485,495,497,498,499,500,502,505,506,507,514,515,519,524,525,527,528],docuement:460,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,235,237,238,241,242,243,246,247,250,252,254,255,257,260,267,271,272,273,274,275,277,278,279,291,292,293,294,295,296,304,305,306,310,312,315,317,335,338,340,342,343,347,350,351,352,355,356,357,358,363,364,365,367,368,370,376,377,378,379,380,387,388,389,394,395,396,397,398,399,401,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,426,427,428,429,430,433,434,436,437,438,440,441,443,444,445,446,448,450,451,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,493,494,495,497,498,499,500,501,504,505,507,508,509,510,511,514,515,518,519,524,529],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,331,387,389,393,395,408,417,428,458,459,477,480,481,482,485,497,499],dof:[3,8,123,156,157,158,171,219,317,525],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[387,497],doi:[6,230,298],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,231,232,250,253,257,271,272,300,312,317,322,347,352,353,377,378,388,393,415,448,492,494,497,501,514],domin:[1,418,511],don:[0,8,9,12,13,15,127,181,213,237,255,356,443,466,495,497,519],donadio:339,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,241,242,244,246,251,252,254,255,262,271,277,278,279,291,292,294,296,297,299,300,301,303,306,314,317,319,321,335,338,339,340,342,344,345,358,360,376,377,378,386,388,389,392,393,395,403,416,426,427,428,435,441,442,443,448,450,451,458,475,478,479,484,492,493,494,495,498,501,502,505,515,516,518,519,524,525],donor:425,dot:[153,174,213,237,249,270],doti:[399,456],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,231,244,305,356,360,376,378,392,393,399,419,424,446,458,459,493,497,501,505,510,524,525],dover:216,down:[3,6,7,8,11,39,75,229,246,254,335,351,418,448,466,496,516],downhil:[384,385],download:[5,7,8,9,11,12,13,16,251,427,457],downsid:6,downward:314,dozen:[8,9,12,118,210,458,459],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[],dpde:264,dpdtheta:[40,88,89,414],dpdtheta_i:[240,241,242],dproduct:396,dr_ewald:[130,319],drag:[],dragforc:257,drai:[206,269,307],drain:[250,351,386],dramat:[9,61,202,226,227,228,229,231,271,335,338,339,378,448,466,494],drautz:399,draw:206,drawback:306,drawn:[42,203,206,207,247,492],drayleigh:[269,307],dreid:[],dreiding:[],drfourth:115,drho:[124,394,416,450,451],drift:[6,113,115,238,247,248,250,254,255,267,315,335,506,514,518],drive:[11,12,214,229,231,249,271,298,304,317,354,388],driven:[6,190],driver:[6,12,14,210,244,251],drop:[3,207,413],droplet:426,drsquar:115,drude:[],drudes:[255,518],dry:243,dsecriptor:427,dsf:[],dsmc:[],dstyle:303,dt_collis:257,dt_lb:257,dt_md:257,dt_srd:335,dtilt:[61,231],dtneb:511,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518],especi:[8,15,166,178,210,217,225,246,307,312,315,316,393,494,516],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,299,351,378,395,409,431,482,502,515],essential:[8,276],essex:28,establish:[95,250],estim:[1,3,6,10,12,37,41,56,99,153,216,225,236,269,318,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,257,271,307,308,310,351,417,419,422,456,481,485,523],eta_dot:271,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:271,etap_dot:271,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,231,232,244,246,247,254,271,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,207,235,255,269,307,514,515],eu2:177,eu3:177,euler:[318,386,388],eulerian:216,euqat:469,europhi:257,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,237,247,249,250,252,253,254,255,299,305,308,318,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,294],evanseck:[6,19,184,404,509],evapor:[],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,231,232,235,238,252,255,269,271,272,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,199,225,257,429,486],event:[],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,253,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,238,243,244,246,248,250,251,252,257,258,267,271,272,276,287,293,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[238,248,257,300,492],evolv:[257,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,247,248,254,255,256,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,231,236,241,247,254,255,256,272,284,285,295,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,228,299,318],examp:[495,524],exampl:[],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,231,236,243,271,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,225,231,271,335,459,505],excel:418,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,231,239,245,246,249,252,254,256,271,272,273,274,275,276,277,278,279,280,281,284,285,289,291,292,294,295,296,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[221,418],exchang:[2,3,6,8,63,64,210,216,217,238,246,250,254,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,258,267,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[271,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,251,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:247,exemplifi:418,exert:[6,252,255,287,312,354,355,356,378],exhaust:[216,392,524],exhibit:[100,238,250,271,385,418,506],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,232,246,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,203,225,376,392,495,496,505,514,515,516,524],exlanatori:3,exp6:[],exp:[],expand:[],expans:[12,152,197,203,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,237,246,248,268,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,207,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,224,232,251,260,270,304,316,317,384,388,413,448,506,511],experienc:[6,12,15,259,260],experiment:[16,246,377,393,511],expert:12,expertis:7,expir:[515,516],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,231,271,287,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,203,204,219,270,298,426,491,494,495,497,506],explanatori:[3,8,128,203,204,218,219,222,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,231,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,231,239,245,247,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,306,307,309,310,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,459,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,318,420,456,477,485,489,511,524],expos:11,exposit:[216,413,415],express:[6,152,164,178,211,212,229,268,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,233,237,238,244,245,246,248,249,250,252,254,256,269,271,276,285,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,210,515],extent:[1,3,41,42,45,59,75,176,180,203,215,225,252,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,271,305,306,307,317,335,386,387,390,391,393,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,231,271,345,418,481,518],extrema:439,extreme:418,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,266,337,349,515,524],f_ij:456,f_indent:223,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:269,f_r:[255,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,215,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,248,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,231,232,238,246,251,254,256,257,269,271,272,276,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,229,232,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:251,fall:[3,6,207,222,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,232,271,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:254,farrel:[480,482],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,232,246,248,252,268,269,271,273,274,275,276,277,278,279,288,291,292,294,295,296,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,15,16,39,203,204,282,307,318,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,231,239,245,249,253,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,304,308,309,310,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:228,favorit:7,fbmc:342,fcc:[],fcm:[288,524],fcold:238,fdirect:235,fdotr:427,fdt:[],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[],fecr:416,feedback:[7,251],feel:[7,251,252,260,298,356,358,388,448],fehlberg:318,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:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,238,255,271,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,260,506],fewest:3,fextern:244,feynman:300,fff:495,ffield:[408,419,458,459,466],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:238,ficiti:475,fictiti:[6,213,214,237,244,248,300,316,409,431,435,475],field1:[498,502],field2:498,field:[],fifth:[6,331,420,452],figshar:298,figur:[1,3,8,12,15,307,494,495,519],fij:412,file0:298,file1:[11,13,242,298,346,360,387,502,504,508],file2:[11,13,242,346,360,387,502,504,508],file:[],file_from:205,filen:387,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,241,242,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,203,204,207,499,504,529],filepo:314,fill:[7,9,178,206,303,347,380,389,399,446,459,500,519],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,241,242,243,246,270,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,213,237,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,202,268,500],finish:[6,11,41,225,360,374,376,377,390,392,393,484,502,524,525],finit:[],finni:[7,416,476],finverse:235,fiorin:[9,230],fire:[],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,241,242,246,247,252,257,268,269,270,271,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,199,241,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[],fix_deposit:3,fix_flux:216,fix_heat:238,fix_id:[3,229,269,271,273,274,275,276,277,278,279,304,307],fix_manifoldforc:519,fix_modifi:[],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[229,271],fixextern:244,fixid:[206,216],fji:412,flag1:[234,391],flag2:[234,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,234,251,254,258,260,267,268,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:234,flagvf:[401,440,441],flat:[6,15,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,206,219,230,248,272,343,350,418,481,515],flip:[3,6,231,271,354,355],floor:524,flop:12,floralwhit:207,flow:[],fluctuat:[6,66,95,229,246,247,254,257,271,276,298,299,304,322,345,347,370,414],fluid:[],fluid_veloc:261,flush:[3,207,514],flux:[],flv:206,fly:[7,9,12,41,206,210,216,221,232,235,317,321,348,399,446,515,518],fmackai:9,fmag:233,fmass:300,fmax:[386,515],fmomentum:235,fmsec:[2,207,254,255,268,271,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:235,fnve:238,fnvt:235,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,298,467],fold:[15,333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,235,236,240,241,242,244,246,247,248,251,253,254,255,257,260,269,271,276,277,278,279,291,292,294,296,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,203,206,244,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,17],forc:[],force_uvm:16,forceatom:260,forcefield:[316,425],forcegroup:257,forcezero:384,ford:412,forestgreen:207,forev:75,forget:[255,518],forgiv:271,fork:[],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,207,210,211,212,227,247,248,254,256,260,268,294,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,247,248,254,271,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,241,242,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:242,former:[6,12,39,41,207,225,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,213,237,254,271,294,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,237,249,250,252,254,255,268,298,299,305,314,320,328,333,335,338,339,340,349,352,353,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,244,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,203,228,230,238,246,251,257,263,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,269,347,370,387,388,446,492],fourier:[],fourth:[6,15,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:253,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,202,206,207,217,226,227,228,229,269,303,307,314,315,318,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,251,314],fraig:42,frame:[91,152,207,216,269,307,354,422],framer:[206,207],framework:[5,248,394,467],franc:9,frattl:238,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,211,212,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,219,228,235,246,248,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,206],freez:[],frenkel:[6,238,246,345],freq:215,frequenc:[3,6,15,39,113,207,221,285,299,300,307,312,318,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,207,226,227,238,243,343,350,448,483,504,516],fri:[269,307],friction:[4,5,6,9,10,42,210,248,254,307,312,317,347,351,353,423,507],friedrich:324,from:[],front:[269,307,354],frontend:[206,311],frozen:[6,123,182,245,247,255,389,421],fs2:[6,99],fscale:251,fstr:524,fstring:495,fstyle:353,ftol:[386,388,492,511],fuchsia:207,fuction:409,fudg:321,fugac:246,fugacity_coeff:246,fulfil:6,full:[1,2,3,6,9,12,15,16,37,39,40,99,206,220,221,230,238,257,298,318,377,378,393,399,416,418,419,422,459,48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,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,203,252,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:260,innermost:[37,56,75,391,478,479,506],innernod:260,innner:437,inordin:348,inorgan:[6,485],inp:[230,360,467,485],input1:[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:[3,5,7,8,9,12,61,178,210,232,246,252,303,377,467,475,495,501,518],insertion:[3,232,246,303],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,232,233,238,243,246,252,257,260,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[257,433,495,511],insight:[6,13],instabl:[257,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[],instanc:[6,9,11,211,230,248,354,421,426,448,456,495,518],instantan:[6,65,228,229,247,248,271,276,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,216,426,494],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,246,254,257,260,261,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,459,476,483,492,500,504,511,513,518,524],institut:[9,251,302],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:271,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,232,237,239,243,244,246,249,254,267,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,232,234,244,246,247,248,251,254,255,256,257,299,302,303,306,307,312,317,318,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[],integral:[300,450,451],integrate_ulsph:[],intel:[],intel_coprocessor:15,intel_cpu:12,intel_cpu_intelmpi:15,intel_cpu_mpich:15,intel_cpu_openpmi:15,intel_phi:12,intend:[3,6,8,12,13,35,221,247,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,236,243,250,260,269,271,276,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,210,515],intepol:524,inter:[17,42,63,64,158,181,182,203,228,254,256,270,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,245,246,251,252,254,256,260,285,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,203,270,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[],interfer:[12,271,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,206,270,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],intern:[],internal:[3,206,212,303,524],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:253,interpenetr:443,interpentr:[470,471,473],interpol:[6,14,37,56,110,199,206,207,216,241,242,257,298,377,378,388,399,448,450,451,459,472,478,479,480],interpret:[2,6,11,197,206,222,423,468,492,495,511,524],interrupt:307,intersect:[3,6,130,207,356,358,500],intersert:356,interspers:386,interstiti:[176,446],intertia:[3,103],interv:[3,6,99,205,220,254,271,307,312,313,326,466,472,492,511,524],intestieti:130,intial:[6,393,395],intiial:[41,502],intiti:[3,334],intra:317,intra_energi:246,intramolecular:[28,154,246],introduc:[6,9,100,117,206,238,271,307,312,317,370,377,394,409,418,431,435,439,477,511,524],introduct:[],intuit:380,inv:[130,177,319],invalid:[3,12,75,97,181,285,388,440,441,499],invari:[117,145,150,152],invent:321,invers:[],inverse:518,invert:[1,6,182,299],invis:356,invoc:[176,228,393,463,465,495],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,243,244,245,246,247,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,268,270,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,317,319,320,321,323,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,361,363,364,366,367,370,372,376,377,378,379,380,386,388,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,427,431,432,433,434,435,436,437,438,439,440,441,444,448,449,452,453,455,459,460,461,463,465,467,468,477,478,480,481,482,483,485,486,487,488,489,491,494,495,496,498,500,502,505,506,508,509,511,514,515,518,524,525],invokd:3,invoke:[3,12,16],involv:[3,6,7,8,12,65,119,126,127,128,158,182,210,217,226,246,257,302,305,310,335,377,385,386,388,398,415,422,429,477,480,482,493,494,500,502,506,511,512],ioff:[387,497],ion:[6,7,9,160,297,331,347,378,399,410,419,421,443,446,466,476,482,489,497,518],ionic:[6,9,400,402,410,418,419,453,466,518],ioniz:[408,418],ionocoval:9,iparam:[3,227],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,41,60,225,229,231,271,317],irrelev:452,irrespect:[440,441],irrevers:[235,318],is_act:[3,524],is_avail:[3,524],is_defin:[3,524],isbn:488,isele:[377,378],isenthalp:[9,271,272,273,274,275],ismail:[377,378,403,435],isn:[3,8,11,12,238,250],iso:[3,229,235,255,271,272,273,274,275,276,277,278,279,304,312,317,518],isobar:[9,271,272,277,278,279,322,414],isodem:418,isoenerget:[9,322,414],isoenthalp:[322,414],isol:[3,181,358,423],isomorph:300,isotherm:[9,246,271,272,277,278,279,304,322,414],isotop:306,isotrop:[6,100,254,304,377,378,401,422,440,441],isovolum:319,isralewitz:323,issu:[1,3,6,9,11,12,13,14,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,61,75,77,87,113,123,155,165,184,185,187,188,189,190,192,193,195,196,199,206,213,224,228,229,231,232,237,238,239,245,246,249,254,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,300,304,306,309,310,317,320,321,334,338,339,340,345,355,357,360,361,363,364,366,367,370,372,378,387,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,475,477,478,480,481,482,483,485,487,488,489,497,499,500,506,509,514,515,516,524,525],issue:216,ital:[458,459],itali:13,item:[6,7,8,41,203,207,225],iter:[3,6,12,39,41,65,205,213,214,224,225,229,235,237,244,252,287,293,299,308,309,317,321,332,342,358,360,376,384,385,386,388,392,466,492,502,506,511,515,516,524],iterat:[12,386],ith:[75,128,131,218,219,220,221,222,223,337,349,515,524],itself:[2,3,6,7,8,9,11,12,13,17,42,61,99,118,169,203,205,206,207,208,220,221,230,235,255,270,311,317,347,358,360,387,388,409,419,422,426,427,450,451,478,479,495,501,504,505,509,524,529],itset:507,ityp:[3,57,126,127,178,215,227,310,486],itype1:127,itype2:127,itypen:127,ivector:8,ivori:207,ixcm:317,ixi:[42,317,387],ixx:[42,103,317,387,524],ixy:[103,387,524],ixz:[42,103,317,387,524],iycm:317,iyi:[42,103,317,387,524],iyz:[42,103,317,387,524],izcm:317,izrailev:323,izumi:481,izz:[42,103,317,387,524],j0jt:99,j20:220,j_m:152,jackson:447,jacobi:3,jacobsen:385,jacs:[6,184,509],jagreat:13,jame:[9,18],janssen:298,januari:443,jaramillo:[7,9,13,418],jarzynski:323,jatempl:9,jcc:9,jcp:352,jec:13,jeff:13,jeffer:15,jello:271,jensen:[254,377],jeremi:[9,445],jerom:9,jewett:13,jiang:[255,518],jiao:[9,13],jiht:[7,9],jik:399,jim:7,jku:[7,9],jmake:12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415,509],reconstruct:[3,230,466],record:[208,230,323],recov:[229,238,271],recreat:359,rectangl:[41,225,380],rectangular:[7,41,64,180,225,246,380,497,499,501],rectilinear:[130,177,204],rector:53,recurs:[41,225,399,484],recust:41,recv:494,red:[2,206,207,228,300],redefin:[3,499,505,524],redirect:12,redo:12,reduc:[],reduct:[17,18,128,130,177,269,307,377],redund:419,ree:471,reed:[269,307],rees:[7,9,13],ref:[344,345,385],refactor:6,refer:[],referenc:[3,6,12,65,71,75,125,131,203,204,210,220,246,306,349,378,409,425,452,460,495,515,524],reflect:[],refman:9,reformat:7,refresh:216,reg:500,regard:[6,61,268,321,322,327,455,459],regardless:[14,75,178,181,202,222,231,254,271,273,274,275,277,278,279,304,317,328,335,393,494,500,507],regim:[6,343,350,410,506],region:[],region_spher:8,region_styl:356,regist:[8,127,154,330],regoin:6,regress:524,regspher:178,regstrip:358,regul:6,regular:[1,3,41,64,96,176,180,203,206,217,225,246,306,347,378,410,429,494,497,499,501],reigon:524,reinder:15,reinhardt:[344,345],reject:[178,228,458,512],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,207,210,217,225,231,232,235,238,246,252,255,267,268,294,298,303,312,314,315,318,323,331,335,337,342,343,347,354,358,377,378,386,418,422,423,440,441,443,460,488,498,506,511,515,518,525],relat:[],relationship:[6,241,308,360,377,466,488,518,524],relax:[],releas:[0,5,7,8,13,226],relect:[3,448],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,207,211,212,215,216,217,218,219,220,221,222,223,225,226,227,231,232,236,238,239,243,245,246,247,250,251,257,258,259,261,262,263,264,265,267,268,270,280,281,282,283,284,285,286,287,288,289,290,293,297,301,302,303,305,306,311,313,314,315,319,321,328,333,335,336,337,342,343,346,347,348,349,350,351,352,353,354,355,357,358,377,382,386,396,397,401,407,409,410,412,413,415,418,421,422,423,424,425,430,432,433,434,436,437,438,440,441,448,449,450,451,455,460,468,475,478,479,487,488,489,494,510,525],reli:[3,12,309,418,459,489,497,507],reloc:12,reltol:318,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,231,254,255,262,271,272,277,278,279,291,292,294,296,301,302,326,335,338,339,340,346,347,358,360,368,371,387,399,418,426,439,446,448,476,492,497,498,502,507,509,511,515,516,518,519,524,525],remaina:399,remaind:[9,178,203,232,303,335,348,482,497],remap:[3,6,12,61,63,75,161,178,202,231,252,268,294,377,497,498,499],remedi:[6,518],rememb:[2,519],remot:519,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,243,254,255,260,263,267,269,271,277,278,279,291,292,294,296,302,308,317,318,319,321,335,338,339,340,342,358,377,388,412,441,446,497,500,508,509,519,524,525],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,359,508,519],render:[12,13,203,206,207],rendon:[271,272],reneighbor:[3,8,12,39,59,75,225,246,335,348,358,413,514,515],renssela:302,renumb:75,reorder:[3,12,39,494],rep:512,repeat:[2,6,206,207,228,229,246,318,327,380,399,480,482,484,492,511],repeatedli:2,repel:252,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,232,254,276,305,306,312,314,353,393,395,409,423,433,450,451,478,498,499,504,505,515,524,525,527,529],replic:[],replica:[],replica_fil:12,report:[],repositori:[],reprens:347,repres:[1,3,6,8,9,12,14,40,41,42,61,70,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,235,242,247,249,254,257,271,300,302,304,312,317,318,319,323,331,332,347,349,356,378,388,394,399,422,429,439,440,441,443,444,445,453,456,458,459,483,484,492,494,497,507,509,512,518,524,527],represent:[3,6,8,9,59,61,146,180,203,247,248,300,347,399,418,422,446,460,497,500,518],reprocess:502,reproduc:[3,15,271,353,409,416,423],repul:443,repuls:[6,7,35,40,45,46,119,252,308,352,353,356,395,399,407,409,413,418,420,423,425,439,443,447,466,475,482,485,488,489,507],reqir:[308,310],request:[3,6,8,12,41,113,181,199,203,251,257,315,322,335,337,375,377,448,458,459,492,502,507,511,516,519,524,525,527],requir:[],rerun:[],rescal:[],research:[5,7,88,89,240,257,261,322,446,492,511],resembl:[312,519],resepct:6,reserv:[12,251,518],reservoir:[99,238,246,250,254,347],reset:[],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[],resid:13,residu:251,residue1:389,resist:[6,251],resolut:[221,466,478,479],resolv:[229,300,335,441,519],resort:3,resourc:[7,394,416],respa:[3,15,213,214,224,233,236,237,249,251,252,266,271,298,309,316,320,323,331,332,333,334,351,352,356,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,505,506,516,517,524],respecifi:446,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,231,238,239,245,249,252,254,255,257,271,273,274,275,276,277,278,279,280,281,287,289,291,292,294,296,308,309,310,317,319,321,323,331,334,347,352,355,361,363,364,366,367,370,372,375,377,378,383,386,387,392,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,452,453,455,459,460,461,465,466,467,468,477,478,480,481,482,483,485,487,488,489,494,498,507,510,516,518,524,526,527,529],respon:9,respond:[6,7,161,231,418,455],respons:[6,7,269,343,350],resquar:[],rest:[6,8,12,38,58,200,306,310,316,373,399,441,443,490,514,515,518],restart1:300,restart2:300,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,62,63,113,178,211,212,266,306,323,331,332,337,359,514,515],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,230,269,316,334,430],restratin:316,restrict:[],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,199,202,203,204,206,207,210,213,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,235,238,239,241,245,246,247,249,254,255,257,261,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,295,296,299,300,308,309,310,314,315,317,318,320,321,335,343,344,345,347,348,349,352,353,355,357,360,361,363,364,366,367,370,372,377,378,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,443,444,446,448,449,450,451,452,453,455,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,497,499,500,502,506,507,508,509,511,523,524,525],resum:524,retain:[2,226,227,395,399,446,494],retart:[32,50,191,368],retir:[3,458],retreiv:8,retriev:[6,8,244,444,445,524],reus:[3,509],rev:[6,13,66,74,100,117,121,152,153,166,217,248,254,256,269,271,272,276,294,299,309,312,317,323,335,339,342,344,345,350,385,399,407,408,409,412,416,417,418,422,423,428,433,440,441,442,443,445,450,451,456,460,467,477,480,481,482,485,492],revers:[2,6,8,95,189,228,252,271,297,298,308,327,343,344,350,388,439,506,518],review:[152,308,323,342,446,457,467,492,511,518,519],rewind:376,rewrap:203,rewrit:[5,12],rewritten:18,rezwanur:455,rfac0:[152,467],rfactor:335,rfile:317,rg0:333,rgb:207,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[450,451,478,479],rho0:[443,463,465,473,474],rho0_meam:443,rho:[],rho_0:[473,474],rho_alpha_beta:416,rho_bkgd:443,rho_colloid:352,rho_e:347,rho_fin:346,rho_i:[444,445],rho_initi:346,rho_ref_meam:443,rho_wal:352,rhodo:[9,10],rhodopsin:[1,10,15],rhohi:303,rholo:303,rhosum:[],rhot:238,rhs:318,ribier:385,richard:9,richardson:317,richi:[9,18],rick:[308,309,408,466],rick_and_stuart:309,ridg:[9,18],right:[3,6,11,12,41,154,178,196,198,202,204,225,228,252,257,268,297,298,318,360,380,409,497,500,507,519,524],rightmost:[41,225],rigid:[],rigidid:129,rigidifi:317,rii:[97,98],rij:[100,117,226,227,298,413,414,450,451,475],rin:[425,436,437],ring:[],rino:[77,485],rinv:377,rirj:[353,423],risi:[152,467],risk:[8,316,506],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rk4:318,rkf45:318,rlo:[450,451,478,479],rmask:[3,524],rmass:[3,306],rmax:[75,179,226],rmdir:508,rmin0:[152,467],rmin:[75,179,227,433],rms:[318,377,378],rmsd:346,rnemd:6,robert:9,robin:207,robust:[384,385,386,459],rock:443,rockett:456,rod:317,rodata:12,rodnei:312,roi:7,role:[6,342],roll:12,ronchetti:117,room:[59,61],root:[11,95,97,98,205,342,346,416,504],rosati:39,rose:443,ross:443,rosski:300,rosybrown:207,rot:[6,99,300,316,342,525],rotat:[],rotate:327,rotation:117,rotaton:500,rough:[6,178,206,357],roughli:[7,10,12,41,161,206,221,246,254,255,263,270,271,285,304,317,335,338,339,342,378,388,393,462,464,499,506],round:[1,3,12,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,42,43,45,46,47,48,49,51,53,54,56,75,123,155,165,184,185,187,188,189,190,192,193,195,196,199,207,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,429,431,432,433,434,435,436,437,438,439,440,444,449,450,451,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,499,500,506,523,524],rous:247,rout:[95,425,439],routin:[5,6,8,11,14,15,37,39,56,96,182,257,446,457,478,479,510],roux:[6,235,255,483,518],row:[6,68,69,71,73,79,84,86,98,102,103,114,116,119,125,126,127,129,131,158,166,173,175,176,177,219,220,222,223,260,317,347,349,357,418],royalblu:207,rozero:443,rperp:[268,327],rpi:302,rpm:12,rrespa:[1,3,5,7,8,15,211,212,268,271,389,394,395,396,397,398,400,401,402,403,404,405,407,408,40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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","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":226,"default":[36,39,40,55,59,60,61,63,64,75,95,96,100,112,113,115,117,118,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,231,232,236,243,246,247,252,254,255,256,257,258,260,266,269,271,272,276,294,295,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[221,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,adding:519,addition:[12,13,519],addtorqu:214,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:215,arrai:6,aspher:[6,90,156,273,277,281,282,291],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:224,awpmd:[9,396],axel:519,balanc:[41,225],barostat:6,basal:70,bcc:298,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,274,278,283,292,398],body:9,bond:[8,13,72,73,226,227,228,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,229],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:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,230],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,custom:[8,203,204],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,43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\ No newline at end of file diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 383a0c005..4a883fe52 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,303 +1,303 @@ LAMMPS Users Manual - + "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line

LAMMPS Documentation :c,h3 -13 Jul 2016 version :c,h4 +15 Jul 2016 version :c,h4 Version info: :h4 The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on "this page of the WWW site"_bug. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page). If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of LAMMPS. :ulb,l If you browse the HTML doc pages included in your tarball, they describe the version you have. :l The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of every patch. :l There is also a "Developer.pdf"_Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS. :ule,l LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at http://lammps.sandia.gov has more information about the code and its uses. :link(bug,http://lammps.sandia.gov/bug.html) :link(sjp,http://www.sandia.gov/~sjplimp) :line The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation. Once you are familiar with LAMMPS, you may want to bookmark "this page"_Section_commands.html#comm at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands. "PDF file"_Manual.pdf of the entire manual, generated by "htmldoc"_http://freecode.com/projects/htmldoc "Introduction"_Section_intro.html :olb,l 1.1 "What is LAMMPS"_intro_1 :ulb,b 1.2 "LAMMPS features"_intro_2 :b 1.3 "LAMMPS non-features"_intro_3 :b 1.4 "Open source distribution"_intro_4 :b 1.5 "Acknowledgments and citations"_intro_5 :ule,b "Getting started"_Section_start.html :l 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b 2.2 "Making LAMMPS"_start_2 :b 2.3 "Making LAMMPS with optional packages"_start_3 :b 2.4 "Building LAMMPS via the Make.py script"_start_4 :b 2.5 "Building LAMMPS as a library"_start_5 :b 2.6 "Running LAMMPS"_start_6 :b 2.7 "Command-line options"_start_7 :b 2.8 "Screen output"_start_8 :b 2.9 "Tips for users of previous versions"_start_9 :ule,b "Commands"_Section_commands.html :l 3.1 "LAMMPS input script"_cmd_1 :ulb,b 3.2 "Parsing rules"_cmd_2 :b 3.3 "Input script structure"_cmd_3 :b 3.4 "Commands listed by category"_cmd_4 :b 3.5 "Commands listed alphabetically"_cmd_5 :ule,b "Packages"_Section_packages.html :l 4.1 "Standard packages"_pkg_1 :ulb,b 4.2 "User packages"_pkg_2 :ule,b "Accelerating LAMMPS performance"_Section_accelerate.html :l 5.1 "Measuring performance"_acc_1 :ulb,b 5.2 "Algorithms and code options to boost performace"_acc_2 :b 5.3 "Accelerator packages with optimized styles"_acc_3 :b 5.3.1 "GPU package"_accelerate_gpu.html :ulb,b 5.3.2 "USER-INTEL package"_accelerate_intel.html :b 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b 5.3.4 "USER-OMP package"_accelerate_omp.html :b 5.3.5 "OPT package"_accelerate_opt.html :ule,b 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b "How-to discussions"_Section_howto.html :l 6.1 "Restarting a simulation"_howto_1 :ulb,b 6.2 "2d simulations"_howto_2 :b 6.3 "CHARMM and AMBER force fields"_howto_3 :b 6.4 "Running multiple simulations from one input script"_howto_4 :b 6.5 "Multi-replica simulations"_howto_5 :b 6.6 "Granular models"_howto_6 :b 6.7 "TIP3P water model"_howto_7 :b 6.8 "TIP4P water model"_howto_8 :b 6.9 "SPC water model"_howto_9 :b 6.10 "Coupling LAMMPS to other codes"_howto_10 :b 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b 6.13 "NEMD simulations"_howto_13 :b 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b 6.17 "Walls"_howto_17 :b 6.18 "Elastic constants"_howto_18 :b 6.19 "Library interface to LAMMPS"_howto_19 :b 6.20 "Calculating thermal conductivity"_howto_20 :b 6.21 "Calculating viscosity"_howto_21 :b 6.22 "Calculating a diffusion coefficient"_howto_22 :b 6.23 "Using chunks to calculate system properties"_howto_23 :b 6.24 "Setting parameters for pppm/disp"_howto_24 :b 6.25 "Polarizable models"_howto_25 :b 6.26 "Adiabatic core/shell model"_howto_26 :b 6.27 "Drude induced dipoles"_howto_27 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l "Additional tools"_Section_tools.html :l "Modifying & extending LAMMPS"_Section_modify.html :l 10.1 "Atom styles"_mod_1 :ulb,b 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b 10.3 "Compute styles"_mod_3 :b 10.4 "Dump styles"_mod_4 :b 10.5 "Dump custom output options"_mod_5 :b 10.6 "Fix styles"_mod_6 :b 10.7 "Input script commands"_mod_7 :b 10.8 "Kspace computations"_mod_8 :b 10.9 "Minimization styles"_mod_9 :b 10.10 "Pairwise potentials"_mod_10 :b 10.11 "Region styles"_mod_11 :b 10.12 "Body styles"_mod_12 :b 10.13 "Thermodynamic output options"_mod_13 :b 10.14 "Variable options"_mod_14 :b 10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b "Python interface"_Section_python.html :l 11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b 11.2 "Overview of using Python from a LAMMPS script"_py_2 :b 11.3 "Building LAMMPS as a shared library"_py_3 :b 11.4 "Installing the Python wrapper into Python"_py_4 :b 11.5 "Extending Python with MPI to run in parallel"_py_5 :b 11.6 "Testing the Python-LAMMPS interface"_py_6 :b 11.7 "Using LAMMPS from Python"_py_7 :b 11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b "Errors"_Section_errors.html :l 12.1 "Common problems"_err_1 :ulb,b 12.2 "Reporting bugs"_err_2 :b 12.3 "Error & warning messages"_err_3 :ule,b "Future and history"_Section_history.html :l 13.1 "Coming attractions"_hist_1 :ulb,b 13.2 "Past versions"_hist_2 :ule,b :ole :link(intro_1,Section_intro.html#intro_1) :link(intro_2,Section_intro.html#intro_2) :link(intro_3,Section_intro.html#intro_3) :link(intro_4,Section_intro.html#intro_4) :link(intro_5,Section_intro.html#intro_5) :link(start_1,Section_start.html#start_1) :link(start_2,Section_start.html#start_2) :link(start_3,Section_start.html#start_3) :link(start_4,Section_start.html#start_4) :link(start_5,Section_start.html#start_5) :link(start_6,Section_start.html#start_6) :link(start_7,Section_start.html#start_7) :link(start_8,Section_start.html#start_8) :link(start_9,Section_start.html#start_9) :link(cmd_1,Section_commands.html#cmd_1) :link(cmd_2,Section_commands.html#cmd_2) :link(cmd_3,Section_commands.html#cmd_3) :link(cmd_4,Section_commands.html#cmd_4) :link(cmd_5,Section_commands.html#cmd_5) :link(pkg_1,Section_packages.html#pkg_1) :link(pkg_2,Section_packages.html#pkg_2) :link(acc_1,Section_accelerate.html#acc_1) :link(acc_2,Section_accelerate.html#acc_2) :link(acc_3,Section_accelerate.html#acc_3) :link(acc_4,Section_accelerate.html#acc_4) :link(howto_1,Section_howto.html#howto_1) :link(howto_2,Section_howto.html#howto_2) :link(howto_3,Section_howto.html#howto_3) :link(howto_4,Section_howto.html#howto_4) :link(howto_5,Section_howto.html#howto_5) :link(howto_6,Section_howto.html#howto_6) :link(howto_7,Section_howto.html#howto_7) :link(howto_8,Section_howto.html#howto_8) :link(howto_9,Section_howto.html#howto_9) 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:link(mod_6,Section_modify.html#mod_6) :link(mod_7,Section_modify.html#mod_7) :link(mod_8,Section_modify.html#mod_8) :link(mod_9,Section_modify.html#mod_9) :link(mod_10,Section_modify.html#mod_10) :link(mod_11,Section_modify.html#mod_11) :link(mod_12,Section_modify.html#mod_12) :link(mod_13,Section_modify.html#mod_13) :link(mod_14,Section_modify.html#mod_14) :link(mod_15,Section_modify.html#mod_15) :link(py_1,Section_python.html#py_1) :link(py_2,Section_python.html#py_2) :link(py_3,Section_python.html#py_3) :link(py_4,Section_python.html#py_4) :link(py_5,Section_python.html#py_5) :link(py_6,Section_python.html#py_6) :link(err_1,Section_errors.html#err_1) :link(err_2,Section_errors.html#err_2) :link(err_3,Section_errors.html#err_3) :link(hist_1,Section_history.html#hist_1) :link(hist_2,Section_history.html#hist_2) diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 7e96336d5..2bbff42b9 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -1,143 +1,143 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line pair_style brownian command :h3 pair_style brownian/omp command :h3 pair_style brownian/poly command :h3 pair_style brownian/poly/omp command :h3 [Syntax:] pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF :pre style = {brownian} or {brownian/poly} mu = dynamic viscosity (dynamic viscosity units) flaglog = 0/1 log terms in the lubrication approximation on/off flagfld = 0/1 to include/exclude Fast Lubrication Dynamics effects cutinner = inner cutoff distance (distance units) cutoff = outer cutoff for interactions (distance units) t_target = target temp of the system (temperature units) seed = seed for the random number generator (positive integer) flagHI (optional) = 0/1 to include/exclude 1/r hydrodynamic interactions flagVF (optional) = 0/1 to include/exclude volume fraction corrections in the long-range isotropic terms :ul [Examples:] pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) pair_coeff 1 1 2.05 2.8 pair_coeff * * :pre [Description:] -Styles {brownian} and {brownain/poly} compute Brownian forces and +Styles {brownian} and {brownian/poly} compute Brownian forces and torques on finite-size spherical particles. The former requires monodisperse spherical particles; the latter allows for polydisperse spherical particles. These pair styles are designed to be used with either the "pair_style lubricate"_pair_lubricate.html or "pair_style lubricateU"_pair_lubricateU.html commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters {mu}, {flaglog}, {flagfld}, {cutinner}, and {cutoff} should be specified consistent with the settings in the lubrication pair styles. For details, refer to either of the lubrication pair styles. The {t_target} setting is used to specify the target temperature of the system. The random number {seed} is used to generate random numbers for the thermostatting procedure. The {flagHI} and {flagVF} settings are optional. Neither should be used, or both must be defined. :line The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands, or by mixing as described below: cutinner (distance units) cutoff (distance units) :ul The two coefficients are optional. If neither is specified, the two cutoffs specified in the pair_style command are used. Otherwise both must be specified. :line 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 "this section"_Section_accelerate.html 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_start.html#start_3 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"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "this section"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Mixing, shift, table, tail correction, restart, rRESPA info]: For atom type pairs I,J and I != J, the two cutoff distances for this pair style can be mixed. The default mix value is {geometric}. See the "pair_modify" command for details. This pair style does not support the "pair_modify"_pair_modify.html shift option for the energy of the pair interaction. The "pair_modify"_pair_modify.html table option is not relevant for this pair style. This pair style does not support the "pair_modify"_pair_modify.html tail option for adding long-range tail corrections to energy and pressure. This pair style writes its information to "binary restart files"_restart.html, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. This pair style can only be used via the {pair} keyword of the "run_style respa"_run_style.html command. It does not support the {inner}, {middle}, {outer} keywords. :line [Restrictions:] These styles are part of the COLLOID package. They are only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. Only spherical monodisperse particles are allowed for pair_style brownian. Only spherical particles are allowed for pair_style brownian/poly. [Related commands:] "pair_coeff"_pair_coeff.html, "pair_style lubricate"_pair_lubricate.html, "pair_style lubricateU"_pair_lubricateU.html [Default:] The default settings for the optional args are flagHI = 1 and flagVF = 1.