diff --git a/doc/Manual.html b/doc/Manual.html index f6108a323d..3adb6bf047 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,478 +1,443 @@ - - - -LAMMPS Users Manual - - - - - - - - - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + LAMMPS Documentation — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

- -

LAMMPS Documentation -

-

28 Aug 2015 version -

-

Version info: -

-

The LAMMPS "version" is the date when it was released, such as 1 May + +

+
+
+ +
+ + + +
+
+
+ +

+

LAMMPS Documentation

+
+

10 Aug 2015 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 +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 +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 +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 +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 +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 -

-

-

-
  1. -Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +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/Manual.html.html b/doc/Manual.html.html new file mode 100644 index 0000000000..7957fdb51c --- /dev/null +++ b/doc/Manual.html.html @@ -0,0 +1,318 @@ + + + + +LAMMPS Users Manual + + + + + + + + + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ +
+ +

+ +

LAMMPS Documentation +

+

28 Aug 2015 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). +

+ +

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 +

+

+

+
  1. +Introduction + + +
  2. Getting started + + +
  3. Commands + + +
  4. Packages + + +
  5. Accelerating LAMMPS performance + + +
  6. How-to discussions + + +
  7. Example problems + +
  8. Performance & scalability + +
  9. Additional tools + +
  10. Modifying & extending LAMMPS + + +
  11. Python interface + + +
  12. Errors + + +
  13. Future and history + + + +
+ + + + + + + + diff --git a/doc/Manual.txt b/doc/Manual.txt index c59b8eda2b..b0857e6c32 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -28 Aug 2015 version :c,h4 +10 Aug 2015 version :c,h4 Version info: :h4 @@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: // comment + :numbered: Section_intro Section_start @@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` // comment -* :ref:`search` // comment +* :ref:`genindex` +* :ref:`search` END_RST --> diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 77995418d3..8a306ce57b 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -968,14 +968,14 @@ used if LA smd/ulsph/strain/rate smd/ulsph/stress smd/vol -temp/drude +tally -temp/eff +temp/drude +temp/eff temp/deform/eff temp/region/eff temp/rotate xrd -  diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 6f9eefc691..e2ab30d7ea 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -758,6 +758,7 @@ package"_Section_start.html#start_3. "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, "smd/ulsph/stress"_compute_smd_ulsph_stress.html, "smd/vol"_compute_smd_vol.html, +"tally"_compute_tally.html, "temp/drude"_compute_temp_drude.html, "temp/eff"_compute_temp_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html, diff --git a/doc/Section_modify.html b/doc/Section_modify.html index ffa54a0417..5f2be86a78 100644 --- a/doc/Section_modify.html +++ b/doc/Section_modify.html @@ -474,8 +474,8 @@ per-atom kinetic energy.

class. See compute.h for details.

--++ @@ -520,11 +520,21 @@ class. See compute.h for details.

- + + + +
init
restore_bias_all same as before, but for all atoms in group (optional)
memory_usage
pair_tally_callbackcallback function for tally-style computes (optional).
memory_usage tally memory usage (optional)
+

Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides *examples*_compute_tally.html for utilizing this mechanism.

@@ -1098,7 +1108,7 @@ the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
  • If you want your contribution to be added as a user-contributed -feature, and it’s a single file (actually a *.cpp and *.h file) it can +feature, and it’s a single file (actually a *.cpp and *.h file) it can rapidly be added to the USER-MISC directory. Send us the one-line entry to add to the USER-MISC/README file in that dir, along with the 2 source files. You can do this multiple times if you wish to @@ -1148,7 +1158,7 @@ directories under examples/USER for examples of input scripts other users provided for their packages.
  • If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp +its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index a5068f80fe..e3df8f59ce 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -275,8 +275,17 @@ remove_bias: remove velocity bias from one atom (optional) remove_bias_all: remove velocity bias from all atoms in group (optional) restore_bias: restore velocity bias for one atom after remove_bias (optional) restore_bias_all: same as before, but for all atoms in group (optional) +pair_tally_callback: callback function for {tally}-style computes (optional). memory_usage: tally memory usage (optional) :tb(s=:) +Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides {examples}_compute_tally.html for utilizing this mechanism. + :line 10.4 Dump styles :link(mod_4),h4 diff --git a/doc/Section_packages.html b/doc/Section_packages.html index d1730c62df..e66095d9b5 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -712,7 +712,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.

  • -h5md +lib/h5md USER-INTEL Vectorized CPU and Intel(R) coprocessor styles @@ -882,7 +882,21 @@ on how to build LAMMPS with both kinds of auxiliary libraries.

    -  +USER-TALLY +Pairwise tallied computes +Axel Kohlmeyer (Temple U) +compute +USER/tally + + + + + +        diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 8e01c6bbbb..768b9797d5 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -123,7 +123,7 @@ USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"c USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, - USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - -USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, h5md +USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - @@ -136,6 +136,7 @@ USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_st USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - +USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, - :tb(ea=c) :link(atc,http://lammps.sandia.gov/pictures.html#atc) diff --git a/doc/compute_tally.html b/doc/compute_tally.html new file mode 100644 index 0000000000..fe48bc13ce --- /dev/null +++ b/doc/compute_tally.html @@ -0,0 +1,266 @@ + + + + + + + + + + + compute force/tally command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute force/tally command

    +
    +
    +

    compute pe/tally command

    +
    +
    +

    compute stress/tally command

    +
    +

    Syntax

    +
    compute ID group-ID style group2-ID
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • style = force/tally or pe/tally or stress/tally
      • +
    • group2-ID = group ID of second (or same) group
      • +
    +
    +
    +

    Examples

    +
    compute 1 lower force/tally upper
+compute 1 left pe/tally right
+compute 1 lower stress/tally lower
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates properties between two groups of +atoms by accumulating them from pairwise non-bonded computations. The +two groups can be the same. This is similar to compute group/group only that the data is +accumulated directly during the non-bonded force computation. The +computes force/tally, pe/tally, stress/tally, and +heat/flux/tally are primarily provided as example how to program +additional, more sophisticated computes using the tally mechanism.

    +
    +

    The pairwise contributions are computing via a callback that the +compute registers with the non-bonded pairwise force computation. +This limits the use to systems that have no bonds, no Kspace, and no +manybody interactions. On the other hand, the computation does not +have to compute forces or energies a second time and thus can be much +more efficient. The callback mechanism allows to write more complex +pairwise property computations.

    +
    +

    Output info:

    +

    Compute pe/tally calculates a global scalar (the energy) and a per +atom scalar (the contributions of the single atom to the global +scalar). Compute force/tally calculates a global scalar (the force +magnitude) and a per atom 3-element vector (force contribution from +each atom). Compute stress/tally calculates a global scalar +(average of the diagonal elements of the stress tensor) and a per atom +vector (the 6 elements of stress tensor contributions from the +individual atom).

    +

    Both the scalar and vector values calculated by this compute are +“extensive”.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-TALLY package. It is only enabled +if LAMMPS was built with that package. See the Making LAMMPS section for more info.

    +

    Not all pair styles can be evaluated in a pairwise mode as required by +this compute. For example, 3-body and other many-body potentials, +such as Tersoff and +Stillinger-Weber cannot be used. EAM +potentials only include the pair potential portion of the EAM +interaction when used by this compute, not the embedding term. Also +bonded or Kspace interactions do not contribute to this compute.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_tally.txt b/doc/compute_tally.txt new file mode 100644 index 0000000000..bdd0385dc5 --- /dev/null +++ b/doc/compute_tally.txt @@ -0,0 +1,84 @@ +"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 + +compute force/tally command :h3 +compute pe/tally command :h3 +compute stress/tally command :h3 + +[Syntax:] + +compute ID group-ID style group2-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +style = {force/tally} or {pe/tally} or {stress/tally} +group2-ID = group ID of second (or same) group :ul + +[Examples:] + +compute 1 lower force/tally upper +compute 1 left pe/tally right +compute 1 lower stress/tally lower :pre + +[Description:] + +Define a computation that calculates properties between two groups of +atoms by accumulating them from pairwise non-bonded computations. The +two groups can be the same. This is similar to "compute +group/group"_compute_group_group.html only that the data is +accumulated directly during the non-bonded force computation. The +computes {force/tally}, {pe/tally}, {stress/tally}, and +{heat/flux/tally} are primarily provided as example how to program +additional, more sophisticated computes using the tally mechanism. + +:line + +The pairwise contributions are computing via a callback that the +compute registers with the non-bonded pairwise force computation. +This limits the use to systems that have no bonds, no Kspace, and no +manybody interactions. On the other hand, the computation does not +have to compute forces or energies a second time and thus can be much +more efficient. The callback mechanism allows to write more complex +pairwise property computations. + +:line + +[Output info:] + +Compute {pe/tally} calculates a global scalar (the energy) and a per +atom scalar (the contributions of the single atom to the global +scalar). Compute {force/tally} calculates a global scalar (the force +magnitude) and a per atom 3-element vector (force contribution from +each atom). Compute {stress/tally} calculates a global scalar +(average of the diagonal elements of the stress tensor) and a per atom +vector (the 6 elements of stress tensor contributions from the +individual atom). + +Both the scalar and vector values calculated by this compute are +"extensive". + +[Restrictions:] + +This compute is part of the USER-TALLY package. It is only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Not all pair styles can be evaluated in a pairwise mode as required by +this compute. For example, 3-body and other many-body potentials, +such as "Tersoff"_pair_tersoff.html and +"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html +potentials only include the pair potential portion of the EAM +interaction when used by this compute, not the embedding term. Also +bonded or Kspace interactions do not contribute to this compute. + +[Related commands:] + +{compute group/group}_compute_group_group.html, {compute +heat/flux}_compute_heat_flux.html + +[Default:] none + diff --git a/doc/genindex.html b/doc/genindex.html index 8462cb4f0f..7ef4cf69a7 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -440,6 +440,10 @@ +
    compute force/tally +
    + +
    compute group/group
    @@ -535,12 +539,12 @@
    compute pressure
    + +
    compute property/atom
    -
    -
    compute property/chunk
    diff --git a/doc/searchindex.js b/doc/searchindex.js index 883c7a7f7e..52484df8c3 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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afterward:3,afterword:41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,190,215,230,277,332,345,356,406,407,450,452,453,455,457,462,469,471,481,483],against:[11,12,13,64,216,356,420,421],aggreg:[6,12,65,68,69,79,92,108,115,230,246,289,291,304,450,482],aggress:[230,469],agilio:[9,13],agre:[3,8,184,354,363,394,421],agreement:[5,7],ahd:391,ahead:325,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:189,akohlmei:[7,9,13,191,231],aktulga:[7,9,284,421],al2o3_001:[118,292],al3:163,ala:237,alain:9,alat:[272,408],alb:[418,440,442],albeit:290,albert:9,alchem:[87,158],alcohol:321,alcu:[362,367],alcu_eam:418,alderton:380,alejandr:[250,251],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,190,199,209,212,215,237,239,240,262,274,291,294,313,314,318,321,326,352,353,354,358,361,385,407,425,427,450,452,469],alia:12,alias:[1,347],aliceblu:190,align:[6,12,29,41,71,166,184,205,209,232,349,455,458,476],alkali:385,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,191,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,243,245,246,248,250,251,252,253,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,302,303,305,306,307,308,309,310,313,314,315,316,317,318,319,320,321,323,324,325,326,327,328,329,330,331,332,333,336,341,344,345,346,347,348,349,351,354,355,356,357,358,360,361,362,363,364,366,367,368,370,371,372,373,374,376,377,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,401,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,470,472,473,474,476,480,481,482,483,484,485],allen:[29,87,380,388],allentildeslei:87,allign:3,allindex:330,alloc:[3,5,6,8,9,11,12,60,224,320,355,357,361,416,421,455,463],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,189,190,191,193,194,196,198,199,200,202,203,204,205,206,207,209,211,212,213,214,215,216,220,221,224,226,227,228,229,231,234,237,240,241,245,247,250,251,272,276,278,279,280,281,285,291,292,294,295,297,298,302,306,313,314,315,316,318,319,320,321,322,323,329,331,333,341,346,347,349,354,355,356,357,360,361,364,367,368,369,370,371,372,377,383,385,389,390,391,392,401,406,407,412,418,421,422,425,427,436,445,447,450,453,455,457,458,459,460,461,462,465,467,468,469,472,473,474,481,482],almost:[2,3,12,60,232,281,318,347,358,361,436],alo:377,alon:[6,7,212,287,420,421,453],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,189,212,232,237,238,242,247,249,281,291,294,295,299,303,304,313,317,318,324,327,329,349,352,353,354,356,377,380,389,392,395,397,401,408,420,421,439,455,458,465,466,481],alonso:[409,410],alpha:[6,12,51,194,237,273,281,286,354,362,365,368,377,381,383,384,386,391,396,397,408,413,417,441,443,473,476],alpha_:443,alpha_c:405,alpha_i:[428,443],alpha_ialpha_j:443,alpha_lj:405,alphabet:[2,3,22,37,44,55,63,172,183,193,333,341,355,374,437,455],alphanumer:[3,63,193,280,288,331,355,481],alreadi:[3,7,8,12,42,164,165,167,188,198,202,205,206,209,211,215,241,279,281,306,329,355,356,381,390,392,399,407,436,445,448,451,455,456,460,465,481],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,191,193,194,195,196,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,221,224,225,226,227,228,230,231,234,235,236,237,247,248,250,251,252,253,254,255,256,261,264,265,267,268,269,270,272,273,274,276,277,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,299,300,303,304,306,309,310,311,312,313,317,318,319,320,322,324,327,329,331,333,338,341,344,346,347,349,350,351,354,355,356,357,358,360,361,367,371,372,374,378,379,380,381,383,384,385,388,389,391,392,393,401,405,406,408,412,414,416,417,418,419,422,423,425,431,432,434,435,436,437,438,439,440,441,442,443,450,452,453,454,455,456,457,458,459,460,462,463,464,465,467,468,469,470,473,474,475,476,477,479,480,481,482,483,485],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,15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7,219,226,227,232,234,235,240,246,250,255,256,267,268,270,273,277,282,288,289,291,292,295,303,304,306,308,309,310,311,313,314,316,323,327,332,349,355,366,384,385,388,389,395,406,407,408,409,410,438,440,441,442,444,458,465,476,481],centimet:480,central:[3,61,70,76,77,116,122,140,240,272,294,304,355,414,420,421,455],centro:[],centroid:[3,274,444,465],cerda:346,ceriotti2:228,ceriotti:[13,228,233],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,189,201,202,203,204,205,206,207,212,224,225,291,293,307,320,331,338,345,357,392,412,421,443,457,461,476,481],certainli:232,cerutti:347,cfg:[3,6,7,13,187,188,189,190,191],cfile:421,cfl:[128,296],cfor:295,cg_type:423,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:294,ch2lmp:[],ch3:294,ch5md:188,chain3:357,chain:[],challeng:[6,295],chalopin:286,champaign:[231,346,347,406],chandler:[362,383],chandrasekhar:[6,397],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,191,193,194,195,196,197,199,200,205,206,208,209,210,211,212,213,214,215,216,220,221,223,225,228,230,231,232,234,236,237,238,240,246,247,248,250,251,252,253,254,255,256,262,267,268,269,270,272,273,277,278,280,281,285,288,289,290,291,293,294,295,306,309,310,311,312,314,315,316,317,318,319,321,324,327,329,347,352,354,356,359,361,381,385,389,392,406,407,408,412,420,421,437,450,451,452,453,455,456,457,458,459,460,461,463,464,465,466,467,470,473,477,479,480,481,482,483],change_box:[],changeabl:187,channel:[4,196],chapter:[274,347],charact:[2,3,6,12,38,41,56,63,184,187,189,190,191,193,209,280,288,331,355,360,385,396,418,420,421,439,452,453,457,462,463,481,483,484,485],character:[6,67,70,116,140,428,450,469],characterist:[235,306,315],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,191,193,194,195,200,216,221,226,280,282,283,284,288,308,321,346,347,355,368,370,376,377,379,380,383,385,386,392,397,401,405,415,420,421,437,442,443,445,447,448,455,456,460,465,467,476,480,481],charmm2lammp:13,charmm:[],chartreus:190,cheap:306,cheaper:[220,388,422],check:[3,6,8,11,12,15,17,39,41,71,91,184,200,205,209,210,211,216,223,226,232,233,290,294,306,314,316,321,329,331,345,354,355,356,357,358,361,382,393,396,412,421,436,450,452,453,455,463,469,472,473],checkf:184,checkqeq:421,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,214,219,227,228,235,237,249,250,251,268,269,274,278,281,283,291,295,306,309,310,313,314,315,316,323,332,340,342,346,347,353,356,363,368,372,373,376,377,378,380,381,385,387,388,390,391,397,401,402,405,408,411,412,415,436,443,464,467,469,476],chemic:[9,118,158,163,187,199,200,226,282,287,288,313,347,420,421,432],chemistri:[9,281,282,284,367,385,420,421],chen:318,cheng:376,chenoweth:[420,421],chenoweth_2008:[420,421],chi:[92,153,186,272,282,284,386,388,482],chiefli:419,child:8,chip:[7,12,17,361,468],chipot:214,chiral:340,chmod:[11,12],cho:408,chocol:[7,190],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,202,205,206,209,212,215,216,228,234,237,248,250,274,282,291,313,341,347,352,353,356,358,361,392,405,412,416,455,464,465,468,469,475,476,480],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,189,210,211,212,213,216,223,234,237,248,250,252,253,254,255,256,278,306,310,324,346,347,353,445,450,452,464,470],chose:[440,442],chosen:[2,3,6,12,17,140,164,167,176,184,189,195,200,213,216,223,226,227,235,237,248,250,254,274,277,288,306,310,313,314,319,321,322,328,347,348,353,361,385,389,395,396,399,423,440,450,464,469,476],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,202],chute:[4,10,229],ciccotti:294,cieplak:[6,170,467],cii:203,cij:203,circl:302,circular:[3,6,143,185],circumst:18,circumv:286,citat:[],cite:[3,7,8,12,234],cko:2,cl1:163,clarendon:[29,380],clarifi:[7,440,442],clariti:331,clark:415,class2:[],classic:[0,3,5,6,7,8,9,224,274,281,286,318,342,385],classifi:[9,437],claus:453,clean:[6,12,14,15,17,463],cleanli:[454,484],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:459,click:[2,11,22,37,44,55,164,172,183,189,231,333,341,356,374,437],client:[231,233],climb:[249,356,469],clinic:[7,13],clo:[153,186,482],clock:[12,450,469],clockwis:324,close:[3,6,11,12,13,39,41,67,141,167,187,211,212,213,228,235,237,250,268,291,294,324,327,345,347,350,352,353,356,361,363,367,377,378,408,412,424,426,442,459,465,476,478],closer:[3,41,116,162,186,187,209,213,217,315,356],closest:[211,272,291,321,388,422,436,445],cloud:476,clovertown:18,clsuter:72,clump1:[276,291],clump2:[276,291],clump3:[276,291],clump:291,cluster:[],clutter:[3,9],cmap:455,cmatrix:228,cmax:408,cmd:[11,12,274,466],cmin:408,cmm:[],cn1:203,cn2:203,cna:[],cnn:203,cnr:[9,13],cnt:[392,459],co2:[40,163,294,355],coars:[7,9,29,36,40,54,176,276,291,306,390,423,467],coarser:[347,481],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,332,333,338,374,392,396,412,425,427,429,455,457],coeffcient:455,coeffici:[],coefficienct:381,coefficient0:383,coefficient1:383,coeffieci:[6,365],coeffincientn:383,coexist:[9,226,385],cohes:[6,386,408],coincid:[122,327,372,406,407,450],colberg:188,cold:[6,149,230,357,476],coldest:314,coleman8:9,coleman:[9,118,163,292],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,190,202,214,240,246,276,286,289,291,329,346,355,357,375,395,455,462,468,474,485],collid:[220,306,328],colliex:163,collinear:[3,276],collis:[3,237,306,324,328,382,389,448],colllis:306,colloid:[],colombo:39,colon:[191,329,456],color1:190,color2:190,color:[3,9,41,187,189,190,209,227,281,286],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,190,193,201,202,203,204,205,206,207,240,247,248,281,291,307,308,318,328,387,391,420,421,456,470,472,481],colvar:[],colvarmodul:12,com:[],comamnd:215,comand:[212,457],comannd:361,comb3:[],comb:[],comb_1:283,comb_2:283,combiant:378,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,189,199,204,231,240,250,274,280,310,319,327,330,332,346,347,349,353,361,375,377,378,385,386,392,404,405,428,438,440,442,447,458,463,476,481],come:[],comfort:[12,13],comm:[0,3,12,61,73,188,231,233,234,347,356,361,381,412,417,439],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,235,291,318,355,356,362,383,384,386,396,408,414,421,428,438,439,440,441,442,452,453,455,476,481],commerci:7,commmand:[3,6,12,59,107,269,449,450,452,469,484],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,189,191,342,390,399,428,440,442,455,458,467],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,189,190,209,210,211,213,214,215,231,233,237,239,240,241,250,273,280,282,283,284,291,306,318,329,346,357,358,359,361,382,416,452,453,457,464,465,483,485],communc:346,comp:[7,188,233,234,294,347,356,385,412,417,422,435,439,441],compact:[63,193,374,437],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,190,219,282,329,331,346,347,354,356,408,450,469,470,476,480],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,332,333,341,373,437],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,191,195,201,202,203,204,205,206,207,209,273,285,310,313,320,323,326,346,361,393,412,439,452,453,481],compens:[6,210,211,289,357,385],compet:317,competit:347,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,189,191,231,317,347,361,455,456,460],compl:17,complain:[12,17],complement:408,complementari:[7,377,397],complet:[3,6,9,12,15,41,59,71,190,205,209,214,240,274,277,280,306,317,319,331,345,356,361,386,425,427,444,450,455,460,463,467,469,472,476,481],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,237,302,327,344,356,385,439,453,455,458,481],compli:[313,317],complic:[6,7,9,12,13,200,226,453],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,189,190,196,197,201,202,203,204,205,206,207,208,212,213,215,216,221,224,229,233,234,237,240,242,246,247,249,250,251,254,255,256,267,268,270,271,273,274,275,278,289,291,293,294,295,299,300,303,306,309,310,311,313,320,321,326,327,328,346,349,353,354,355,356,361,381,385,389,406,407,425,427,428,455,456,465,473,481,482],componenet:6,composit:[6,200,237,383],compound:[376,385,386],compres:[71,114,202],compress:[3,6,9,12,59,71,114,167,187,189,190,202,215,248,254,278,281],compris:[40,327,395,422,444],compton:[118,163],comptu:[3,6],compuat:347,comput:[],computation:[3,6,210,211,318,367],computational:476,compute_arrai:8,compute_fep:[195,405],compute_group_group:226,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,292],compute_scalar:8,compute_temp:8,compute_ti:195,compute_vector:8,compute_xrd:163,concaten:[2,3,484],concav:327,concentr:383,concept:[6,144,154,202,464],conceptu:[3,6,71,152,213,215,356,377,392,408,460],concern:[6,73,87,188,227],concis:[11,317],conclud:12,concret:8,concurr:[9,16,347],conden:[318,440,442],condens:[6,146,318,363,379,383,397],condit:[],conducit:6,conduct:[],cone:458,confid:[3,469],config:[12,187,452],configfil:214,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,189,193,213,214,215,216,220,226,233,234,262,274,282,317,344,354,356,363,367,384,408,438,440,442,450,455,457,458,469],confin:[455,469],conflict:[3,12,40,412,453],conform:[3,6,13,59,212,213,249,290,295,317,340,356,385,467],confus:3,conjuct:381,conjug:[7,8,234,353,385,420,421],conjunct:[6,7,71,86,87,114,147,152,158,164,168,190,194,195,234,237,241,262,277,278,282,283,284,286,291,306,314,321,326,346,347,356,368,370,374,377,381,385,391,397,412,415,423,443,455,458,462,476,485],connect:[3,6,87,149,167,212,231,276,291,294,303,356,378,389,436,442,452,453,459,476],conput:3,consecut:[3,11,12,39,71,164,190,194,195,216,231,232,377,397,401,450,456,458],consequ:[1,6,318,396,469],conserv:[3,193,200,212,219,220,227,230,234,236,237,241,246,248,250,262,291,294,309,310,314,321,322,326,356,380,381,389,403,464,469],consid:[6,9,70,71,78,87,115,149,150,167,187,190,194,195,201,203,205,209,211,212,216,238,251,273,291,313,314,317,318,321,347,374,385,392,421,422,436,450,451,453,456,457,458,460,463,465,473,476,481],consider:[6,8,234,235,309,310,311,361,464],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,191,196,197,202,215,216,219,221,224,227,234,235,236,247,250,252,253,254,255,256,257,258,260,261,262,263,265,266,267,268,269,270,278,281,286,288,290,291,309,310,311,312,322,346,347,349,355,356,361,363,367,369,375,377,385,388,392,406,407,408,412,422,425,427,439,445,453,455,456,458,459,460,467,476,481],consistent_fe_initi:199,consit:291,constant:[],constitu:[3,6,240,291,323,327,375,422],constitut:[425,427],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,193,202,216,226,227,232,240,244,276,277,289,291,294,304,314,321,354,355,385,460,467,476],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,163,213,250,273,290,327,357,361,380,412,436,438,439,458,459,481],constructor:8,consult:421,consum:[1,286,416,481],consumpt:344,contact:[],contact_stiff:[424,426],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,189,190,191,193,194,195,199,201,202,203,204,205,206,207,209,214,216,221,228,232,233,234,235,237,248,262,272,273,276,277,279,281,284,288,291,292,296,306,313,317,318,327,328,331,345,347,355,356,359,360,362,363,364,367,376,377,380,383,384,385,392,393,408,414,418,419,420,421,428,438,439,440,441,442,443,450,451,452,453,455,456,457,458,460,462,464,467,469,472,473,476,481,483,485],content:[12,18,421,471,473],context:[3,6,8,12,17,117,190,210,211,216,276,288,322,353,447,455,462,471,480,481,482],contibut:70,contigu:452,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,190,193,194,195,200,202,203,204,205,206,207,209,212,213,214,215,216,226,227,228,230,231,232,234,235,236,242,247,248,250,252,253,254,255,256,267,268,269,270,275,277,280,281,291,292,295,305,306,308,315,316,318,324,327,331,345,360,361,367,381,382,399,402,420,421,422,425,427,441,450,453,455,457,458,463,469,472,473,481,483],continuum:[6,7,9,199,318,425,427],contour_integr:199,contract:[59,213,215,250,278,291],contradictori:3,contrain:294,contraint:262,contrari:[228,235],contrast:[1,6,42,55,64,149,215,329,425,427,447,484],contrib:318,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,195,200,201,202,203,204,205,206,207,213,226,234,237,240,241,245,251,268,269,276,277,285,288,291,292,294,320,346,354,356,364,381,382,383,385,392,406,407,412,420,421,467,473,476],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,173,187,189,193,199,200,209,213,214,215,230,231,234,235,250,252,253,254,255,256,278,283,291,297,298,309,310,311,318,322,344,346,358,385,388,420,421,424,426,438,442,450,452,464,470,471],control_typ:199,controlfil:421,convect:91,conveni:[6,12,29,187,191,207,292,349,428,481],convent:[3,8,9,29,175,182,183,190,290,303,330,383,385,481],converg:[3,6,41,88,187,189,191,196,209,212,213,221,224,254,281,283,286,290,294,352,353,354,356,376,377,397,450,462,469],convers:[3,8,140,189,190,200,203,278,346,377,378,379,385,397,401,405,415,453,469,480],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,189,190,207,248,329,332,334,337,340,349,356,362,383,440,442,448,453,455,456,457,462,472,476,480,481,483,485],convex:327,convinc:[7,12],cook:9,cooki:7,cool:[7,154,230,289],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,202,205,206],coord2:[3,114,202,205,206],coord3:[3,114,202,205,206],coord:[],coordiat:354,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,191,193,196,201,202,204,205,206,209,210,211,212,213,214,215,216,219,221,222,224,226,229,230,231,232,233,234,235,247,249,250,252,253,255,256,268,271,272,273,276,277,278,288,289,291,293,294,295,300,303,304,305,306,308,316,317,318,325,326,328,329,349,354,355,356,361,362,363,366,384,450,455,456,458,460,463,465,469,476,481,482],coordn:[114,202],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,189,318,356,374,420,453],copper:448,coproccesor:16,coprocessor:[1,4,7,9,16,17,361,468],coproprocessor:17,copy_arrai:8,copyright:[7,8,276],coral:190,core:[],core_shel:146,coreshel:[6,9,370,377,379],cornel:[6,170,467],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,189,327,328,349,444,455],cornflowerblu:190,cornsilk:190,corpor:16,corr:376,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,189,215,228,234,250,251,268,276,278,281,317,323,327,346,356,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,455,470,473,476],correction_max_iter:199,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,190,196,216,221,224,235,244,250,251,284,291,294,303,305,324,327,356,357,361,379,407,452,453,455,465,480,482],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,189,190,194,195,196,202,204,205,206,208,211,213,215,222,224,225,229,234,237,238,246,247,248,250,252,253,254,255,256,257,262,265,267,268,270,273,274,278,283,291,293,294,309,311,313,322,323,324,326,327,328,330,332,333,334,335,336,337,340,342,347,351,353,355,356,362,363,365,368,369,370,371,372,373,374,375,376,377,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,412,413,414,415,417,418,420,421,422,423,428,429,438,439,440,441,442,444,446,447,448,450,452,453,455,456,458,468,469,470,472,473,476,481],correspondingli:[406,407,464],cosin:[],cosineshift:27,cosmo:[228,233],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,189,190,202,205,206,209,210,211,223,250,283,318,346,347,359,377,397,401,412,438,452,464],costheta0:[438,440,442],costheta:418,costli:[11,88,228,357],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,189,190,194,195,200,202,203,205,209,215,224,233,280,281,282,286,289,291,293,306,307,313,317,318,319,323,327,329,331,338,343,345,352,354,357,361,364,387,391,392,420,421,451,452,453,455,457,459,462,463,471,476,481,482],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,282,284,319,346,347,354,361,368,370,371,372,373,376,377,378,379,380,385,389,390,392,397,401,405,412,415,420,421,423,437,442,443,447,460,467,473,476,480],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,196,197,200,202,204,205,206,208,209,216,221,223,226,232,250,262,277,294,309,310,327,347,354,355,356,358,361,387,391,412,473,481],counter:[324,450,461,463,469],counterbal:230,counterpart:[187,291,450],counterproduct:18,coupl:[],courant:296,cours:[3,8,126,128,158,187,194,195,227,290,303,317,323,325,326,328,329,347,406,429,452,455,468,476,481,483],coval:[6,29,385,408,476],covari:228,cover:[6,71,184,190,199,237,385,395,444],coverag:[71,205],cpc:233,cpp:[1,3,6,8,9,11,12,13,87,187,194,195,224,294],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,190,193,219,235,319,344,347,361,374,437,450,468,469,472,473,474],cpuremain:473,cr2:163,cr3:163,crack:[4,357],crada:[5,7],crai:[5,7,13,18,187],crash:[3,12,357,476],craympi:361,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:199,create_faceset:199,create_group:188,create_nodeset:199,createatom:[],creation:[],crimson:190,critchlei:276,criteria:[3,116,165,189,190,210,211,212,245,354,417,444,457,460,481],criterion:[12,41,121,162,164,167,200,209,212,226,262,283,296,324,329,354,356,376,385,389,460,469,470],criterioni:469,critic:[48,49,248,313,318,354],cross:[3,12,22,71,89,143,172,187,189,201,205,211,215,247,249,268,291,299,303,305,314,321,333,349,356,372,381,382,383,390,391,392,397,399,401,418,423,425,427,440,442,455,459,465,483],crossov:1,crossterm:455,crozier:[0,7,13],crucial:281,crystal:[4,6,13,73,272,273,316,357,459,473,476],crystallin:[6,273,349,441,476],crystallis:313,crystallogr:[118,163],crystallograph:[349,473],crystallographi:[118,163,349],cs1:163,cs_chunk:6,cs_im:[40,455],cs_re:[40,455],csanyi:[140,419,428],cscl:408,csequ:6,csh:[11,12,374],cshrc:[11,12],csic:[384,438,440,442],csinfo:6,csisi:[384,438,440,442],csld:[],cst:383,cstherm:6,cstyle:452,csvr:[],ctcm:[362,383],ctemp_cor:219,cterm:295,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:408,cube:[6,41,162,167,209,219,327,349,476],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:367,cummul:[3,6,207,210,211,212,214,223,228,234,236,306,309,310,311,312,314,321,391,473],cumul:[6,200,202,204,205,206,220,226,234,248,250,254,262,291,292,356],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,191,194,195,199,200,202,205,206,207,209,210,211,212,213,214,215,216,220,221,224,226,228,231,232,234,240,247,250,251,255,256,262,267,268,270,276,282,283,285,288,289,290,291,294,295,296,297,298,299,300,302,304,305,306,309,310,311,317,318,321,322,323,324,325,326,328,329,331,344,345,346,347,350,351,353,354,355,356,361,367,374,376,380,383,385,386,389,393,396,406,407,408,409,410,412,418,420,421,424,425,426,427,429,440,442,443,445,450,451,452,453,455,456,457,458,459,461,462,463,465,467,469,470,472,473,481,482,483,484,485],curv:[6,164,226,273],curvatur:[388,422,448],custom:[],cut0:453,cut1:464,cut2:464,cut:[],cuthi:[272,284],cutinn:[369,406,407],cutlo:[272,284],cutmax:418,cutoff1:[373,380,397,401,405,415,423],cutoff2:[368,370,371,373,379,380,397,401,405,415,423],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,211,212,217,272,281,282,284,286,288,291,306,319,323,327,329,346,347,354,357,358,359,361,362,363,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,453,457,460,464,476],cutoffa:384,cutoffc:384,cuu3:383,cval:163,cvd:313,cvel:295,cvff:[],cwiggl:[3,247,323,326,328,481],cyan:[2,189,190],cycl:[3,226,248,250,251,254],cyclic:[3,184],cygwin:12,cylind:[3,4,189,232,277,324,327,458],cylindr:[6,232,303,324],cypress:361,cyrot:367,cyrstal:273,d3q15:237,d3q19:237,d_double_doubl:15,d_e:318,d_flag2:280,d_flag:280,d_name:[113,187,280,308,465],d_single_doubl:15,d_single_singl:15,d_sx:280,d_sy:280,d_sz:280,daan:316,dai:12,daili:12,daivi:268,damag:[],dammak:286,damp:[3,6,193,198,234,235,236,241,250,251,254,278,281,286,291,309,310,322,324,325,353,354,356,368,370,372,377,380,385,389,397,405,415,423,437,443,469,476],damp_com:235,damp_drud:235,dampen:[291,476],dampflag:[324,389],dan:17,danger:[3,12,226,329,381,473],dangl:167,daniel:9,darden:[347,380],darkblu:190,darkcyan:190,darken:189,darkgoldenrod:190,darkgrai:190,darkgreen:190,darkkhaki:190,darkmagenta:190,darkolivegreen:190,darkorang:190,darkorchid:190,darkr:190,darksalmon:190,darkseagreen:190,darkslateblu:190,darkslategrai:190,darkturquois:190,darkviolet:190,dasgupta:282,dash:[389,472],dat:[6,91,184,199,451],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,292],dataset:292,datatyp:3,date:[0,6,12,13,420,421,481],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,203],davi:323,david:[9,19,346,347,440,442],daw:[383,418],dbg:14,dcd:[3,6,7,187,188,189,190,191,274,456,460],ddim:186,deactiv:405,dealt:233,debug:[6,7,11,12,13,14,17,118,122,163,164,274,279,344,346,361,393,412,445,453,454,457,462,465,472,481],deby:[],decai:[377,448],decid:[3,6,12,16,71,247,280,291,319,470],decipher:349,declar:188,declin:306,decod:189,decompos:[87,428],decomposit:[3,5,7,18,62,199,274],decoupl:[6,476],decreas:[3,187,196,197,212,215,221,224,234,317,346],decrement:295,deepli:343,deeppink:190,deepskyblu:190,def:[12,13,453],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,190,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,219,220,221,224,225,226,229,232,233,234,235,236,237,245,247,249,250,251,252,253,254,255,256,258,259,260,263,265,266,267,268,269,270,272,273,274,276,277,278,280,282,284,289,291,292,293,294,296,300,304,306,308,309,310,311,312,314,315,316,318,320,321,323,324,325,326,327,328,329,331,332,333,334,335,336,337,340,341,342,344,346,347,349,351,353,354,355,356,357,358,359,360,361,363,364,365,366,368,369,370,371,372,373,374,375,377,378,380,381,382,384,385,387,388,389,390,391,392,393,395,397,398,399,400,401,402,403,404,405,406,407,411,412,413,414,415,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,453,455,456,458,459,460,461,464,465,466,467,469,470,472,473,476,477,478,479,480,481,482],definit:[2,3,6,8,12,13,78,80,116,140,190,202,203,204,205,206,207,215,232,254,292,308,320,323,326,328,330,341,344,355,364,367,375,385,395,418,425,427,428,444,453,455,457,464,466,480,481],defint:473,deform:[],deg2theta:163,deg:476,degener:[3,276],degrad:[8,18,273,347,464],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,189,202,212,219,226,228,229,234,235,240,250,251,254,255,256,267,268,270,274,276,290,291,294,309,310,311,316,332,334,337,340,342,354,380,383,391,465,473,476,482],degress:[144,202],del:469,delai:[3,6,12,357,382,473],deleg:392,delet:[2,3,7,8,12,54,57,60,63,162,167,168,193,202,203,204,205,206,207,210,212,223,226,250,292,309,310,329,331,345,355,357,360,412,455,456,458,466,467,472,477,479,481,482],delete_atom:[],delete_bond:[],delete_el:199,deli:186,delimit:[453,481],deloc:[251,385],delr:408,delt_lo:469,delta:[],delta_1:367,delta_3:367,delta_7:367,delta_conf:3,delta_ij:[408,418],delta_mu:[3,200],delta_pi:367,delta_r:418,delta_sigma:367,delx:186,delz:186,demand:286,demo:11,demon:271,demonstr:[281,408],den:277,dendrim:391,denniston:[9,237,239,240,241,273],denomin:[7,169],denot:[118,219,235,273,284,286,377,390,392,421,425,427],dens:[71,212,385],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,194,195,199,202,205,206,209,215,224,237,240,243,244,273,277,278,282,318,323,349,351,355,362,367,383,408,409,410,418,422,431,433,434,435,455,464,465,473,480],density_continu:427,density_summ:427,depart:[0,7],departur:[248,281],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,190,193,194,195,196,197,200,202,204,205,207,208,209,211,213,221,222,225,228,229,230,232,234,235,237,239,240,247,250,252,253,254,255,256,257,265,267,268,270,272,283,286,288,291,293,294,300,306,309,310,311,313,315,317,318,320,322,323,326,327,328,329,331,332,333,334,335,336,337,340,342,347,349,354,355,357,358,359,361,362,363,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,408,409,411,413,414,415,417,418,420,421,422,423,428,429,437,438,439,440,441,442,443,444,446,447,448,450,452,455,457,458,461,465,467,469,472,473,475,481,482],dependend:6,depflag:12,dephas:[450,469],depos:216,deposit:[],deprec:282,depth:[51,143,189,318,388,422],dequidt:9,der:[87,107,375,376,405,420,421,447,476],deriv:[6,7,8,38,56,63,87,140,158,184,203,213,215,226,234,247,250,252,253,254,255,256,272,278,282,286,315,316,318,323,324,327,353,355,363,367,375,380,385,386,390,399,403,404,408,420,421,437,439,447,476],derjagin:447,derlet:272,descend:190,descent:[7,353],descib:[40,282],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,188,193,194,195,202,203,204,205,206,207,209,212,213,214,215,216,218,219,227,228,231,232,233,234,235,236,237,239,240,241,245,249,250,251,254,261,269,272,274,279,280,281,282,283,284,291,295,303,306,307,308,309,310,311,312,313,314,315,316,321,323,324,326,331,346,347,349,352,353,354,355,356,360,363,364,366,368,369,370,372,373,374,375,376,377,380,383,385,386,388,389,390,392,397,398,399,400,401,402,403,404,405,406,407,408,411,417,418,419,420,421,422,423,428,429,436,437,438,439,440,441,442,443,446,447,448,450,452,453,455,456,458,459,465,468,469,472,481,482,483],descript:[],descriptor:[140,187,393],deserno:347,design:[0,3,6,7,8,9,11,13,14,15,17,118,146,149,163,199,212,218,219,250,251,272,273,292,313,318,364,365,366,369,372,377,379,385,405,406,407,409,410,418,421,439,464],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,200,202,207,213,215,224,226,227,234,235,236,240,250,268,276,277,278,279,282,286,291,294,306,309,310,311,312,317,324,338,343,346,347,349,352,354,355,356,381,383,391,406,407,438,440,442,451,452,453,455,459,464,469,470,472,473,481,482,483],desk:7,desktop:[4,6,7,10,12,17,189],despit:476,destabil:367,destre:340,destroi:[11,39,210,211],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,189,190,193,194,195,199,202,203,204,205,207,209,211,212,213,214,215,216,224,226,227,228,229,231,232,234,236,237,241,247,248,249,250,251,252,253,254,255,256,260,262,267,268,269,270,273,276,277,278,280,281,283,284,285,291,294,306,309,310,311,312,313,314,316,317,318,319,320,321,322,329,331,333,341,346,347,350,354,355,357,358,361,362,363,364,366,367,369,371,372,373,374,375,376,377,380,381,385,386,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,408,411,412,417,420,421,422,428,429,437,444,446,447,453,455,456,457,458,460,461,464,465,467,470,473,474,481,482,485],detect:[2,3,12,61,63,86,225,277,317,356,376,391,396,450,452,455,466,469,481],determ:361,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,189,190,191,192,196,197,198,201,202,203,204,205,206,207,208,209,213,215,216,219,221,226,229,230,232,234,235,240,245,247,248,250,255,256,267,268,270,272,274,278,281,288,289,290,291,292,293,296,298,300,306,309,310,311,313,319,320,323,324,325,326,327,328,329,341,346,347,349,355,357,358,361,363,364,371,376,380,382,383,387,389,392,393,401,408,412,421,422,436,439,443,447,452,455,456,458,460,462,465,469,471,472,474,480,481,482],detil:108,devan:[9,423],devanathan:442,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,231,254,276,281,282,285,363,367,385,410,457],devemi:9,deviat:[248,254,272,387],deviator:9,devic:[1,3,12,15,17,231,361],device_typ:361,devin:[283,376],devis:410,dfactor:189,dff:476,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,347],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,285],dhi:[59,186,215,277],dhug:[248,281],dhugoniot:[248,281],dia:408,diagnost:[],diagon:[3,6,83,140,141,213,250,278,291,321,425,427],diagonalstyl:428,diagram:[41,118,163,183,209,274],diallo:391,diam:[189,190,277,355],diamet:[3,6,40,113,164,187,189,190,194,195,234,277,291,306,322,324,355,375,388,389,395,399,422,444,447,455,456,465],diamond:[349,385,408],diamter:[40,277],dick:6,dicsuss:247,dictat:[200,248],did:[3,12,354,381,382,383,389,412,440,442,463],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,160,320,346],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,142,143,144,145,147,150,151,152,153,154,156,157,158,164,165,167,172,183,184,186,187,189,190,193,195,198,200,202,204,209,210,211,212,213,214,215,219,225,226,227,228,229,230,231,234,235,237,247,250,251,252,253,255,256,258,260,263,265,266,267,270,272,274,276,278,281,282,283,286,289,291,294,295,303,304,306,309,310,311,314,315,316,318,321,322,323,324,327,331,332,341,343,345,346,347,349,350,352,353,355,356,358,359,360,361,362,363,367,371,372,374,375,376,381,383,385,388,389,390,392,395,397,398,400,401,408,409,410,411,412,414,418,420,421,422,423,424,425,427,428,429,437,438,439,440,442,444,447,448,449,450,452,453,455,457,458,459,460,463,464,465,467,469,470,472,473,474,476,480,481,482,483],differenti:[1,3,6,29,184,346,377,418,441],difficult:[213,274,361,391,464],difficulti:[294,420],diffract:[],diffus:[],digit:[2,3,190,331],dih_table1:184,dih_table2:184,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:211,dihydrid:385,dij:294,dilat:[],dim1:3,dim2:3,dim:[3,59,71,142,145,146,147,150,151,152,153,154,156,164,186,205,215,232,324,349,408,458,480,481,482],dimdim:481,dimems:273,dimens:[],dimension:[3,39,112,118,140,142,144,145,146,147,150,151,152,153,154,156,163,185,202,205,249,273,318,349,352,356,418,455,465],dimensionless:[105,121,122,124,127,129,131,136,140,318,347,428,447],dimentionless:135,dimer:[6,291,408],dimgrai:190,dimstr:[41,209],dinola:[278,309],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,187,308,476],dir1:466,dir2:466,dir:[1,3,4,8,11,12,248,272,281,305,418,420,421,453,466,481],dirac:140,direc:418,direct:[],directli:[3,6,8,9,11,12,87,113,140,187,188,189,196,221,228,232,237,273,292,310,322,324,325,326,327,349,353,361,362,363,368,370,371,377,380,383,385,397,401,412,415,423,436,453,465,466,467,473,481],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,191,214,233,276,282,285,302,306,315,316,356,360,362,363,367,374,376,377,383,384,386,393,394,405,408,409,410,414,418,419,420,421,428,438,440,441,442,453,455,456,457,466,481],disabl:[3,12,16,318,396,453,468],disadvantag:[6,209],disallow:[187,215,250],disappear:457,discard:[2,3,41,71,205,209,319,327,452,457,458],discontinu:[9,184,354,403],discourag:408,discov:[13,319],discret:[6,8,40,42,189,190,234,237],discuss:[],disk:[6,84,85,157,185,216,226,277,453],disloc:70,disord:[39,70],disp:[],dispar:422,disperion:[380,401],dispers:[3,6,7,9,162,273,346,347,371,380,401,406,412,421,439],displac:[],displace_atom:[],displace_box:59,displacemet:458,displai:[11,13,22,37,44,55,172,183,187,189,333,341,374,437],dispters:3,dissip:[6,227,234,273,315,316,369,381,389,406,407,437],dissolut:210,dist:[6,69,91,108,117,187,274,290,382,436,450,482],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,153,159,162,164,165,166,167,171,186,187,189,190,198,202,205,206,210,211,212,213,215,216,217,220,226,232,237,247,248,249,250,254,262,272,273,277,281,282,289,290,291,294,295,299,303,304,305,306,313,314,316,317,318,321,323,324,325,326,327,328,332,346,347,349,352,354,356,357,358,361,364,365,366,367,368,369,370,371,372,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,391,395,396,397,398,399,400,401,402,403,404,405,406,407,408,411,412,413,414,415,416,417,418,420,421,422,423,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,450,453,455,458,464,465,469,473,476,480,482],distinct:[6,219,288,346,422],distinguish:[6,86,140,240,385],distort:362,distrbut:362,distribut:[],distro:[111,374,417,418],ditto:[8,11,12,14,15,16,17,18,115,211,453],div:8,divd:117,diverg:[3,12,39,291,316,457,476,483],divid:[3,6,16,41,91,112,117,126,128,141,161,162,172,183,190,202,203,204,209,215,272,314,321,326,346,354,356,386,421,464,472,481],divis:[6,237,367,395,405,452,455,473,481],dl_poli:7,dlambda:158,dlammps_async_imd:231,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,189],dlammps_gzip:[3,12,187,189,317,455,456,460],dlammps_jpeg:[3,12,189],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,189],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,187],dlen:465,dlmp_intel_offload:[12,16],dlo:[59,186,215,277],dlvo:[7,375,447],dm_lb:237,dmax:[306,352],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,143,144,157,159,161,164,165,166,172,183,187,188,189,190,191,193,194,195,200,201,202,203,204,205,206,207,216,226,234,235,245,250,251,255,256,260,267,268,269,270,277,280,291,303,306,309,310,311,320,324,327,329,331,333,341,345,354,355,356,361,362,363,366,374,376,377,383,384,386,391,392,394,395,408,409,410,412,414,417,418,419,428,437,438,440,442,444,453,455,456,457,458,460,463,464,465,472,473,481,482,483,484],docuement:422,dodgerblu:190,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,143,144,147,152,154,158,163,164,165,166,168,170,172,177,183,184,186,187,188,189,190,193,199,200,202,205,208,209,211,212,213,215,219,221,223,226,227,230,232,234,235,237,240,246,250,251,252,253,255,256,267,268,269,270,278,279,280,284,286,289,291,306,309,311,313,314,318,321,322,323,326,327,328,329,334,335,337,338,340,345,346,347,348,349,355,356,357,362,363,364,365,366,367,369,371,372,373,375,376,377,378,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,399,400,402,403,404,406,407,408,409,410,412,418,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,451,452,453,455,456,457,458,459,462,463,465,466,467,468,469,472,473,476,481,485],doegenomestolif:7,doesn:[3,7,8,12,164,187,200,205,206,303,355,357,361,363,376,384,394,420,421,438,440,441,442,455,457],dof:[3,8,112,143,144,157,202,291,482],dof_per_atom:[144,202],dof_per_chunk:[144,202],doff:[355,455],doi:[6,214],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,153,163,166,186,188,189,190,193,200,209,213,215,216,230,233,237,250,251,274,286,291,318,323,324,346,347,356,361,382,412,450,452,455,459,472],domin:[1,385,469],don:[0,8,11,12,13,116,167,196,221,235,280,327,408,453,455],donadio:310,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,158,161,164,167,184,187,189,190,199,200,202,204,205,206,207,209,210,211,212,213,215,216,224,226,231,232,234,235,242,250,255,256,267,268,270,271,273,274,275,280,288,291,292,294,306,309,310,311,313,315,316,329,331,345,346,347,354,356,357,360,361,363,371,383,392,393,394,401,407,408,412,420,436,439,444,450,451,452,453,456,459,460,463,473,474,476,481,482],donor:391,dot:[141,160,196,221,229,249],doti:[367,418],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,215,224,279,327,331,345,347,360,361,367,386,390,420,421,451,455,459,463,468,481,482],dover:199,down:[3,6,7,8,11,39,71,213,234,306,322,361,385,412,454,474],downhil:[352,353],download:[5,7,8,9,11,12,13,17,231,393,419],downsid:6,downward:288,dozen:[8,12,107,193,420,421],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:243,dproduct:364,dr_ewald:[118,292],drag:[],dragforc:237,drai:[248,281],drain:[230,322,354],dramat:[59,186,210,211,212,213,215,250,306,309,310,347,361,412,452],drautz:367,draw:189,drawback:280,drawn:[187,189,190,227,450],drayleigh:[248,281],dreid:[],drfourth:105,drho:[113,362,383],drift:[6,103,105,227,228,234,235,246,289,306,464,472,476],drive:[11,12,197,213,215,229,250,272,278,291,325,356],driven:[6,176],driver:[6,12,14,15,193,224,231],drop:[3,190,381],droplet:392,drsquar:105,drude:[],dry:223,dsecriptor:393,dsf:[],dsmc:[],dstyle:277,dt_collis:237,dt_lb:237,dt_md:237,dt_srd:306,dtilt:[59,215],dtneb:469,dtqm:281,dtype:[115,211],dual:[17,306,361],dudarev:163,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,142,143,145,147,150,151,152,153,154,156,157,159,163,164,167,168,187,189,193,196,197,204,208,210,211,212,213,214,215,216,221,222,223,224,227,228,231,232,234,235,236,237,240,241,242,246,247,248,249,250,254,262,272,275,277,289,290,291,293,303,305,306,307,309,310,311,312,313,315,316,318,322,323,325,326,327,329,347,352,354,356,357,358,378,381,383,387,388,392,406,407,412,418,420,422,423,436,439,440,442,445,447,448,450,452,455,456,457,464,469,472,473,474,476,481,482],duffi:318,duin:[9,282,287,420,421],duke:347,dummi:[12,29,441],dump1:460,dump2:460,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:188,dump_modifi:[],dumpcustom:8,dumptimestep:460,dunbrack:[6,20,170,372,467],dunweg:[234,236],duplic:[2,3,14,15,16,17,18,19,41,42,165,209,228,272,455,480],dupont:[5,7,13],durat:[37,55,142,143,145,146,147,149,150,151,152,153,156,157,183,190,202,226,286,318,341,389,437],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,146,165,168,184,187,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,249,250,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,299,303,304,305,306,307,308,309,310,311,312,313,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1,286,291,319,323,324,327,357,361,377,416,455,459,460],enpub:383,enrti:12,ensembl:[],ensight:6,ensur:[3,6,140,187,200,213,226,227,250,296,317,347,367,382,405,436,438],enter:[57,154,386,469],enthalpi:[123,252,253,383,472,473,481],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,144,163,164,190,193,194,195,202,205,206,209,212,214,223,226,227,230,234,235,246,250,252,253,254,255,256,272,274,276,289,291,304,318,320,331,361,380,401,412,439,455,463,464],entireti:[395,444],entiti:[6,8,40,42,187,291],entri:[3,8,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,190,204,205,206,214,281,329,355,367,384,408,414,421,428,438,439,440,441,442],entropi:469,entry1:[38,56,190,374,439],entry2:190,entryn:190,enumer:[165,187],enumuer:6,env:361,environ:[1,3,6,11,12,16,17,18,189,228,233,272,361,362,367,374,376,384,385,418,440,452,466,481],epair:[107,190,387,391,420,421,473],epen:[420,421],epfl:[228,233],epp:380,epq:380,eps0:447,eps14:405,epsilon0:442,epsilon:[3,6,36,45,46,50,53,54,87,170,194,195,226,291,306,323,327,352,354,366,372,373,375,377,378,379,380,388,390,391,392,395,396,397,398,399,400,401,402,403,404,405,411,415,422,423,432,438,444,446,447,464,476,480],epsilon_0:448,epsilon_14:372,epsilon_:422,epsilon_d:378,epsilon_i:[388,412,422],epsilon_i_:422,epsilon_i_a:[388,422],epsilon_i_b:[388,422],epsilon_i_c:[388,422],epsilon_ij:412,epsilon_j:[388,412,422],epsilon_j_:422,epsilon_j_a:[388,422],epsilon_j_b:[388,422],epsilon_j_c:[388,422],epsilon_lj:422,epton:417,eqch:159,eqeq:[420,421],eqp:380,eqq:380,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,189,190,193,194,195,196,197,200,203,204,207,208,209,213,215,216,221,226,227,229,230,232,234,235,237,240,241,247,248,254,264,272,274,277,279,281,282,283,286,288,290,291,293,295,300,302,309,310,311,314,315,316,318,320,321,323,326,328,329,331,345,354,356,357,358,360,361,376,381,387,388,391,406,411,418,420,421,422,424,425,426,428,429,439,444,448,451,452,453,455,457,458,462,463,466,469,471,473,481,482],equat:[3,6,7,8,9,91,112,118,163,172,183,193,213,219,220,228,234,235,237,240,248,249,250,251,254,268,272,274,281,282,286,294,306,314,318,321,323,324,326,328,340,346,347,375,380,381,385,386,389,394,406,407,408,412,422,425,427,431,432,434,435,443,448,476],equi:251,equidist:249,equil:[3,282,350,462,485],equilater:465,equilibr:[3,4,5,6,7,9,59,91,164,193,200,203,212,213,226,248,250,251,268,269,281,282,283,284,314,315,316,321,376,377,420,421,451,465],equilibria:321,equilibribum:[210,211],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,213,215,226,227,228,235,237,250,254,268,281,286,290,294,295,303,306,313,314,316,321,332,334,337,340,376,408,414,476],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:199,equival:[6,12,13,59,124,125,133,138,162,166,190,204,207,213,215,226,234,250,268,278,290,291,326,381,385,440,442,455,458,463,464,473,476],equlibrium:6,equliibr:[282,284],er3:163,eradiu:[40,113,385,455],eras:[293,315],erat:[215,407],erc:377,erfc:[377,397,412],erforc:113,erg:480,erhart:[200,383,440,442],ermscal:364,ernst:9,eror:3,eros:408,erose_form:408,erot:[],errata:[440,442],erratum:323,erron:3,error:[],erta:389,ervel:[113,455],escap:[216,476],especi:[8,11,16,152,164,193,200,209,226,281,286,289,290,361,452],espresso:[9,285],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,203,254,273,322,347,363,377,397,442,460,473],essex:29,establish:[87,230],estim:[1,3,6,10,12,38,41,56,91,141,199,209,220,248,306,313,346,347,352,412,421,439,469,473],esu:480,esub:408,eta:[6,237,250,281,282,284,322,384,386,388,418,441,480],eta_dot:250,eta_ij:418,eta_ji:386,etag:[40,455],etail:473,etap:250,etap_dot:250,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,189,190,193,199,200,201,202,204,205,206,207,210,211,215,216,224,226,227,234,250,277,288,292,318,319,327,331,345,346,354,355,356,357,359,383,384,392,405,407,416,420,421,438,440,442,450,453,455,456,457,462,464,465,469,471,472,473,476,480,481,483,485],ethernet:18,etol:[354,356,450,469],etot0:281,etot:[6,94,96,97,110,141,150,190,219,235,248,281,472,473],eu2:163,eu3:163,euler:[354,356],eulerian:199,euqat:430,europhi:237,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,189,190,194,195,196,197,199,201,202,203,204,205,206,207,208,215,221,227,229,230,232,233,234,235,273,279,282,293,296,300,309,310,311,320,323,326,328,329,331,346,347,352,354,361,412,418,424,426,439,450,451,453,457,458,460,462,463,464,465,469,471,473,481,482],evalut:[331,453],evan:[152,268],evanseck:[6,20,170,372,467],evapor:[],evaul:[8,354],evdwl:[107,420,421,473],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,190,193,194,195,200,201,202,204,205,206,207,209,210,211,213,215,216,219,232,235,248,250,251,273,286,288,291,292,302,306,314,318,321,323,327,329,339,346,352,354,356,361,366,385,386,389,392,412,422,445,455,456,458,460,461,462,464,465,467,470,472,473,474,476,485],evenli:[3,41,141,184,209,237,395,445,455],event:[],eventu:[3,6,12,15,166,282,469],ever:[54,56,233,306],evera:[375,388,422,437],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,191,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,220,223,224,226,228,230,231,232,237,238,246,250,251,254,271,272,273,277,278,279,280,281,282,283,284,286,288,289,291,292,294,295,306,308,309,310,311,312,313,314,317,318,319,320,321,329,331,345,347,356,357,358,361,381,382,392,405,420,421,433,449,450,451,455,457,459,460,462,463,464,469,470,471,473,481,485],everyth:[8,107],everywher:[116,399],eviri:385,evolut:[228,237,274,450],evolv:[237,274,319],ewald:[2,3,5,6,7,8,12,88,110,118,141,319,346,347,354,368,370,371,377,380,385,397,401,415,423,437,439,457],ewald_disp:380,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,209,212,227,228,234,235,236,277,286,287,306,318,333,346,374,457,462,469,483,485],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,194,195,204,209,215,220,227,234,235,236,251,261,262,269,273,281,306,311,312,325,361,374,381,383,389,392,395,406,412,439,457,458,465,469,481],exager:476,examin:[6,8,9,212,273],examp:[453,481],exampl:[],exce:[3,6,16,17,18,41,58,71,166,202,205,206,209,213,215,220,223,250,273,297,298,306,354,361,455,481],exceed:[3,41,59,209,215,250,306,463],excel:385,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,190,193,196,202,203,204,208,209,213,215,222,225,226,229,232,234,236,250,251,252,253,254,255,256,257,261,262,265,267,268,269,270,274,283,284,291,293,294,303,306,309,311,312,318,322,329,331,332,333,334,335,336,337,340,341,342,346,347,349,351,355,356,357,359,360,361,362,363,365,368,369,370,371,372,373,374,375,376,377,379,380,381,383,384,385,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,407,409,413,414,415,417,420,421,422,423,429,437,438,439,440,441,442,444,446,447,448,450,452,453,455,457,458,460,463,464,465,466,467,469,473,476,480,481,482,484],excess:385,exchang:[2,3,6,8,9,61,62,193,199,200,226,234,283,291,314,318,321,346,361,385,470],exchange:346,excit:[9,385],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,202,205,210,211,238,246,276,289,291,313,324,329,354,355,357,369,389,392,406,407,412,436,467],exclus:[1,3,9,12,16,87,361,376,412,464,474],excurs:450,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,189,231,285,331,345,348,360,451,453,463,466,469,481],exemplari:227,exemplifi:385,exert:[6,232,235,286,325,326,327,347],exhaust:[199,360,481],exhibit:[250,353,385,464],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,190,193,198,208,211,213,216,226,276,277,279,329,332,334,335,337,341,350,355,361,392,420,445,451,453,455,456,457,466,467,468,481,482,483],exit:[2,3,11,12,41,57,187,209,345,360,453,454,463,472,481],exlanatori:3,exp:[],expand:[],expans:[12,140,187,466],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,209,221,226,228,247,272,278,280,281,286,291,329,347,357,374,408,412,450,453,455,457,460,464,469,481],expens:[6,10,71,190,272,276,291,318,329,346,347,357,361,453],experi:[6,13,15,17,208,216,231,240,249,278,290,291,352,356,381,412,464,469],experienc:[6,12,239,240],experiment:[346,361,469],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,189,190,193,202,203,207,209,211,213,215,250,272,280,291,303,329,331,345,346,349,355,356,360,366,383,395,429,444,448,453,456,457,460,462,465,476,481,485],explan:[3,6,59,113,140,187,202,249,272,392,449,452,453,455,464],explanatori:[3,8,117,187,201,202,204,205,206,291,355,452,481],explantori:[3,287],explic:411,explicit:[6,9,11,22,44,77,87,113,116,158,172,194,195,215,297,298,333,351,363,364,367,372,374,383,385,396,406,443,449,452,456,459],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,190,196,205,208,215,222,225,227,229,234,250,252,253,254,255,256,257,265,267,268,270,280,281,283,291,293,294,309,311,312,318,322,332,334,335,336,337,340,342,355,361,362,363,365,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,386,387,388,389,390,391,392,395,396,397,398,399,400,401,402,403,404,405,406,409,412,413,414,415,417,422,423,429,430,431,432,433,434,435,437,438,439,440,441,442,443,444,446,447,448,455,457,464,465,467,468,474,476],explictli:[16,468],exploit:[9,15,17,274],explor:[118,163],expon:[3,282,284,383,388,391,405,411,423],exponenti:[87,418,438,448,469,481],expos:11,exposit:[199,381,382],express:[6,140,150,164,194,195,213,247,272,282,318,324,331,367,383,385,399,408,428,437,481],expressiont:367,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,193,196,197,200,207,208,214,217,221,224,225,226,228,229,230,232,234,236,248,250,254,262,272,273,289,290,291,293,295,300,303,305,309,310,311,312,313,315,316,318,320,323,327,328,388,408,421,422,428,472,473],extent:[1,3,41,45,57,71,162,166,187,198,205,209,232,325,328,346,349,363,424,426,439,452,455,458],exterior:[3,6,327],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,190,204,209,211,250,279,280,281,291,306,354,355,358,359,380,389,392,395,408,412,452,453,455,458,467,476,481],extract:[3,6,11,13,36,63,87,107,115,117,119,194,195,284,356,377,386,408,428,453,460,472],extract_atom:11,extract_comput:[11,453],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,189,213,215,250,316,385,441,476],extrema:405,extrins:199,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,320],f_a:[440,441,442],f_ave:117,f_c:441,f_f:442,f_fix_id:281,f_harm:316,f_i:418,f_id:[6,71,117,119,187,193,201,202,203,204,205,206,207,245,308,320,473,481],f_ij:418,f_indent:207,f_int:315,f_jj:91,f_k:418,f_langevin:318,f_max:[281,286],f_msst:248,f_r:[235,440,441,442],f_sigma:367,f_solid:316,f_ss:6,f_temp:235,face:[3,6,57,59,71,152,162,166,198,205,206,323,325,326,327,328,349,388,408,422,455,458],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,228,306,316,389,467],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,189,190,194,195,203,209,213,215,216,226,231,234,236,237,248,250,251,254,274,278,290,294,296,298,306,310,314,321,322,323,327,337,347,349,361,363,364,367,368,370,372,377,378,379,381,385,389,392,396,397,408,412,414,415,421,423,429,438,443,452,455,458,459,464,467,469,470,473,476,480,481],factori:[3,453],factoriz:346,fail:[3,11,12,59,168,213,216,346,354,356,379,421,453],failur:[121,425],fairli:[11,412,464,469],faken:73,falcon:231,fall:[3,6,190,204,277,453],fals:[86,329,331,481],fame:8,famili:452,familiar:[0,11],fan:418,far:[3,6,12,17,57,59,61,86,187,190,191,209,210,211,213,216,250,272,290,291,306,323,334,337,352,356,357,444,453,455,460,473],farago:234,farrel:[440,442],farther:187,fashion:[6,8,41,71,164,190,193,194,195,200,205,209,211,216,226,228,232,247,248,250,252,253,254,255,256,264,267,268,269,270,280,281,283,291,295,299,305,308,316,318,322,323,324,326,328,356,392,406,458,467,481,484],fasolino:394,fast:[6,7,9,12,13,17,39,187,259,281,319,346,347,369,406,407,437,439,457,462,464,473,482,485],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,190,193,196,208,209,222,225,229,233,234,250,252,253,254,255,256,257,265,267,268,270,278,282,283,291,293,294,306,309,311,313,315,318,322,332,334,335,336,337,340,342,346,347,358,359,361,362,363,365,367,368,369,370,371,372,373,374,375,376,377,380,381,383,384,386,387,388,389,390,391,392,395,397,398,399,400,401,402,403,404,405,406,409,413,414,415,417,422,423,429,437,438,439,440,441,442,444,446,447,448,450,464,468,476],fastest:[6,14,17,152,205,318,319,361,452],fatal:[3,472],fault:[70,421],faulti:12,fava:388,favor:212,favorit:7,fbmc:313,fcc:[],fcm:[264,481],fdirect:219,fdotr:393,fdti:87,fe2:163,fe3:163,fe_md_boundari:199,featu:8,featur:[],fecr:383,feedback:[7,231],feel:[7,231,232,240,272,327,329,356,412],felling:410,felt:327,femtosecond:480,fene:[],fennel:[377,397],fep:[],ferguson:[6,170,467],fermi:[1,12,15,150,361,442],fermion:[9,385],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,191,201,202,203,204,205,206,207,235,250,277,280,282,294,320,346,354,355,356,363,452,455,460,464,466,474,481,483],fewer:[1,3,11,15,16,61,240,464],fewest:3,fextern:224,feynman:274,fff:453,ffield:[376,386,420,421],ffmpeg:[3,12,189],ffplai:189,fft:[1,3,7,12,14,15,88,109,110,141,273,346,347,464],fft_inc:[12,347],fft_lib:12,fft_path:12,fftbench:[346,474],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,196,197,221,224,228,274,290,377,397,401,436],field1:[456,460],field2:456,field:[],fifth:[303,414],figur:[1,3,8,11,12,281,452,453],fij:380,file0:272,file1:[11,13,272,317,331,355,460,462,466],file2:[11,13,317,331,355,460,462,466],file:[],file_from:188,filenam:[3,12,13,38,41,56,184,187,189,190,191,199,202,203,204,205,206,207,209,214,272,276,279,282,283,284,287,288,291,292,317,318,343,344,345,356,362,363,367,377,383,384,386,394,408,409,410,414,418,419,420,421,428,438,439,440,441,442,451,452,453,456,457,462,466,473,481,483,484,485],filennam:462,filep:[3,187,190,457,462,485],filepo:288,fill:[7,164,189,277,318,349,357,367,421,458],filter:[190,199],final_integr:8,final_integrate_respa:8,finchham:[6,146,379],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,191,200,212,213,223,226,249,272,278,286,290,352,354,356,357,377,392,397,401,408,437,439,476,481],find_custom:8,fine:[16,17,168,196,221,316,357,361,481],finer:[140,164,481],finest:346,finger:[164,186,247,458],finish:[6,11,41,209,331,343,345,346,358,360,361,444,460,481,482],finit:[],finni:[7,383,437],finvers:219,fiorin:[9,214],fire:[352,353,354,356,469],firebrick:190,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,191,193,200,202,203,204,205,206,207,209,212,215,226,227,232,237,247,248,249,250,272,274,279,280,281,283,288,291,294,295,303,304,306,307,308,315,316,317,318,320,324,329,331,332,338,349,354,355,356,357,360,361,362,363,366,367,368,370,372,374,376,377,383,385,386,389,390,393,394,396,397,401,406,407,408,410,412,414,418,420,421,428,436,438,439,440,441,442,450,451,452,453,455,456,457,460,462,464,467,468,469,472,473,476,481,482,483,485],fischer:[6,9,19,20,170,372,467],fit:[3,6,9,12,38,56,184,290,306,363,367,394,408,412,432,439,441,463,481],five:[73,150,281,355,367,409,455,469],fix:[],fix_adapt:[158,195,405],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,200,277],fix_evapor:200,fix_flux:199,fix_gcmc:[200,355],fix_gl:228,fix_gld:228,fix_grav:277,fix_id:[3,213,248,250,252,253,254,255,256,278,281],fix_modifi:[],fix_mov:[186,324],fix_nh:8,fix_npt:228,fix_nvt:[200,226],fix_poem:[3,6],fix_pour:[3,216],fix_qbmsst:9,fix_qeq:[3,376],fix_rattl:294,fix_reax_bond:420,fix_rigid:[240,366],fix_saed_vtk:292,fix_setforc:8,fix_shak:294,fix_srd:3,fix_styl:254,fix_temp_rescal:312,fixedpoint:[213,250],fixextern:224,fixid:199,fji:380,flag1:[218,359],flag2:[218,359],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,189,190,191,207,212,214,218,231,234,238,240,246,247,273,280,291,303,305,306,313,317,326,329,344,347,355,359,360,361,363,391,396,408,436,450,452,453,455,456,457,459,460,461,465,481],flag_buck:371,flag_coul:[371,380,401],flag_lj:[380,401],flagfld:[369,406,407],flaghi:[3,369,406,407],flaglog:[369,406,407],flagn:218,flagvf:[369,406,407],flat:[6,318,323,324,328],flavor:[2,7,12],fld:[9,323,369,406,407],flen:364,flex_press:364,flexibl:[3,6,8,165,189,202,205,214,228,251,314,321,385,441,473],flip:[3,6,215,250,325,326],floor:481,flop:12,floralwhit:190,flow:[],fluctuat:[6,64,87,213,226,227,234,237,250,254,272,273,316,318,340],fluid:[],fluid_veloc:241,flush:[3,190,472],flux:[],flv:189,fly:[7,9,12,41,189,193,199,216,219,291,294,319,367,473,476],fmackai:9,fmag:217,fmass:274,fmax:[354,473],fmomentum:219,fmsec:[2,190,234,235,247,250,278,291,309,310,464,475,480,482],fname:345,fno:12,fnorm:[354,473],fnpt:219,fnvt:219,foce:392,fock:364,focu:294,fogarti:[9,284,421],foil:[140,272,428],fold:[304,464],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,190,193,199,200,201,202,203,204,205,206,207,209,214,215,216,219,220,224,226,227,228,231,233,234,235,237,240,248,250,254,255,256,267,268,270,273,274,276,279,280,281,282,284,286,288,290,291,292,294,308,309,310,311,314,315,316,317,318,320,321,329,330,334,335,336,337,340,342,344,349,351,354,355,356,361,362,363,364,365,366,367,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,425,427,428,429,430,431,432,433,434,435,436,438,439,440,441,442,443,444,446,447,448,450,452,453,455,456,457,458,460,462,463,464,467,469,470,471,476,481,482,484],foo:[4,8,11,12,187,189,224,453,466,481],foot:6,footprint:[12,361],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:240,forcefield:[290,391],forcegroup:237,forcezero:352,ford:380,forestgreen:190,forev:71,forget:[235,476],forgiv:250,fork:[12,187],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,190,193,194,195,211,227,228,234,236,240,247,268,273,284,286,290,291,318,323,327,332,333,340,351,353,355,356,363,364,367,374,383,385,387,391,392,396,408,410,414,415,418,420,421,422,428,429,437,439,440,441,442,447,449,452,453,455,460,465,472,476,481],formal:[6,78,80,91,227,228,234,250,274,306,314],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,191,202,204,205,206,207,209,211,273,276,280,282,284,287,291,292,302,317,318,329,330,333,351,355,356,362,363,367,374,383,386,396,408,410,419,420,421,423,428,439,445,452,453,455,456,457,460,471,472,473,481,483],former:[6,12,16,39,41,190,209,318,322,367,369,461,467,481],formerli:[7,13],formul:[1,40,64,141,196,221,234,250,268,282,284,290,294,317,346,363,367,383,385,388,408,417],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,194,195,196,197,202,203,204,207,208,215,221,229,230,232,234,235,247,272,273,279,288,293,300,304,306,309,310,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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.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump 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/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":210,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,189,190,191,192,194,195,196,198,199,200,202,205,206,207,210,211,213,214,215,216,220,223,226,227,232,234,235,236,237,238,240,245,248,250,251,254,268,269,273,274,277,278,279,280,281,283,286,288,289,291,292,306,308,313,314,315,316,319,321,323,325,329,341,344,346,347,349,350,352,353,355,357,358,359,361,364,367,369,385,406,407,412,420,421,436,437,450,451,452,455,456,458,460,462,463,464,467,469,471,472,473,474,475,480,482,483,484],"function":481,"long":[368,370,371,372,373,377,379,380,397,401,405,415,423],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[194,195],addforc:196,addit:[12,13],addtorqu:197,adiabat:6,adjust_dt:296,adp:362,airebo:363,alloi:383,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:198,arrai:6,aspher:[6,82,143,252,255,258,259,267],atc:[9,199],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,198,200,201,280,481],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:208,awpmd:[9,364],balanc:[41,209],barostat:6,basal:67,beck:365,berendsen:[278,309],between:6,binary2txt:13,bodi:[6,8,42,68,260,366],bond:[8,13,69,210,211,212,287],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:367,born:[368,379],boundari:[7,57],box:[6,58,213],brownian:369,buck:[370,371,379],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,372,405],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,202],citat:7,class2:[21,43,171,332,373],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[323,375,447],colvar:[9,13,214],com:[74,75,145],comb3:376,comb:[283,376],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,481],compute_modifi:102,condit:7,conduct:[6,314],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:203,cosin:[23,24,25,26,27,28,173],cossq:334,coul:[368,370,371,372,373,377,378,379,390,397,401,405,415,423],coupl:6,creat:211,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:310,csvr:310,cubic:399,cuda:[9,14,109,112,142,151,196,208,222,225,229,250,257,293,294,309,311,322,368,370,372,373,383,389,390,397,398,400,403,413,438,440],custom:8,cut:[49,364,370,373,377,380,385,387,397,398,405,411,415],cvff:335,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[377,397],deform:[147,148,215],delete_atom:167,delete_bond:168,delta:24,deposit:216,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,9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,peri:417,period:25,phonon:[9,13,273],pimd:274,piston:325,planeforc:275,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:417,poem:276,point:282,polariz:6,poli:[369,406,407],polym:13,polymorph:418,post:7,potenti:[2,6,8],pour:277,pppm:6,prd:450,pre:7,press:278,pressur:112,previou:12,print:[279,451],problem:[3,4],process:[6,7],processor:452,profil:152,properti:[6,113,114,115,280],pymol_aspher:13,python:[11,13,453],qbmsst:281,qeq:[282,283,284],qmmm:[9,285],qtb:[9,286],quadrat:182,quantiti:6,quartic:[35,54],quip:419,quit:454,ramp:153,rattl:294,rdf:116,read_data:455,read_dump:456,read_restart:457,reax:[13,284,287,288,420,421],reaxc:9,rebo:363,recent:289,reduc:117,refer:481,reflect:326,region:[8,117,154,155,327,458,481],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,191,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,225,226,227,228,229,230,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,286,287,288,289,291,292,293,295,296,297,298,299,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,477,478,479,481,482,483,484,485],relax:213,replic:459,replica:[6,7],report:3,requir:12,rerun:460,rescal:[311,312],reset:220,reset_timestep:461,resquar:422,restart2data:13,restart:[6,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,462],restrain:290,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],rho:126,rhosum:433,rigid:[6,83,98,240,291],ring:340,rotat:156,rule:2,run:[6,11,12,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328,463],run_styl:464,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,423],self:305,serial:11,set:[6,465],setforc:293,setvel:300,shake:294,share:[11,12],shell:[6,466],shield:282,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:282,slice:119,sllod:[268,269],small:291,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,295,296,297,298,299,300,302,424,425,426,427],smooth:[403,404],sna:140,snad:140,snap:428,snapshot:6,snav:140,soft:[405,429],solver:2,sourc:7,spatial:[205,206],spc:6,speci:288,special:[7,412,481],special_bond:467,sph:[9,430,431,432,433,434,435],sphere:[84,85,157,206,240,253,256,265,270],spheric:6,spline:[409,410],spring:[303,304,305,316],squar:28,srd:[306,328],srp:436,standard:9,start:[12,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],state:308,stationari:244,stop:[194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,219,220,221,222,223,224,225,226,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,320,321,322,323,324,325,326,327,328],store:[307,308],strategi:1,streitz:377,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:468,summari:6,swap:[200,212],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485],system:6,tabl:[0,6,38,56,184,439,440],tad:469,taitwat:[434,435],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,309,310,311,312],temper:470,temperatur:6,tersoff:[440,441,442],test:11,tfmc:313,thermal:[6,314],thermo:[6,471],thermo_modifi:472,thermo_styl:473,thermodynam:[6,8],thermostat:6,thole:443,time:[6,207],timer:474,timestep:475,tip3p:6,tip4p:[6,377,397,401,405],tip:12,tlsph:425,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:317,tool:13,torqu:159,transform:219,tri:[266,444],tri_surfac:426,triangle_mesh_vertic:134,triclin:6,tstat:381,ttm:318,tune:319,type:7,ulsph:427,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:342,uncomput:477,undump:478,unfix:479,unit:480,user:[9,12,14,16,18],vacf:160,val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\ No newline at end of file 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,456,457,458,459,461,462,464,466,468,470,473,474,477,481,482,483,484,485,486],afterrun:464,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,451,453,454,456,458,463,470,472,482,484],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,451,483],aggress:[231,470],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,451,453,470],alia:12,alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,456,459,477],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,473,474,475,477,481,482,483,484,485,486],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,456,464],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,402,407,408,413,419,422,423,426,428,437,446,448,451,454,456,458,459,460,461,462,463,466,468,469,470,473,474,482,483],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,454],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,456,459,466,467,482],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,474,477],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,456],alphanumer:[3,63,194,281,289,332,356,482],alreadi:[3,7,8,12,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,446,449,452,456,457,461,466,482],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,386,389,390,392,393,394,402,406,407,409,413,415,417,418,419,420,423,424,426,432,433,435,436,437,438,439,440,441,442,443,444,451,453,454,455,456,457,458,459,460,461,463,464,465,466,468,469,470,471,474,475,476,477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3,426,428,430,456,458],coeffcient:456,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,451],colberg:189,cold:[6,150,231,358,477],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,456,463,469,475,486],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,449],colllis:307,colloid:[],colombo:39,colon:[192,330,457],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,457,471,473,482],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,458],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,448,459,464,477,482],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,453,454,456,477,482],commerci:7,commmand:[3,6,12,59,107,270,450,451,453,470,485],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,456,459,468],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,347,358,359,360,362,383,417,453,454,458,465,466,484,486],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,451,470,471,477,481],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,453,454,482],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,456,457,461],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,451,456,461,464,468,470,473,477,482],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,454,456,459,482],compli:[314,318],complic:[6,7,9,12,13,201,227,454],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,456,457,466,474,482,483],componenet:6,composit:[6,201,238,384],compound:[377,386,387],compres:[71,114,203],compress:[3,6,9,12,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:477,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,485],concav:328,concentr:384,concept:[6,145,155,203,465],conceptu:[3,6,71,153,214,216,357,378,393,409,461],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348],conden:[319,441,443],condens:[6,147,319,364,380,384,398],condit:[],conducit:6,conduct:[],cone:459,confid:[3,470],config:[12,188,453],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,451,456,458,459,470],confin:[456,470],conflict:[3,12,40,413,454],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,468],confus:3,conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,456,459,463,477,486],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,453,454,460,477],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,451,457,459],consequ:[1,6,319,397,470],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,465,470],consid:[6,9,70,71,78,87,115,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,451,452,454,457,458,459,461,464,466,474,477,482],consider:[6,8,235,236,310,311,312,362,465],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,446,454,456,457,459,460,461,468,477,482],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,461,468,477],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,459,460,475,482],constructor:8,consult:422,consum:[1,287,417,482],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,451,452,453,454,456,457,458,459,461,463,465,468,470,473,474,477,482,484,486],content:[12,18,422,472,474],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,448,456,463,472,481,482,483],contibut:70,contigu:453,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,451,454,456,458,459,464,470,473,474,482,484],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,448,485],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,468,474,477],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,451,453,465,471,472],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,482],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,482],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,451,463,470],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,454,470,481],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,449,454,456,457,458,463,473,477,481,482,484,486],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,451,456,457,459,461,464,466,470,477,482,483],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,454],copper:449,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,469],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,468],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,328,329,350,445,456],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,447,448,449,456,471,474,477],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,453,454,456,466,481,483],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,447,448,449,451,453,454,456,457,459,469,470,471,473,474,477,482],correspondingli:[407,408,465],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,453,465],costheta0:[439,441,443],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,201,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,452,453,454,456,458,460,463,464,472,477,482,483],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,448,461,468,474,477,481],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,474,482],counter:[325,451,462,464,470],counterbal:231,counterpart:[188,292,451],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,453,456,469,477,482,484],coval:[6,29,386,409,477],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,451,469,470,473,474,475],cpuremain:474,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,477],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,458,461,482],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,461,470,471],criterioni:470,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,456,460,466,484],crossov:1,crossterm:456,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,358,460,474,477],crystallin:[6,274,350,442,477],crystallis:314,crystallogr:[118,164],crystallograph:[350,474],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,456],cs_re:[40,456],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443],csinfo:6,csisi:[385,439,441,443],csld:[],cst:384,cstherm:6,cstyle:453,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,477],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,474],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,161,163,166,169,188,189,190,191,192,195,196,200,201,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256,257,263,268,269,271,277,283,284,286,289,290,291,292,295,296,297,298,299,300,301,303,305,306,307,310,311,312,318,319,322,323,324,325,326,327,329,330,332,345,346,347,348,351,352,354,355,356,357,362,368,375,377,381,384,386,387,390,394,397,407,408,409,410,411,413,419,421,422,425,426,427,428,430,441,443,444,446,451,452,453,454,456,457,458,459,460,462,463,464,466,468,470,471,473,474,482,483,484,485,486],curv:[6,165,227,274],curvatur:[389,423,449],custom:[],cut0:454,cut1:465,cut2:465,cut:[],cuthi:[273,285],cutinn:[370,407,408],cutlo:[273,285],cutmax:419,cutoff1:[374,381,398,402,406,416,424],cutoff2:[369,371,372,374,380,381,398,402,406,416,424],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,212,213,218,273,282,283,285,287,289,292,307,320,324,328,330,347,348,355,358,359,360,362,363,364,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,454,458,461,465,477],cutoffa:385,cutoffc:385,cuu3:384,cval:164,cvd:314,cvel:296,cvff:[],cwiggl:[3,248,324,327,329,482],cyan:[2,190,191],cycl:[3,227,249,251,252,255],cyclic:[3,185],cygwin:12,cylind:[3,4,190,233,278,325,328,459],cylindr:[6,233,304,325],cypress:362,cyrot:368,cyrstal:274,d3q15:238,d3q19:238,d_double_doubl:15,d_e:319,d_flag2:281,d_flag:281,d_name:[113,188,281,309,466],d_single_doubl:15,d_single_singl:15,d_sx:281,d_sy:281,d_sz:281,daan:317,dai:12,daili:12,daivi:269,damag:[],dammak:287,damp:[3,6,194,199,235,236,237,242,251,252,255,279,282,287,292,310,311,323,325,326,354,355,357,369,371,373,378,381,386,390,398,406,416,424,438,444,470,477],damp_com:236,damp_drud:236,dampen:[292,477],dampflag:[325,390],dan:17,danger:[3,12,227,330,382,474],dangl:168,daniel:9,darden:[348,381],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:283,dash:[390,473],dat:[6,91,185,200,452],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,293],dataset:293,datatyp:3,date:[0,6,12,13,421,422,482],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:324,david:[9,19,347,348,441,443],daw:[384,419],dbg:14,dcd:[3,6,7,188,189,190,191,192,275,457,461],ddim:187,deactiv:406,dealt:234,debug:[6,7,11,12,13,14,17,118,122,164,165,275,280,345,347,362,394,413,446,454,455,458,463,466,473,482],deby:[],decai:[378,449],decid:[3,6,12,16,71,248,281,292,320,471],decipher:350,declar:189,declin:307,decod:190,decompos:[87,429],decomposit:[3,5,7,18,62,200,275],decoupl:[6,477],decreas:[3,188,197,198,213,216,222,225,235,318,347],decrement:296,deepli:344,deeppink:191,deepskyblu:191,def:[12,13,454],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,220,221,222,225,226,227,230,233,234,235,236,237,238,246,248,250,251,252,253,254,255,256,257,259,260,261,264,266,267,268,269,270,271,273,274,275,277,278,279,281,283,285,290,292,293,294,295,297,301,305,307,309,310,311,312,313,315,316,317,319,321,322,324,325,326,327,328,329,330,332,333,334,335,336,337,338,341,342,343,345,347,348,350,352,354,355,356,357,358,359,360,361,362,364,365,366,367,369,370,371,372,373,374,375,376,378,379,381,382,383,385,386,388,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,412,413,414,415,416,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,454,456,457,459,460,461,462,465,466,467,468,470,471,473,474,477,478,479,480,481,482,483],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,216,233,255,293,309,321,324,327,329,331,342,345,356,365,368,376,386,396,419,426,428,429,445,454,456,458,465,467,481,482],defint:474,deform:[],deg2theta:164,deg:477,degener:[3,277],degrad:[8,18,274,348,465],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,213,220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,466,474,477,483],degress:[145,203],del:470,delai:[3,6,12,358,383,474],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,456,457,459,467,468,473,478,480,482,483],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[454,482],deloc:[252,386],delr:409,delt_lo:470,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:[3,201],delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,456,465,466,474,481],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,447,448,449,451,453,456,458,459,462,466,468,470,473,474,476,482,483],dependend:6,depflag:12,dephas:[451,470],depos:217,deposit:[],deprec:283,depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,448,477],deriv:[6,7,8,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,448,477],derjagin:448,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,447,448,449,451,453,454,456,457,459,460,466,469,470,473,482,483,484],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,465],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,147,165,178,187,201,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,452,453,454,456,460,465,470,471,473,474,482,483,484],desk:7,desktop:[4,6,7,10,12,17,190],despit:477,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,447,448,454,456,457,458,459,461,462,465,466,468,471,474,475,482,483,486],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,451,453,456,467,470,482],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,448,453,456,457,459,461,463,466,470,472,473,475,481,482,483],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,458],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:477,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,448,456,457,466],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,464],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,448,449,450,451,453,454,456,458,459,460,461,464,465,466,468,470,471,473,474,475,477,481,482,483,484],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,465],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,459,481,482,483],dimdim:482,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,456,466],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,448],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,477],dir1:467,dir2:467,dir:[1,3,4,8,11,12,249,273,282,306,419,421,422,454,467,482],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,454,466,467,468,474,482],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,454,456,457,458,467,482],disabl:[3,12,16,319,397,454,469],disadvantag:[6,210],disallow:[188,216,251],disappear:458,discard:[2,3,41,71,206,210,320,328,453,458,459],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,454],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440],displac:[],displace_atom:[],displace_box:59,displacemet:459,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,451,483],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,454,456,459,465,466,470,474,477,481,483],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,454],div:8,divd:117,diverg:[3,12,39,292,317,458,477,484],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,465,473,482],divis:[6,238,368,396,406,453,456,474,482],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,456,457,461],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:466,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlvo:[7,376,448],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,454,456,457,458,459,461,464,465,466,473,474,482,483,484,485],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,142,144,145,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,452,453,454,456,457,458,459,460,463,464,466,467,468,469,470,473,474,477,482,486],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,456,458],dof:[3,8,112,144,145,158,203,292,483],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,456],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,451,453,456,460,473],domin:[1,386,470],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,454,456],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,451,452,453,454,457,460,461,464,474,475,477,482,483],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,452,456,460,464,469,482,483],dover:200,down:[3,6,7,8,11,39,71,214,235,307,323,362,386,413,455,475],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,453],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,451],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,465,473,477],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:470,dtqm:282,dtype:[115,212],dual:[17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,446,448,449,451,453,456,457,458,465,470,473,474,475,477,482,483],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:461,dump2:461,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:461,dunbrack:[6,20,171,373,468],dunweg:[235,237],duplic:[2,3,14,15,16,17,18,19,41,42,166,210,229,273,456,481],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,166,169,185,188,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,250,251,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,2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,448],electron:[3,6,7,9,13,40,96,97,113,118,149,151,156,194,200,219,220,236,237,252,262,270,285,313,319,354,356,363,365,377,381,384,386,387,409,419,420,443,449,456,477,481],electron_integr:200,electron_temperatur:200,electron_unit:386,electroneg:[6,283,284,285,377,387],electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,201,227,283,285,286,320,347,348,376,381,386,398,406,408,422,448],eleftheri:292,elem1:[387,409,429],elem2:[387,409,429],element1:[289,363,384],element2:[289,363,384],element:[3,6,7,8,12,13,63,81,89,103,105,112,117,119,134,140,141,142,143,144,145,146,147,148,152,153,154,155,157,158,161,188,189,190,191,192,194,200,204,205,208,274,289,314,321,363,364,368,377,384,385,386,387,393,394,395,409,410,411,415,419,420,421,422,429,439,441,442,443,477,482,485],elementn:[363,384],elementset:200,elev:470,elif:[140,332],elig:[3,201,211,212,224,227,392],elimin:[3,6,71,228,235,236,292,295,316,317,451],elj:381,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,144,186],ellipsoid:[3,4,6,7,13,40,42,82,113,130,144,165,186,188,235,253,256,259,260,268,292,307,352,355,389,408,423,438,456,466,484],ellipsoidflag:456,elong:[220,236,474],elp:[421,422],els:[3,7,8,12,71,107,116,117,119,189,190,202,203,204,205,206,207,208,227,251,292,307,319,320,321,330,332,347,393,455,467,482,485],elsewher:[8,248,307,409,420,421,422,468,474,482],elt:409,emac:[],email:[0,3,5,7,8,11,387],emb:[3,9,328],emb_lin_neg:409,embed:[3,5,7,11,12,13,29,88,142,163,319,363,384,387,406,409,410,411,419,438,446,454],embt:172,emi:[7,9],emol:[421,422,474],emphas:390,empir:[200,311,364,386],emploi:[9,274,287,442],empti:[3,57,71,167,292,347,358,397,456,467,468,482],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,96,97,98,99,100,101,105,109,111,112,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,147,149,151,152,156,157,159,163,171,172,174,175,176,177,178,179,180,182,183,184,185,188,189,191,192,194,195,196,197,198,199,201,207,209,211,212,213,215,217,222,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,244,245,247,249,251,252,253,254,255,256,257,258,259,260,261,262,264,266,267,268,269,270,271,273,274,275,277,278,282,283,284,285,286,287,288,289,291,292,294,295,296,297,298,299,300,301,303,304,306,307,310,312,313,314,315,316,317,319,320,322,323,324,325,326,328,331,333,335,336,337,338,339,341,342,343,348,355,357,361,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,454,457,458,463,465,475,482,486],enclos:[2,6,12,167,188,280,332,409,452,454,464,482],encod:[13,39,42,188,190,191,281,393],encompass:[3,6,40,57,59,116,166,303,321,438,459],encount:[3,8,12,59,205,361,461,482],encourag:[7,8,286,305],end12i:113,end12x:113,end12z:113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,205,207,208,213,216,220,228,233,235,236,237,250,251,252,263,279,291,292,296,307,310,311,312,313,315,318,319,322,326,329,330,346,347,356,357,361,362,382,384,389,423,426,428,429,430,444,446,451,454,456,457,458,459,461,463,464,468,472,474,477,482,486],end_of_step:8,endbondtors:[3,172,178,456],endif:8,energet:[213,364,422],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,353,354,355,357,358,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,451,454,456,461,465,466,468,470,472,473,474,477,481,482,485],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,453,482,483],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,451],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,456,460,461],enpub:384,enrti:12,ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439],enter:[57,155,387,470],enthalpi:[123,253,254,384,473,474,482],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,456,464,465],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443],entropi:470,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,453,467,482],epair:[107,191,388,392,421,422,474],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:448,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,447,448,465,477,481],epsilon_0:449,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,449,452,453,454,456,458,459,463,464,467,470,472,474,482,483],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,449,477],equi:252,equidist:250,equil:[3,283,351,463,486],equilater:466,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,452,466],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,477],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,456,459,464,465,474,477],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,456],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:481,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,456],escap:[217,477],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,453],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,461,474],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,470,474],esu:481,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,481],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,456],etail:474,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,451,454,456,457,458,463,465,466,470,472,473,474,475,477,481,482,484,486],ethernet:18,etol:[355,357,451,470],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,473,474],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,451,452,454,458,459,461,463,464,465,466,470,472,474,482,483],evalut:[332,454],evan:[153,269],evanseck:[6,20,171,373,468],evapor:[],evaul:[8,355],evdwl:[107,421,422,474],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,456,457,459,461,462,463,465,466,468,471,473,474,475,477,486],evenli:[3,41,141,185,210,238,396,446,456],event:[],eventu:[3,6,12,15,167,283,470],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,450,451,452,456,458,460,461,463,464,465,470,471,472,474,482,486],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,451],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,458],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,458,463,470,484,486],exactli:[3,6,12,14,17,38,41,56,59,71,91,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,458,459,466,470,482],exager:477,examin:[6,8,9,213,274],examp:[454,482],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,456,482],exceed:[3,41,59,210,216,251,307,464],excel:386,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,447,448,449,451,453,454,456,458,459,461,464,465,466,467,468,470,474,477,481,482,483,485],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,471],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,468],exclus:[1,3,9,12,16,87,362,377,413,465,475],excurs:451,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,452,454,464,467,470,482],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,482],exhibit:[251,354,386,465],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,446,452,454,456,457,458,467,468,469,482,483,484],exit:[2,3,11,12,41,57,188,210,346,361,454,455,464,473,482],exlanatori:3,exp:[],expand:[],expans:[12,140,188,467],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,451,454,456,458,461,465,470,482],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,454],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,465,470],experienc:[6,12,240,241],experiment:[347,362,470],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,449,454,457,458,461,463,466,477,482,486],explan:[3,6,59,113,140,188,203,250,273,393,450,453,454,456,465],explanatori:[3,8,117,188,202,203,205,206,207,292,356,453,482],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,450,453,457,460],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,447,448,449,456,458,465,466,468,469,475,477],explictli:[16,469],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,449,470,482],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,482],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,473,474],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,453,456,459],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,453,454,456,459,468,477,482],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,454,461,473],extract_atom:11,extract_comput:[11,454],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,477],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,474,482],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,456,459],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,468],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,453,456,459,460,465,468,470,471,474,477,481,482],factori:[3,454],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,454],failur:[121,426],fairli:[11,413,465,470],faken:73,falcon:232,fall:[3,6,191,205,278,454],fals:[86,330,332,482],fame:8,famili:453,familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,454,456,461,474],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,459,468,482,485],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,458,463,465,474,483,486],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,447,448,449,451,465,469,477],fastest:[6,14,17,153,206,319,320,362,453],fatal:[3,473],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,482],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:481,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,468],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,453,456,461,465,467,475,482,484],fewer:[1,3,11,15,16,61,241,465],fewest:3,fextern:225,feynman:275,fff:454,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,465],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,475],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[457,461],field2:457,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,453,454],fij:381,file0:273,file1:[11,13,273,318,332,356,461,463,467],file2:[11,13,318,332,356,461,463,467],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,452,453,454,457,458,463,467,474,482,484,485,486],filennam:463,filep:[3,188,191,458,463,486],filepo:289,fill:[7,165,190,278,319,350,358,368,422,459],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,477,482],find_custom:8,fine:[16,17,169,197,222,317,358,362,482],finer:[140,165,482],finest:347,finger:[165,187,248,459],finish:[6,11,41,210,332,344,346,347,359,361,362,445,461,482,483],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,470],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,201,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,451,452,453,454,456,457,458,461,463,465,468,469,470,473,474,477,482,483,484,486],fischer:[6,9,19,20,171,373,468],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,464,482],five:[73,151,282,356,368,410,456,470],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,451,453,454,456,457,458,460,461,462,466,482],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,474],flip:[3,6,216,251,326,327],floor:482,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,473],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,474,477],fmackai:9,fmag:218,fmass:275,fmax:[355,474],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,465,476,481,483],fname:346,fno:12,fnorm:[355,474],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,465],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,453,454,456,457,458,459,461,463,464,465,468,470,471,472,477,482,483,485],foo:[4,8,11,12,188,190,225,454,467,482],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,477],forgiv:251,fork:[12,188],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,212,228,229,235,237,241,248,269,274,285,287,291,292,319,324,328,333,334,341,352,354,356,357,364,365,368,375,384,386,388,392,393,397,409,411,415,416,419,421,422,423,429,430,438,440,441,442,443,448,450,453,454,456,461,466,473,477,482],formal:[6,78,80,91,228,229,235,251,275,307,315],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,205,206,207,208,210,212,274,277,281,283,285,288,292,293,303,318,319,330,331,334,352,356,357,363,364,368,375,384,387,397,409,411,420,421,422,424,429,440,446,453,454,456,457,458,461,472,473,474,482,484],former:[6,12,16,39,41,191,210,319,323,368,370,462,468,482],formerli:[7,13],formul:[1,40,64,141,197,222,235,251,269,283,285,291,295,318,347,364,368,384,386,389,409,418],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,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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.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump 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/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,451,452,453,456,457,459,461,463,464,465,468,470,472,473,474,475,476,481,483,484,485],"function":482,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,482],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,448],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,482],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92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per:6,perform:[1,10],peri:418,period:25,phonon:[9,13,274],pimd:275,piston:326,planeforc:276,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:418,poem:277,point:283,polariz:6,poli:[370,407,408],polym:13,polymorph:419,post:7,potenti:[2,6,8],pour:278,pppm:6,prd:451,pre:7,press:279,pressur:112,previou:12,print:[280,452],problem:[3,4],process:[6,7],processor:453,profil:153,properti:[6,113,114,115,281],pymol_aspher:13,python:[11,13,454],qbmsst:282,qeq:[283,284,285],qmmm:[9,286],qtb:[9,287],quadrat:183,quantiti:6,quartic:[35,54],quip:420,quit:455,ramp:154,rattl:295,rdf:116,read_data:456,read_dump:457,read_restart:458,reax:[13,285,288,289,421,422],reaxc:9,rebo:364,recent:290,reduc:117,refer:482,reflect:327,region:[8,117,155,156,328,459,482],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,226,227,228,229,230,231,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,287,288,289,290,292,293,294,296,297,298,299,300,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,350,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,465,466,468,469,470,471,472,473,474,475,476,478,479,480,482,483,484,485,486],relax:214,replic:460,replica:[6,7],report:3,requir:12,rerun:461,rescal:[312,313],reset:221,reset_timestep:462,resquar:423,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,463],restrain:291,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],rho:126,rhosum:434,rigid:[6,83,98,241,292],ring:341,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],run_styl:465,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,424],self:306,serial:11,set:[6,466],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,467],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,482],special_bond:468,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:469,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],system:6,tabl:[0,6,38,56,185,440,441],tad:470,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:471,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,472],thermo_modifi:473,thermo_styl:474,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:475,timestep:476,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:13,torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:343,uncomput:478,undump:479,unfi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\ No newline at end of file diff --git a/doc/timer.html b/doc/timer.html index fc618f8c89..18b7b91604 100644 --- a/doc/timer.html +++ b/doc/timer.html @@ -135,12 +135,12 @@
  • args = one or more of off or loop or normal or full or sync or nosync
    • -off = do not collect and print timing information
+off = do not collect or print any timing information
 loop = collect only the total time for the simulation loop
-normal = collect timer information broken down in sections (default)
+normal = collect timer information broken down by sections (default)
 full = like normal but also include CPU and thread utilzation
 sync = explicitly synchronize MPI tasks between sections
-nosync = do not synchronize MPI tasks when collecting timer info (default)
+nosync = do not synchronize MPI tasks between sections (default)
    @@ -152,36 +152,37 @@ timer loop

    Description

    -

    Select to which level of detail LAMMPS is performing internal profiling.

    -

    During regular runs LAMMPS will collect information about how much +

    Select the level of detail LAMMPS performs its CPU timings.

    +

    During a simulation run LAMMPS collects information about how much time is spent in different sections of the code and thus can provide valuable information for determining performance and load imbalance problems. This can be done at different levels of detail and -accuracy. For more information about the timing output, please have a -look at the discussion of screen output.

    +accuracy. For more information about the timing output, see this +discussion of screen output.

    The off setting will turn all time measurements off. The loop -setting will only measure the total time of run loop and not collect -any detailed per section information. With the normal setting, -timing information for individual sections of the code are collected -and also information about load imbalances inside those sections -presented. The full setting adds information about CPU utilization -and thread utilization, when multi-threading is enabled.

    +setting will only measure the total time for a run and not collect any +detailed per section information. With the normal setting, timing +information for portions of the timestep (pairwise calculations, +neighbor list construction, output, etc) are collected as well as +information about load imbalances for those sections across +procsessors. The full setting adds information about CPU +utilization and thread utilization, when multi-threading is enabled.

    With the sync setting, all MPI tasks are synchronized at each timer -call and thus allowing to study load imbalance more accuractly, but -this usually has some performance impact. Using the nosync setting -this can be turned off (which is the default).

    -

    Multiple keywords can be provided and for keywords that are mutually -exclusive, the last one in that group is taking effect.

    +call which meaures load imbalance more accuractly, though it can also +slow down the simulation. Using the nosync setting (which is the +default) turns off this synchronization.

    +

    Multiple keywords can be specified. For keywords that are mutually +exclusive, the last one specified takes effect.

    Warning

    Using the full and sync options provides the most -detailed and accurate timing information, but also can have a -significant negative performance impact due to the overhead of the -many required system calls. It is thus recommended to use these -settings only when making tests to identify the performance. For -calculations with few atoms or a very large number of performance, -even using the normal setting can have a measurable performance -impact. In those cases just use the loop or off setting.

    +detailed and accurate timing information, but can also have a negative +performance impact due to the overhead of the many required system +calls. It is thus recommended to use these settings only when testing +tests to identify performance bottlenecks. For calculations with few +atoms or a very large number of processors, even the normal setting +can have a measurable negative performance impact. In those cases you +can just use the loop or off setting.

    diff --git a/doc/timer.txt b/doc/timer.txt index ced3750d51..d465e450f6 100644 --- a/doc/timer.txt +++ b/doc/timer.txt @@ -13,12 +13,12 @@ timer command :h3 timer args :pre {args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} :l - {off} = do not collect and print timing information + {off} = do not collect or print any timing information {loop} = collect only the total time for the simulation loop - {normal} = collect timer information broken down in sections (default) + {normal} = collect timer information broken down by sections (default) {full} = like {normal} but also include CPU and thread utilzation {sync} = explicitly synchronize MPI tasks between sections - {nosync} = do not synchronize MPI tasks when collecting timer info (default) :pre + {nosync} = do not synchronize MPI tasks between sections (default) :pre [Examples:] @@ -27,43 +27,45 @@ timer loop :pre [Description:] -Select to which level of detail LAMMPS is performing internal profiling. +Select the level of detail LAMMPS performs its CPU timings. -During regular runs LAMMPS will collect information about how much +During a simulation run LAMMPS collects information about how much time is spent in different sections of the code and thus can provide valuable information for determining performance and load imbalance problems. This can be done at different levels of detail and -accuracy. For more information about the timing output, please have a -look at the "discussion of screen output"_Section_start.html#start_8. +accuracy. For more information about the timing output, see this +"discussion of screen output"_Section_start.html#start_8. The {off} setting will turn all time measurements off. The {loop} -setting will only measure the total time of run loop and not collect -any detailed per section information. With the {normal} setting, -timing information for individual sections of the code are collected -and also information about load imbalances inside those sections -presented. The {full} setting adds information about CPU utilization -and thread utilization, when multi-threading is enabled. +setting will only measure the total time for a run and not collect any +detailed per section information. With the {normal} setting, timing +information for portions of the timestep (pairwise calculations, +neighbor list construction, output, etc) are collected as well as +information about load imbalances for those sections across +procsessors. The {full} setting adds information about CPU +utilization and thread utilization, when multi-threading is enabled. With the {sync} setting, all MPI tasks are synchronized at each timer -call and thus allowing to study load imbalance more accuractly, but -this usually has some performance impact. Using the {nosync} setting -this can be turned off (which is the default). +call which meaures load imbalance more accuractly, though it can also +slow down the simulation. Using the {nosync} setting (which is the +default) turns off this synchronization. -Multiple keywords can be provided and for keywords that are mutually -exclusive, the last one in that group is taking effect. +Multiple keywords can be specified. For keywords that are mutually +exclusive, the last one specified takes effect. IMPORTANT NOTE: Using the {full} and {sync} options provides the most -detailed and accurate timing information, but also can have a -significant negative performance impact due to the overhead of the -many required system calls. It is thus recommended to use these -settings only when making tests to identify the performance. For -calculations with few atoms or a very large number of performance, -even using the {normal} setting can have a measurable performance -impact. In those cases just use the {loop} or {off} setting. +detailed and accurate timing information, but can also have a negative +performance impact due to the overhead of the many required system +calls. It is thus recommended to use these settings only when testing +tests to identify performance bottlenecks. For calculations with few +atoms or a very large number of processors, even the {normal} setting +can have a measurable negative performance impact. In those cases you +can just use the {loop} or {off} setting. [Restrictions:] none [Related commands:] + "run post no"_run.html, "kspace_modify fftbench"_kspace_modify.html [Default:]