From 0e5c36676f1dc94e44da763d91388b88797408a0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 7 Mar 2016 17:29:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14724 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 6 +- doc/Section_example.html | 192 ++-- doc/Section_example.txt | 103 +- doc/Section_packages.html | 1544 ++++++++++++++++----------- doc/Section_packages.txt | 1549 ++++++++++++++++----------- doc/Section_perf.html | 124 +-- doc/Section_perf.txt | 95 +- doc/_sources/Section_example.txt | 269 ++--- doc/_sources/Section_packages.txt | 1586 +++++++++++++++++----------- doc/_sources/Section_perf.txt | 101 +- doc/_sources/accelerate_kokkos.txt | 38 +- doc/_sources/pair_brownian.txt | 10 +- doc/_sources/pair_lubricate.txt | 8 +- doc/_sources/pair_lubricateU.txt | 9 +- doc/_sources/pair_peri.txt | 2 +- doc/accelerate_kokkos.html | 18 +- doc/accelerate_kokkos.txt | 10 +- doc/pair_brownian.html | 10 +- doc/pair_brownian.txt | 10 +- doc/pair_lubricate.html | 8 +- doc/pair_lubricate.txt | 8 +- doc/pair_lubricateU.html | 9 +- doc/pair_lubricateU.txt | 9 +- doc/pair_peri.html | 4 +- doc/pair_peri.txt | 2 +- doc/searchindex.js | 2 +- 26 files changed, 3428 insertions(+), 2298 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 75e9a18c08..96d5926acc 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -260,7 +260,11 @@ it gives quick access to documentation for all LAMMPS commands.

  • 6.27. Drude induced dipoles
    • -
  • 7. Example problems
    • +
  • 7. Example problems +
  • 8. Performance & scalability
  • 9. Additional tools
  • 4.2. User packages -PERI +PERI Peridynamics models Mike Parks (Sandia) pair_style peri @@ -490,14 +477,14 @@ name links to a sub-section below with more details.

    -POEMS +POEMS coupled rigid body motion Rudra Mukherjee (JPL) fix poems rigid lib/poems -PYTHON +PYTHON embed Python code in an input script -SRD +SRD stochastic rotation dynamics -VORONOI +VORONOI Voronoi tesselations Daniel Schwen (LANL) compute voronoi/atom @@ -589,7 +576,7 @@ name links to a sub-section below with more details.

    Voro++ -XTC +XTC dumps in XTC format -  +        @@ -616,16 +603,17 @@ name links to a sub-section below with more details.

    The “Authors” column lists a name(s) if a specific person is responible for creating and maintaining the package.

    -

    (1) The FLD package was created by Amit Kumar and Michael Bybee from -Jonathan Higdon’s group at UIUC.

    +

    (1) The COLLOID package includes Fast Lubrication Dynamics pair styles +which were created by Amit Kumar and Michael Bybee from Jonathan +Higdon’s group at UIUC.

    (2) The OPT package was created by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy).

    (3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, and Ellad Tadmor (U Minn).

    -

    (4) The KOKKOS package was created primarily by Christian Trott -(Sandia). It uses the Kokkos library which was developed by Carter -Edwards, Christian, and collaborators at Sandia.

    +

    (4) The KOKKOS package was created primarily by Christian Trott and +Stan Moore (Sandia). It uses the Kokkos library which was developed +by Carter Edwards, Christian Trott, and others at Sandia.

    The “Doc page” column links to either a sub-section of the Section_howto of the manual, or an input script command implemented as part of the package, or to additional @@ -644,8 +632,8 @@ p.s.: are we ever going to get commit messages from you? ;-)

    4.1.1. ASPHERE package

    -

    Contents: Aspherical particle models for ellipsoids, 2d lines, 3d -triangles.

    +

    Contents: Several computes, time-integration fixes, and pair styles +for aspherical particle models: ellipsoids, 2d lines, 3d triangles.

    To install via make or Make.py:

    make yes-asphere
 make machine
@@ -662,13 +650,18 @@ make machine
 
    Make.py -p ^asphere -a machine
 
    
 
    
-
    Supporting info: examples/ASPHERE, examples/ellipse, Section howto
-6.14, pair gayberne
    
+
    Supporting info: Section howto 6.14,
+pair_style gayberne, pair_style resquared,
+doc/PDF/pair_gayberne_extra.pdf,
+doc/PDF/pair_resquared_extra.pdf,
+examples/ASPHERE, examples/ellipse

    4.1.2. BODY package

    -

    Contents:

    +

    Contents: Support for body-style particles. Computes, +time-integration fixes, pair styles, as well as the body styles +themselves. See the body doc page for an overview.

    To install via make or Make.py:

    make yes-body
 make machine
@@ -685,12 +678,14 @@ make machine
 
    Make.py -p ^body -a machine
 
    
 
    
-
    Supporting info: examples/body
    
+
    Supporting info: atom_style body, body,
+pair_style body, examples/body

    4.1.3. CLASS2 package

    -

    Contents:

    +

    Contents: Bond, angle, dihedral, improper, and pair styles for the +COMPASS CLASS2 molecular force field.

    To install via make or Make.py:

    make yes-class2
 make machine
@@ -707,12 +702,16 @@ make machine
 
    Make.py -p ^class2 -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: bond_style class2, angle_style class2, dihedral_style class2, improper_style class2, pair_style lj/class2

    4.1.4. COLLOID package

    -

    Contents:

    +

    Contents: Support for coarse-grained colloidal particles. Wall fix +and pair styles that implement colloidal interaction models for +finite-size particles. This includes the Fast Lubrication Dynamics +method for hydrodynamic interactions, which is a simplified +approximation to Stokesian dynamics.

    To install via make or Make.py:

    make yes-colloid
 make machine
@@ -729,12 +728,19 @@ make machine
 
    Make.py -p ^colloid -a machine
 
    
 
    
-
    Supporting info: examples/colloid, examples/srd
    
+
    Supporting info: fix wall/colloid, pair_style colloid, pair_style yukawa/colloid, pair_style brownian, pair_style lubricate, pair_style lubricateU, examples/colloid, examples/srd

    4.1.5. COMPRESS package

    -

    Contents:

    +

    Contents: Support for compressed output of dump files via the zlib +compression library, using dump styles with a “gz” in their style +name.

    +

    Building with the COMPRESS package assumes you have the zlib +compression library available on your system. The build uses the +lib/compress/Makefile.lammps file in the compile/link process. You +should only need to edit this file if the LAMMPS build cannot find the +zlib info it specifies.

    To install via make or Make.py:

    make yes-compress
 make machine
@@ -751,12 +757,17 @@ make machine
 
    Make.py -p ^compress -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: src/COMPRESS/README, lib/compress/README, dump atom/gz, dump cfg/gz, dump custom/gz, dump xyz/gz

    4.1.6. CORESHELL package

    -

    Contents:

    +

    Contents: Compute and pair styles that implement the adiabatic +core/shell model for polarizability. The compute temp/cs command +measures the temperature of a system with core/shell particles. The +pair styles augment Born, Buckingham, and Lennard-Jones styles with +core/shell capabilities. See Section howto 6.26 for an overview of how to use the +package.

    To install via make or Make.py:

    make yes-coreshell
 make machine
@@ -773,12 +784,15 @@ make machine
 
    Make.py -p ^coreshell -a machine
 
    
 
    
-
    Supporting info: examples/coreshell, Section howto 6.26
    
+
    Supporting info: Section howto 6.26, compute temp/cs,
+pair_style born/coul/long/cs, pair_style buck/coul/long/cs, pair_style
+lj/cut/coul/long/cs”_pair_lj.html, examples/coreshell

    4.1.7. DIPOLE package

    -

    Contents:

    +

    Contents: An atom style and several pair styles to support point +dipole models with short-range or long-range interactions.

    To install via make or Make.py:

    make yes-dipole
 make machine
@@ -795,40 +809,48 @@ make machine
 
    Make.py -p ^dipole -a machine
 
    
 
    
-
    Supporting info: examples/dipole
    
-
    
-
    -
    -

    4.1.8. FLD package

    -

    Contents:

    -

    To install via make or Make.py:

    -
    make yes-fld
-make machine
-
    -
    -
    Make.py -p fld -a machine
-
    -
    -

    To un-install via make or Make.py:

    -
    make no-fld
-make machine
-
    -
    -
    Make.py -p ^fld -a machine
-
    -
    -

    Supporting info:

    +

    Supporting info: atom_style dipole, pair_style lj/cut/dipole/cut, pair_style lj/cut/dipole/long, pair_style lj/long/dipole/long, examples/dipole

    -

    4.1.9. GPU package

    -

    Contents:

    +

    4.1.8. GPU package

    +

    Contents: Dozens of pair styles and a version of the PPPM long-range +Coulombic solver for NVIDIA GPUs. All of them have a “gpu” in their +style name. Section accelerate gpu gives +details of what hardware and Cuda software is required on your system, +and how to build and use this package. See the KOKKOS and USER-CUDA +packages, which also have GPU-enabled styles.

    +

    Building LAMMPS with the GPU package requires first building the GPU +library itself, which is a set of C and Cuda files in lib/gpu. +Details of how to do this are in lib/gpu/README. As illustrated +below, perform a “make” using one of the Makefile.machine files in +lib/gpu which should create a lib/reax/libgpu.a file. +Makefile.linux.* and Makefile.xk7 are examples for different +platforms. There are 3 important settings in the Makefile.machine you +use:

    +
      +
    • CUDA_HOME = where NVIDIA Cuda software is installed on your system
      • +
    • CUDA_ARCH = appropriate to your GPU hardware
      • +
    • CUDA_PREC = precision (double, mixed, single) you desire
      • +
    +

    See example Makefile.machine files in lib/gpu for the syntax of these +settings. See lib/gpu/Makefile.linux.double for ARCH settings for +various NVIDIA GPUs. The “make” also creates a +lib/gpu/Makefile.lammps file. This file has settings that enable +LAMMPS to link with Cuda libraries. If the settings in +Makefile.lammps for your machine are not correct, the LAMMPS link will +fail. Note that the Make.py script has a “-gpu” option to allow the +GPU library (with several of its options) and LAMMPS to be built in +one step, with Type “python src/Make.py -h -gpu” to see the details.

    To install via make or Make.py:

    -
    make yes-gpu
+
    cd ~/lammps/lib/gpu
+make -f Makefile.linux.mixed     # for example
+cd ~/lammps/src
+make yes-gpu
 make machine
 
    
 
    
-
    Make.py -p gpu -a machine
+
    Make.py -p gpu -gpu mode=mixed arch=35 -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
@@ -839,12 +861,16 @@ make machine
 
    Make.py -p ^gpu -a machine
 
    
 
    
-
    Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
    
+
    Supporting info: src/GPU/README, lib/gpu/README, Section acclerate, Section accelerate gpu, Pair Styles section of Section commands 3.5 for any pair style listed with a (g),
+kspace_style, package gpu,
+examples/accelerate, bench/FERMI, bench/KEPLER
    
 
    
 
    
 
    
-
    4.1.10. GRANULAR package
    
-
    Contents:
    
+
    4.1.9. GRANULAR package
    
+
    Contents: Fixes and pair styles that support models of finite-size
+granular particles, which interact with each other and boundaries via
+frictional and dissipative potentials.
    
 
    To install via make or Make.py:
    
 
    make yes-granular
 make machine
@@ -861,12 +887,19 @@ make machine
 
    Make.py -p ^granular -a machine
 
    
 
    
-
    Supporting info: examples/pour, bench/in.chute, Section howto 6.6
    
+
    Supporting info: Section howto 6.6, fix pour, fix wall/gran, pair_style gran/hooke, pair_style gran/hertz/history, examples/pour, bench/in.chute
    
 
    
 
    
 
    
-
    4.1.11. KIM package
    
-
    Contents:
    
+
    4.1.10. KIM package
    
+
    Contents: A pair style that interfaces to the Knowledge Base for
+Interatomic Models (KIM) repository of interatomic potentials, so that
+KIM potentials can be used in a LAMMPS simulation.
    
+
    To build LAMMPS with the KIM package you must have previously
+installed the KIM API (library) on your system.  The lib/kim/README
+file explains how to download and install KIM.  Building with the KIM
+package also uses the lib/kim/Makefile.lammps file in the compile/link
+process.  You should not need to edit this file.
    
 
    To install via make or Make.py:
    
 
    make yes-kim
 make machine
@@ -883,54 +916,72 @@ make machine
 
    Make.py -p ^kim -a machine
 
    
 
    
-
    Supporting info: examples/kim
    
+
    Supporting info: src/KIM/README, lib/kim/README, pair_style kim, examples/kim
    
 
    
 
    
 
    
-
    4.1.12. KOKKOS package
    
-
    Contents:
    
-
    To install via make or Make.py:
    
-
    make yes-kokkow
-make machine
-
    
-
    
-
    Make.py -p kokkow -a machine
+
    4.1.11. KOKKOS package
    
+
    Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
+which run with the Kokkos library to provide optimization for
+multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
+native mode).  All of them have a “kk” in their style name.  Section accelerate kokkos gives details of what
+hardware and software is required on your system, and how to build and
+use this package.  See the GPU, OPT, USER-CUDA, USER-INTEL, USER-OMP
+packages, which also provide optimizations for the same range of
+hardware.
    
+
    Building with the KOKKOS package requires choosing which of 3 hardware
+options you are optimizing for: CPU acceleration via OpenMP, GPU
+acceleration, or Intel Xeon Phi.  (You can build multiple times to
+create LAMMPS executables for different hardware.)  It also requires a
+C++11 compatible compiler.  For GPUs, the NVIDIA “nvcc” compiler is
+used, and an appopriate KOKKOS_ARCH setting should be made in your
+Makefile.machine for your GPU hardware and NVIDIA software.
    
+
    The simplest way to do this is to use Makefile.kokkos_cuda or
+Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
+“make kokkos_cuda” or “make kokkos_omp” or “make kokkos_phi”.  (Check
+the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
+below, you can use the Make.py script with its “-kokkos” option to
+choose which hardware to build for.  Type “python src/Make.py -h
+-kokkos” to see the details.  If these methods do not work on your
+system, you will need to read the Section accelerate kokkos doc page for details of what
+Makefile.machine settings are needed.
    
+
    To install via make or Make.py for each of 3 hardware options:
    
+
    make yes-kokkos
+make kokkos_omp    # for CPUs with OpenMP
+make kokkos_cuda   # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
+make kokkos_phi    # for Xeon Phis
 
    
 
    
+
    Make.py -p kokkos -kokkos omp -a machine           # for CPUs with OpenMP
+Make.py -p kokkos -kokkos cuda arch=35 -a machine  # for GPUs of style arch
+Make.py -p kokkos -kokkos phi -a machine           # for Xeon Phis
    
 
    To un-install via make or Make.py:
    
-
    make no-kokkow
+
    make no-kokkos
 make machine
 
    
 
    
-
    Make.py -p ^kokkow -a machine
+
    Make.py -p ^kokkos -a machine
 
    
 
    
-
    Supporting info:
    
-
    For the KOKKOS package, you have 3 choices when building.  You can
-build with OMP or Cuda or Phi support.  Phi support uses Xeon Phi
-chips in “native” mode.  This can be done by setting the following
-variables in your Makefile.machine:
    
-
      
-
    • for OMP support, set OMP = yes
      • 
-
    • for Cuda support, set OMP = yes and CUDA = yes
      • 
-
    • for Phi support, set OMP = yes and MIC = yes
      • 
-
    
-
    These can also be set as additional arguments to the make command, e.g.
    
-
    make g++ OMP=yes MIC=yes
-
    
-
    
-
    Building the KOKKOS package with CUDA support requires a Makefile
-machine that uses the NVIDIA “nvcc” compiler, as well as an
-appropriate “arch” setting appropriate to the GPU hardware and NVIDIA
-software you have on your machine.  See
-src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
-Makefile.
    
-
    Examples: examples/accelerate, bench/FERMI, bench/KEPLER
    
+
    Supporting info: src/KOKKOS/README, lib/kokkos/README, Section acclerate, Section accelerate kokkos, Pair Styles section of Section commands 3.5 for any pair style listed
+with a (k), package kokkos,
+examples/accelerate, bench/FERMI, bench/KEPLER
    
 
    
 
    
 
    
-
    4.1.13. KSPACE package
    
-
    Contents:
    
+
    4.1.12. KSPACE package
    
+
    Contents: A variety of long-range Coulombic solvers, and pair styles
+which compute the corresponding short-range portion of the pairwise
+Coulombic interactions.  These include Ewald, particle-particle
+particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
    
+
    Building with the KSPACE package requires a 1d FFT library be present
+on your system for use by the PPPM solvers.  This can be the KISS FFT
+library provided with LAMMPS, or 3rd party libraries like FFTW or a
+vendor-supplied FFT library.  See step 6 of Section start 2.2.2 of the manual for details of how
+to select different FFT options in your machine Makefile.  The Make.py
+tool has an “-fft” option which can insert these settings into your
+machine Makefile automatically.  Type “python src/Make.py -h -fft” to
+see the details.
    
 
    To install via make or Make.py:
    
 
    make yes-kspace
 make machine
@@ -947,14 +998,18 @@ make machine
 
    Make.py -p ^kspace -a machine
 
    
 
    
-
    Supporting info:
    
-
    Examples: examples/peptide, bench/in.rhodo
    
-
    Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
    
+
    Supporting info: kspace_style,
+doc/PDF/kspace.pdf, Section howto 6.7, Section howto 6.8, Section howto 6.9, pair_style coul,
+other pair style command doc pages which have “long” or “msm” in their
+style name, examples/peptide, bench/in.rhodo
    
 
    
 
    
 
    
-
    4.1.14. MANYBODY package
    
-
    Contents:
    
+
    4.1.13. MANYBODY package
    
+
    Contents: A variety of many-body and bond-order potentials.  These
+include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
+potentials.  Do a directory listing, “ls src/MANYBODY”, to see
+the full list.
    
 
    To install via make or Make.py:
    
 
    make yes-manybody
 make machine
@@ -972,12 +1027,16 @@ make machine
 
    
 
    
 
    Supporting info:
    
-
    Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
    
+
    Examples: Pair Styles section of Section commands 3.5, examples/comb, examples/eim,
+examples/nb3d, examples/vashishta
    
 
    
 
    
 
    
-
    4.1.15. MC package
    
-
    Contents:
    
+
    4.1.14. MC package
    
+
    Contents: Several fixes and a pair style that have Monte Carlo (MC) or
+MC-like attributes.  These include fixes for creating, breaking, and
+swapping bonds, and for performing atomic swaps and grand-canonical MC
+in conjuction with dynamics.
    
 
    To install via make or Make.py:
    
 
    make yes-mc
 make machine
@@ -994,18 +1053,43 @@ make machine
 
    Make.py -p ^mc -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: fix atom/swap, fix bond/break, fix bond/create, fix bond/swap,
+fix gcmc, pair_style dsmc
    
 
    
 
    
 
    
-
    4.1.16. MEAM package
    
-
    Contents:
    
+
    4.1.15. MEAM package
    
+
    Contents: A pair style for the modified embedded atom (MEAM)
+potential.
    
+
    Building LAMMPS with the MEAM package requires first building the MEAM
+library itself, which is a set of Fortran 95 files in lib/meam.
+Details of how to do this are in lib/meam/README.  As illustrated
+below, perform a “make” using one of the Makefile.machine files in
+lib/meam which should create a lib/meam/libmeam.a file.
+Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
+and Intel Fortran compilers.  The “make” also copies a
+lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps.
+This file has settings that enable the C++ compiler used to build
+LAMMPS to link with a Fortran library (typically the 2 compilers to be
+consistent e.g. both Intel compilers, or both GNU compilers).  If the
+settings in Makefile.lammps for your compilers and machine are not
+correct, the LAMMPS link will fail.  Note that the Make.py script has
+a “-meam” option to allow the MEAM library and LAMMPS to be built in
+one step.  Type “python src/Make.py -h -meam” to see the details.
    
+
    
+
    Note
    
+
    The MEAM potential can run dramatically faster if built with the
+Intel Fortran compiler, rather than the GNU Fortran compiler.
    
+
    
 
    To install via make or Make.py:
    
-
    make yes-meam
+
    cd ~/lammps/lib/meam
+make -f Makefile.gfortran    # for example
+cd ~/lammps/src
+make yes-meam
 make machine
 
    
 
    
-
    Make.py -p meam -a machine
+
    Make.py -p meam -meam make=gfortran -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
@@ -1016,12 +1100,15 @@ make machine
 
    Make.py -p ^meam -a machine
 
    
 
    
-
    Supporting info: examples/meam
    
+
    Supporting info: lib/meam/README, pair_style meam,
+examples/meam
    
 
    
 
    
 
    
-
    4.1.17. MISC package
    
-
    Contents:
    
+
    4.1.16. MISC package
    
+
    Contents: A variety of computes, fixes, and pair styles that are not
+commonly used, but don’t align with other packages.  Do a directory
+listing, “ls src/MISC”, to see the list of commands.
    
 
    To install via make or Make.py:
    
 
    make yes-misc
 make machine
@@ -1038,12 +1125,15 @@ make machine
 
    Make.py -p ^misc -a machine
 
    
 
    
-
    Supporting info: examples/misc
    
+
    Supporting info: compute ti, fix evaporate, fix tmm, fix viscosity, examples/misc
    
 
    
 
    
 
    
-
    4.1.18. MOLECULE package
    
-
    Contents:
    
+
    4.1.17. MOLECULE package
    
+
    Contents: A large number of atom, pair, bond, angle, dihedral,
+improper styles that are used to model molecular systems with fixed
+covalent bonds.  The pair styles include terms for the Dreiding
+(hydrogen-bonding) and CHARMM force fields, and TIP4P water model.
    
 
    To install via make or Make.py:
    
 
    make yes-molecule
 make machine
@@ -1060,12 +1150,20 @@ make machine
 
    Make.py -p ^molecule -a machine
 
    
 
    
-
    Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3
    
+
    Supporting info:atom_style,
+bond_style, angle_style,
+dihedral_style,
+improper_style, pair_style hbond/dreiding/lj, pair_style lj/charmm/coul/charmm, Section howto 6.3, examples/micelle, examples/peptide,
+bench/in.chain, bench/in.rhodo
    
 
    
 
    
 
    
-
    4.1.19. MPIIO package
    
-
    Contents:
    
+
    4.1.18. MPIIO package
    
+
    Contents: Support for parallel output/input of dump and restart files
+via the MPIIO library, which is part of the standard message-passing
+interface (MPI) library.  It adds dump styles with a
+“mpiio” in their style name.  Restart files with an ”.mpiio” suffix
+are also written and read in parallel.
    
 
    To install via make or Make.py:
    
 
    make yes-mpiio
 make machine
@@ -1082,12 +1180,23 @@ make machine
 
    Make.py -p ^mpiio -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: dump, restart,
+write_restart, read_restart
    
 
    
 
    
 
    
-
    4.1.20. OPT package
    
-
    Contents:
    
+
    4.1.19. OPT package
    
+
    Contents: A handful of pair styles with an “opt” in their style name
+which are optimized for improved CPU performance on single or multiple
+cores.  These include EAM, LJ, CHARMM, and Morse potentials.  Section accelerate opt gives details of how to build and
+use this package.  See the KOKKOS, USER-INTEL, and USER-OMP packages,
+which also have styles optimized for CPU performance.
    
+
    Some C++ compilers, like the Intel compiler, require the compile flag
+“-restrict” to build LAMMPS with the OPT package.  It should be added
+to the CCFLAGS line of your Makefile.machine.  Or use Makefile.opt in
+src/MAKE/OPTIONS, via “make opt”.  For compilers that use the flag,
+the Make.py command adds it automatically to the Makefile.auto file it
+creates and uses.
    
 
    To install via make or Make.py:
    
 
    make yes-opt
 make machine
@@ -1104,17 +1213,16 @@ make machine
 
    Make.py -p ^opt -a machine
 
    
 
    
-
    Supporting info: examples/accelerate, bench/KEPLER
    
-
    For the OPT package, your Makefile.machine needs an additional
-settings for CCFLAGS.
    
-
      
-
    • CCFLAGS: add -restrict
      • 
-
    
+
    Supporting info: Section acclerate, Section accelerate opt, Pair Styles section of Section commands 3.5 for any pair style listed
+with an (o), examples/accelerate, bench/KEPLER
    
 
    
 
    
 
    
-
    4.1.21. PERI package
    
-
    Contents:
    
+
    4.1.20. PERI package
    
+
    Contents: Support for the Peridynamics method, a particle-based
+meshless continuum model.  The package includes an atom style, several
+computes which calculate diagnostics, and several Peridynamic pair
+styles which implement different materials models.
    
 
    To install via make or Make.py:
    
 
    make yes-peri
 make machine
@@ -1131,34 +1239,69 @@ make machine
 
    Make.py -p ^peri -a machine
 
    
 
    
-
    Supporting info: examples/peri
    
+
    Supporting info:
+doc/PDF/PDLammps_overview.pdf,
+doc/PDF/PDLammps_EPS.pdf,
+doc/PDF/PDLammps_VES.pdf, atom_style peri, compute damage,
+pair_style peri/pmb, examples/peri
    
 
    
 
    
 
    
-
    4.1.22. POEMS package
    
-
    Contents:
    
+
    4.1.21. POEMS package
    
+
    Contents: A fix that wraps the Parallelizable Open source Efficient
+Multibody Software (POEMS) librar, which is able to simulate the
+dynamics of articulated body systems.  These are systems with multiple
+rigid bodies (collections of atoms or particles) whose motion is
+coupled by connections at hinge points.
    
+
    Building LAMMPS with the POEMS package requires first building the
+POEMS library itself, which is a set of C++ files in lib/poems.
+Details of how to do this are in lib/poems/README.  As illustrated
+below, perform a “make” using one of the Makefile.machine files in
+lib/poems which should create a lib/meam/libpoems.a file.
+Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++
+compilers.  The “make” also creates a lib/poems/Makefile.lammps file
+which you should not need to change.  Note the Make.py script has a
+“-poems” option to allow the POEMS library and LAMMPS to be built in
+one step.  Type “python src/Make.py -h -poems” to see the details.
    
 
    To install via make or Make.py:
    
-
    make yes-poems
+
    cd ~/lammps/lib/poems
+make -f Makefile.g++    # for example
+cd ~/lammps/src
+make yes-poems
 make machine
 
    
 
    
-
    Make.py -p poems -a machine
+
    Make.py -p poems -poems make=g++ -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-poems
+
    make no-meam
 make machine
 
    
 
    
-
    Make.py -p ^poems -a machine
+
    Make.py -p ^meam -a machine
 
    
 
    
-
    Supporting info: examples/rigid
    
+
    Supporting info: src/POEMS/README, lib/poems/README,
+fix_poems, examples/rigid
    
 
    
 
    
 
    
-
    4.1.23. PYTHON package
    
-
    Contents:
    
+
    4.1.22. PYTHON package
    
+
    Contents: A python command which allow you to execute
+Python code from a LAMMPS input script.  The code can be in a separate
+file or embedded in the input script itself.  See Section python 11.2 for an overview of using Python from
+LAMMPS and Section python for other ways to use
+LAMMPS and Python together.
    
+
    Building with the PYTHON package assumes you have a Python shared
+library available on your system, which needs to be a Python 2
+version, 2.6 or later.  Python 3 is not supported.  The build uses the
+contents of the lib/python/Makefile.lammps file to find all the Python
+files required in the build/link process.  See the lib/python/README
+file if the settings in that file do not work on your system.  Note
+that the Make.py script has a “-python” option to allow an alternate
+lib/python/Makefile.lammps file to be specified and LAMMPS to be built
+in one step.  Type “python src/Make.py -h -python” to see the details.
    
 
    To install via make or Make.py:
    
 
    make yes-python
 make machine
@@ -1179,8 +1322,10 @@ make machine
 
    
 
    
 
    
-
    4.1.24. QEQ package
    
-
    Contents:
    
+
    4.1.23. QEQ package
    
+
    Contents: Several fixes for performing charge equilibration (QEq) via
+severeal different algorithms.  These can be used with pair styles
+that use QEq as part of their formulation.
    
 
    To install via make or Make.py:
    
 
    make yes-qeq
 make machine
@@ -1197,18 +1342,38 @@ make machine
 
    Make.py -p ^qeq -a machine
 
    
 
    
-
    Supporting info: examples/qeq
    
+
    Supporting info: fix qeq/*, examples/qeq
    
 
    
 
    
 
    
-
    4.1.25. REAX package
    
-
    Contents:
    
+
    4.1.24. REAX package
    
+
    Contents: A pair style for the ReaxFF potential, a universal reactive
+force field, as well as a fix reax/bonds command
+for monitoring molecules as bonds are created and destroyed.
    
+
    Building LAMMPS with the REAX package requires first building the REAX
+library itself, which is a set of Fortran 95 files in lib/reax.
+Details of how to do this are in lib/reax/README.  As illustrated
+below, perform a “make” using one of the Makefile.machine files in
+lib/reax which should create a lib/reax/libreax.a file.
+Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
+and Intel Fortran compilers.  The “make” also copies a
+lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps.
+This file has settings that enable the C++ compiler used to build
+LAMMPS to link with a Fortran library (typically the 2 compilers to be
+consistent e.g. both Intel compilers, or both GNU compilers).  If the
+settings in Makefile.lammps for your compilers and machine are not
+correct, the LAMMPS link will fail.  Note that the Make.py script has
+a “-reax” option to allow the REAX library and LAMMPS to be built in
+one step.  Type “python src/Make.py -h -reax” to see the details.
    
 
    To install via make or Make.py:
    
-
    make yes-reax
+
    cd ~/lammps/lib/reax
+make -f Makefile.gfortran    # for example
+cd ~/lammps/src
+make yes-reax
 make machine
 
    
 
    
-
    Make.py -p reax -a machine
+
    Make.py -p reax -reax make=gfortran -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
@@ -1219,12 +1384,22 @@ make machine
 
    Make.py -p ^reax -a machine
 
    
 
    
-
    Supporting info: examples/reax
    
+
    Supporting info: lib/reax/README, pair_style reax,
+fix reax/bonds, examples/reax
    
 
    
 
    
 
    
-
    4.1.26. REPLICA package
    
-
    Contents:
    
+
    4.1.25. REPLICA package
    
+
    Contents: A collection of multi-replica methods that are used by
+invoking multiple instances (replicas) of LAMMPS
+simulations. Communication between individual replicas is performed in
+different ways by the different methods.  See Section howto 6.5 for an overview of how to run
+multi-replica simulations in LAMMPS.  Multi-replica methods included
+in the package are nudged elastic band (NEB), parallel replica
+dynamics (PRD), temperature accelerated dynamics (TAD), parallel
+tempering, and a verlet/split algorithm for performing long-range
+Coulombics on one set of processors, and the remainded of the force
+field calcalation on another set.
    
 
    To install via make or Make.py:
    
 
    make yes-replica
 make machine
@@ -1241,12 +1416,18 @@ make machine
 
    Make.py -p ^replica -a machine
 
    
 
    
-
    Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
    
+
    Supporting info: Section howto 6.5,
+neb, prd, tad, temper,
+run_style verlet/split, examples/neb, examples/prd,
+examples/tad
    
 
    
 
    
 
    
-
    4.1.27. RIGID package
    
-
    Contents:
    
+
    4.1.26. RIGID package
    
+
    Contents: A collection of computes and fixes which enforce rigid
+constraints on collections of atoms or particles.  This includes SHAKE
+and RATTLE, as well as variants of rigid-body time integrators for a
+few large bodies or many small bodies.
    
 
    To install via make or Make.py:
    
 
    make yes-rigid
 make machine
@@ -1263,12 +1444,14 @@ make machine
 
    Make.py -p ^rigid -a machine
 
    
 
    
-
    Supporting info: examples/ASPHERE, examples/rigid
    
+
    Supporting info: compute erotate/rigid,
+fix shake, fix rattle, fix rigid/*, examples/ASPHERE, examples/rigid
    
 
    
 
    
 
    
-
    4.1.28. SHOCK package
    
-
    Contents:
    
+
    4.1.27. SHOCK package
    
+
    Contents: A small number of fixes useful for running impact
+simulations where a shock-wave passes through a material.
    
 
    To install via make or Make.py:
    
 
    make yes-shock
 make machine
@@ -1285,12 +1468,15 @@ make machine
 
    Make.py -p ^shock -a machine
 
    
 
    
-
    Supporting info: examples/hugoniostat, examples/msst
    
+
    Supporting info: fix append/atoms, fix msst, fix nphug, fix wall/piston, examples/hugoniostat, examples/msst
    
 
    
 
    
 
    
-
    4.1.29. SNAP package
    
-
    Contents:
    
+
    4.1.28. SNAP package
    
+
    Contents: A pair style for the spectral neighbor analysis potential
+(SNAP), which is an empirical potential which can be quantum accurate
+when fit to an archive of DFT data.  Computes useful for analyzing
+properties of the potential are also included.
    
 
    To install via make or Make.py:
    
 
    make yes-snap
 make machine
@@ -1307,12 +1493,15 @@ make machine
 
    Make.py -p ^snap -a machine
 
    
 
    
-
    Supporting info: examples/snap
    
+
    Supporting info: pair snap, compute sna/atom, compute snad/atom,
+compute snav/atom, examples/snap
    
 
    
 
    
 
    
-
    4.1.30. SRD package
    
-
    Contents:
    
+
    4.1.29. SRD package
    
+
    Contents: Two fixes which implement the Stochastic Rotation Dynamics
+(SRD) method for coarse-graining of a solvent, typically around large
+colloidal-scale particles.
    
 
    To install via make or Make.py:
    
 
    make yes-srd
 make machine
@@ -1329,18 +1518,41 @@ make machine
 
    Make.py -p ^srd -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: fix srd, fix wall/srd, examples/srd, examples/ASPHERE
    
 
    
 
    
 
    
-
    4.1.31. VORONOI package
    
-
    Contents:
    
+
    4.1.30. VORONOI package
    
+
    Contents: A compute voronoi/atom command
+which computes the Voronoi tesselation of a collection of atoms or
+particles by wrapping the Voro++ lib
    
+
    To build LAMMPS with the KIM package you must have previously
+installed the KIM API (library) on your system.  The lib/kim/README
+file explains how to download and install KIM.  Building with the KIM
+package also uses the lib/kim/Makefile.lammps file in the compile/link
+process.  You should not need to edit this file.
    
+
    To build LAMMPS with the VORONOI package you must have previously
+installed the Voro++ library on your system.  The lib/voronoi/README
+file explains how to download and install Voro++.  There is a
+lib/voronoi/install.py script which automates the process.  Type
+“python install.py” to see instructions.  The final step is to create
+soft links in the lib/voronoi directory for “includelink” and
+“liblink” which point to installed Voro++ directories.  Building with
+the VORONOI package uses the contents of the
+lib/voronoi/Makefile.lammps file in the compile/link process.  You
+should not need to edit this file.  Note that the Make.py script has a
+“-voronoi” option to allow the Voro++ library to be downloaded and/or
+installed and LAMMPS to be built in one step.  Type “python
+src/Make.py -h -voronoi” to see the details.
    
 
    To install via make or Make.py:
    
-
    make yes-voronoi
+
    cd ~/lammps/lib/voronoi
+python install.py -g -b -l    # download Voro++, build in lib/voronoi, create links
+cd ~/lammps/src
+make yes-voronoi
 make machine
 
    
 
    
-
    Make.py -p voronoi -a machine
+
    Make.py -p voronoi -voronoi install="-g -b -l" -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
@@ -1351,12 +1563,13 @@ make machine
 
    Make.py -p ^voronoi -a machine
 
    
 
    
-
    Supporting info: examples/voronoi
    
+
    Supporting info: src/VORONOI/README, lib/voronoi/README, compute voronoi/atom, examples/voronoi
    
 
    
 
    
 
    
-
    4.1.32. XTC package
    
-
    Contents:
    
+
    4.1.31. XTC package
    
+
    Contents: A dump xtc command for writing snapshots in the
+XTC format used by the GROMACS MD package.
    
 
    To install via make or Make.py:
    
 
    make yes-xtc
 make machine
@@ -1373,7 +1586,7 @@ make machine
 
    Make.py -p ^xtc -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: dump xtc
    
 
    
 
    
 
    
@@ -1797,143 +2010,152 @@ See details on all of this below for individual packages.
    
 
    
 
    
 
    4.2.1. USER-ATC package
    
-
    Contents:
    
+
    Contents: ATC stands for atoms-to-continuum.  This package implements
+a fix atc command to either couple MD with continuum
+finite element equations or perform on-the-fly post-processing of
+atomic information to continuum fields.  See src/USER-ATC/README for
+more details.
    
+
    To build LAMMPS with this package ...
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package implements a “fix atc” command which can be used in a
-LAMMPS input script.  This fix can be employed to either do concurrent
-coupling of MD with FE-based physics surrogates or on-the-fly
-post-processing of atomic information to continuum fields.
    
-
    See the doc page for the fix atc command to get started.  At the
-bottom of the doc page are many links to additional documentation
-contained in the doc/USER/atc directory.
    
-
    There are example scripts for using this package in examples/USER/atc.
    
-
    This package uses an external library in lib/atc which must be
-compiled before making LAMMPS.  See the lib/atc/README file and the
-LAMMPS manual for information on building LAMMPS with external
-libraries.
    
-
    The primary people who created this package are Reese Jones (rjones at
-sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
-Zimmerman (jzimmer at sandia.gov) at Sandia.  Contact them directly if
-you have questions.
    
-
    Examples: examples/USER/atc
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info:src/USER-ATC/README, fix atc,
+examples/USER/atc
    
+
    Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
+at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
+Contact them directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.2. USER-AWPMD package
    
-
    Contents:
    
+
    Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular
+Dynamics.  This package implements an atom, pair, and fix style which
+allows electrons to be treated as explicit particles in an MD
+calculation.  See src/USER-AWPMD/README for more details.
    
+
    To build LAMMPS with this package ...
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package contains a LAMMPS implementation of the Antisymmetrized
-Wave Packet Molecular Dynamics (AWPMD) method.
    
-
    See the doc page for the pair_style awpmd/cut command to get started.
    
-
    There are example scripts for using this package in examples/USER/awpmd.
    
-
    This package uses an external library in lib/awpmd which must be
-compiled before making LAMMPS.  See the lib/awpmd/README file and the
-LAMMPS manual for information on building LAMMPS with external
-libraries.
    
-
    The person who created this package is Ilya Valuev at the JIHT in
-Russia (valuev at physik.hu-berlin.de).  Contact him directly if you
-have questions.
    
-
    Examples: examples/USER/awpmd
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: src/USER-AWPMD/README, fix awpmd/cut, examples/USER/awpmd
    
+
    Author: Ilya Valuev at the JIHT in Russia (valuev at
+physik.hu-berlin.de).  Contact him directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.3. USER-CG-CMM package
    
-
    Contents:
    
+
    Contents: CG-CMM stands for coarse-grained ??.  This package
+implements several pair styles and an angle style using the coarse
+grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
+(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
+lipids and charged amino acids.  See src/USER-CG-CMM/README for more
+details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
-
    Supporting info:
    
-
    This package implements 3 commands which can be used in a LAMMPS input
-script:
    
-
      
-
    • pair_style lj/sdk
      • 
-
    • pair_style lj/sdk/coul/long
      • 
-
    • angle_style sdk
      • 
-
    
-
    These styles allow coarse grained MD simulations with the
-parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
-(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
-and charged amino acids.
    
-
    See the doc pages for these commands for details.
    
-
    There are example scripts for using this package in
-examples/USER/cg-cmm.
    
-
    This is the second generation implementation reducing the the clutter
-of the previous version. For many systems with electrostatics, it will
-be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
-instead of the combined lj/sdk/coul/long style.  since the number of
-charged atom types is usually small.  For any other coulomb
-interactions this is now required.  To exploit this property, the use
-of the kspace_style pppm/cg is recommended over regular pppm. For all
-new styles, input file backward compatibility is provided.  The old
-implementation is still available through appending the /old
-suffix. These will be discontinued and removed after the new
-implementation has been fully validated.
    
-
    The current version of this package should be considered beta
-quality. The CG potentials work correctly for “normal” situations, but
-have not been testing with all kinds of potential parameters and
-simulation systems.
    
-
    The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com).  Contact him directly if you have questions.
    
-
    Examples: examples/USER/cg-cmm
    
+
    Supporting info: src/USER-CG-CMM/README, pair lj/sdk,
+pair lj/sdk/coul/long, angle sdk,
+examples/USER/cg-cmm
    
+
    Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com).  Contact
+him directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.4. USER-COLVARS package
    
-
    Contents:
    
+
    Contents: COLVARS stands for collective variables which can be used to
+implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
+Sampling and Restraints.  This package implements a fix colvars command which wraps a COLVARS library which
+can perform those kinds of simulations.  See src/USER-COLVARS/README
+for more details.
    
+
    To build LAMMPS with this package ...
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package implements the “fix colvars” command which can be
-used in a LAMMPS input script.
    
-
    This fix allows to use “collective variables” to implement
-Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
-Sampling and Restraints. This code consists of two parts:
    
-
      
-
    • A portable collective variable module library written and maintained
      • 
-
    • by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
      • 
-
    • Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
      • 
-
    • the directory lib/colvars and needs to be compiled first.  The colvars
      • 
-
    • fix and an interface layer, exchanges information between LAMMPS and
      • 
-
    • the collective variable module.
      • 
-
    
-
    See the doc page of fix colvars for more details.
    
-
    There are example scripts for using this package in
-examples/USER/colvars
    
-
    This is a very new interface that does not yet support all
-features in the module and will see future optimizations
-and improvements. The colvars module library is also available
-in NAMD has been thoroughly used and tested there. Bugs and
-problems are likely due to the interface layers code.
-Thus the current version of this package should be considered
-beta quality.
    
-
    The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com).  Contact him directly if you have questions.
    
-
    Examples: examples/USER/colvars
    
-
    Contents:
    
-
    To install via make or Make.py:
    
-
    To un-install via make or Make.py:
    
-
    Supporting info:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info:
+doc/PDF/colvars-refman-lammps.pdf,
+src/USER-COLVARS/README, lib/colvars/README, fix colvars, examples/USER/colvars
    
+
    Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
+fix.  The COLVARS library itself is written and maintained by Giacomo
+Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
+Henin (LISM, CNRS, Marseille, France).  Contact them directly if you
+have questions.
    
 
    
 
    
 
    
 
    4.2.5. USER-CUDA package
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
+
    To build LAMMPS with this package ...
    
+
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
+
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
 GPUs.
    
@@ -1949,253 +2171,227 @@ libraries.
    
 University of Technology Ilmenau, Germany (christian.trott at
 tu-ilmenau.de).  Contact him directly if you have questions.
    
 
    Examples: examples/accelerate, bench/FERMI, bench/KEPLER
    
-
    Contents:
    
-
    To install via make or Make.py:
    
-
    To un-install via make or Make.py:
    
-
    Supporting info:
    
 
    
 
    
 
    
 
    4.2.6. USER-DIFFRACTION package
    
-
    This package contains the commands neeed to calculate x-ray and
-electron diffraction intensities based on kinematic diffraction
-theory.
    
-
    See these doc pages and their related commands to get started:
    
-
-
    The person who created this package is Shawn P. Coleman
-(shawn.p.coleman8.ctr at mail.mil) while at the University of
-Arkansas.  Contact him directly if you have questions.
    
-
    Examples: examples/USER/diffraction
    
-
    Contents:
    
+
    Contents: This packages implements two computes and a fix for
+calculating x-ray and electron diffraction intensities based on
+kinematic diffraction theory.  See src/USER-DIFFRACTION/README for
+more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
-
    Supporting info:
    
+
    Supporting info: compute saed, compute xrd, fix saed.vtk,
+examples/USER/diffraction
    
+
    Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
+the University of Arkansas.  Contact him directly if you have
+questions.
    
 
    
 
    
 
    
 
    4.2.7. USER-DPD package
    
-
    This package implements the dissipative particle dynamics (DPD) method
-under isothermal, isoenergetic, isobaric and isenthalpic conditions.
-The DPD equations of motion are integrated efficiently through the
-Shardlow splitting algorithm.
    
-
    See these doc pages and their related commands to get started:
    
-
-
    There are example scripts for using this package in examples/USER/dpd.
    
-
    The people who created this package are James Larentzos
-(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
-engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
-Contact them directly if you have questions.
    
+
    Contents: DPD stands for dissipative particle dynamics, This package
+implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
+conditions.  The DPD equations of motion are integrated efficiently
+through the Shardlow splitting algorithm.  See src/USER-DPD/README for
+more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
-
    Examples: examples/USER/dpd
    
+
    Supporting info: /src/USER-DPD/README, compute dpd
+compute dpd/atom
+fix_eos/cv fix_eos/table
+fix_shardlow
+pair_dpd/conservative
+pair_dpd/fdt
+pair_dpd/fdt/energy, examples/USER/dpd
    
+
    Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
+Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
+and John Brennan (ARL) (john.k.brennan.civ at mail.mil).  Contact them
+directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.8. USER-DRUDE package
    
-
    Contents:
    
+
    Contents: This package contains methods for simulating polarizable
+systems using thermalized Drude oscillators.  It has computes, fixes,
+and pair styles for this purpose.  See Section howto 6.27 for an overview of how to use the
+package.  See src/USER-DRUDE/README for additional details.  There are
+auxiliary tools for using this package in tools/drude.
    
 
    To install via make or Make.py:
    
-
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package implements methods for simulating polarizable systems
-in LAMMPS using thermalized Drude oscillators.
    
-
    See these doc pages and their related commands to get started:
    
-
-
    There are auxiliary tools for using this package in tools/drude.
    
-
    The person who created this package is Alain Dequidt at Universite
-Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
-Contact him directly if you have questions. Co-authors: Julien Devemy,
-Agilio Padua.
    
-
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
-
    Examples: examples/USER/drude
    
-
    Doc: Section howto 6.27
    
+
    Supporting info: Section howto 6.27,
+src/USER-DRUDE/README, fix drude, fix drude/transform/*, compute temp/drude, pair thole,
+pair lj/cut/thole/long, examples/USER/drude,
+tools/drude
    
+
    Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand
+(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy,
+Agilio Padua.  Contact them directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.9. USER-EFF package
    
-
    Contents:
    
+
    Contents: EFF stands for electron force field.  This package contains
+atom, pair, fix and compute styles which implement the eFF as
+described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
+JCC, 2010. The eFF potential was first introduced by Su and Goddard,
+in 2007.  See src/USER-EFF/README for more details.  There are
+auxiliary tools for using this package in tools/eff; see its README
+file.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: atom_style electron, compute temp/eff, fix langevin/eff, fix nve/eff,
+pair eff/cut, examples/USER/eff, tools/eff
    
 
    Supporting info:
    
-
    This package contains a LAMMPS implementation of the electron Force
-Field (eFF) currently under development at Caltech, as described in
-A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
-2010. The eFF potential was first introduced by Su and Goddard, in
-2007.
    
-
    eFF can be viewed as an approximation to QM wave packet dynamics and
-Fermionic molecular dynamics, combining the ability of electronic
-structure methods to describe atomic structure, bonding, and chemistry
-in materials, and of plasma methods to describe nonequilibrium
-dynamics of large systems with a large number of highly excited
-electrons. We classify it as a mixed QM-classical approach rather than
-a conventional force field method, which introduces QM-based terms (a
-spin-dependent repulsion term to account for the Pauli exclusion
-principle and the electron wavefunction kinetic energy associated with
-the Heisenberg principle) that reduce, along with classical
-electrostatic terms between nuclei and electrons, to the sum of a set
-of effective pairwise potentials.  This makes eFF uniquely suited to
-simulate materials over a wide range of temperatures and pressures
-where electronically excited and ionized states of matter can occur
-and coexist.
    
-
    The necessary customizations to the LAMMPS core are in place to
-enable the correct handling of explicit electron properties during
-minimization and dynamics.
    
-
    See the doc page for the pair_style eff/cut command to get started.
    
-
    There are example scripts for using this package in
-examples/USER/eff.
    
-
    There are auxiliary tools for using this package in tools/eff.
    
-
    The person who created this package is Andres Jaramillo-Botero at
-CalTech (ajaramil at wag.caltech.edu).  Contact him directly if you
-have questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
-
    Examples: examples/USER/eff
    
+
    Author: Andres Jaramillo-Botero at CalTech (ajaramil at
+wag.caltech.edu).  Contact him directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.10. USER-FEP package
    
-
    Contents:
    
+
    Contents: FEP stands for free energy perturbation.  This package
+provides methods for performing FEP simulations by using a fix adapt/fep command with soft-core pair potentials,
+which have a “soft” in their style name.  See src/USER-FEP/README for
+more details.  There are auxiliary tools for using this package in
+tools/fep; see its README file.
    
 
    To install via make or Make.py:
    
-
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package provides methods for performing free energy perturbation
-simulations with soft-core pair potentials in LAMMPS.
    
-
    See these doc pages and their related commands to get started:
    
-
-
    The person who created this package is Agilio Padua at Universite
-Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
-Contact him directly if you have questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
-
    Examples: examples/USER/fep
    
+
    Supporting info: src/USER-FEP/README, fix adapt/fep, compute fep,
+pair_style */soft, examples/USER/fep
    
+
    Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand
+(agilio.padua at univ-bpclermont.fr). Contact him directly if you have
+questions.
    
 
    
 
    
 
    
 
    4.2.11. USER-H5MD package
    
-
    Contents:
    
+
    Contents: H5MD stands for HDF5 for MD.  HDF5 is a binary,
+portable, self-describing file format, used by many scientific
+simulations.  H5MD is a format for molecular simulations, built on top
+of HDF5.  This package implements a dump h5md command
+to output LAMMPS snapshots in this format.  See src/USER-H5MD/README
+for more details.
    
+
    To build LAMMPS with this package ...
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package contains a dump h5md command for
-performing a dump of atom properties in HDF5 format.  HDF5 files are binary, portable and self-describing and can be
-examined and used by a variety of auxiliary tools.  The output HDF5
-files are structured in a format called H5MD, which was designed to
-store molecular data, and can be used and produced by various MD and
-MD-related codes.  The dump h5md command gives a
-citation to a paper describing the format.
    
-
    The person who created this package and the underlying H5MD format is
-Pierre de Buyl at KU Leuven (see http://pdebuyl.be).  Contact him
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: src/USER-H5MD/README, lib/h5md/README, dump h5md
    
+
    Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created
+this package as well as the H5MD format and library.  Contact him
 directly if you have questions.
    
 
    
 
    
 
    
 
    4.2.12. USER-INTEL package
    
-
    Contents:
    
+
    Contents: Dozens of pair, bond, angle, dihedral, and improper styles
+that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
+mode).  All of them have an “intel” in their style name.  Section accelerate intel gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package.  Also see src/USER-INTEL/README for more details. See
+the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
+Phi-enabled styles.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
-
    This package provides options for performing neighbor list and
-non-bonded force calculations in single, mixed, or double precision
-and also a capability for accelerating calculations with an
-Intel(R) Xeon Phi(TM) coprocessor.
    
-
    See this section of the manual to get started:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: examples/accelerate, src/USER-INTEL/TEST
    
 
    Section_accelerate
    
-
    The person who created this package is W. Michael Brown at Intel
-(michael.w.brown at intel.com).  Contact him directly if you have questions.
    
+
    Author: Mike Brown at Intel (michael.w.brown at intel.com).  Contact
+him directly if you have questions.
    
 
    For the USER-INTEL package, you have 2 choices when building.  You can
 build with CPU or Phi support.  The latter uses Xeon Phi chips in
 “offload” mode.  Each of these modes requires additional settings in
@@ -2214,14 +2410,32 @@ your Makefile.machine for CCFLAGS and LINKFLAGS.
    
 
     -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs="gather_scatter_loop_unroll=4""
 
    
-
    Examples: examples/accelerate, bench/KEPLER
    
+
    Examples:
    
 
    
 
    
 
    
 
    4.2.13. USER-LB package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
@@ -2231,30 +2445,32 @@ influenced by hydrodynamic forces.
    
 
    The people who created this package are Frances Mackay (fmackay at
 uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
 Western Ontario.  Contact them directly if you have questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
 
    Examples: examples/USER/lb
    
 
    
 
    
 
    
 
    4.2.14. USER-MGPT package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package contains a fast implementation for LAMMPS of
 quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
@@ -2275,30 +2491,32 @@ Oppelstrup at LLNL.
    
 
    The persons who created the USER-MGPT package are Tomas Oppelstrup
 (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
 Contact them directly if you have any questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
 
    Examples: examples/USER/mgpt
    
 
    
 
    
 
    
 
    4.2.15. USER-MISC package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
@@ -2313,30 +2531,32 @@ compute, pair, etc sections.
    
 src/USER-MISC/README file.
    
 
    You should contact the author directly if you have specific questions
 about the feature or its coding.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
 
    Examples: examples/USER/misc
    
 
    
 
    
 
    
 
    4.2.16. USER-MOLFILE package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
@@ -2357,9 +2577,27 @@ application itself.
    
 
    
 
    
 
    4.2.17. USER-OMP package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
@@ -2379,6 +2617,27 @@ settings for CCFLAGS and LINKFLAGS.
    
 
    
 
    
 
    4.2.18. USER-PHONON package
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
+
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
+
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
    
@@ -2387,30 +2646,32 @@ relations, directly from molecular dynamics simulations.
    
 
    The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
 
    Examples: examples/USER/phonon
    
 
    
 
    
 
    
 
    4.2.19. USER-QMMM package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
@@ -2429,9 +2690,27 @@ without changes to LAMMPS itself.
    
 
    
 
    
 
    4.2.20. USER-QTB package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
@@ -2451,53 +2730,59 @@ bath with the shocked system.
    
 
    The person who created this package is Yuan Shen (sy0302 at
 stanford.edu) at Stanford University.  Contact him directly if you
 have questions.
    
-
    To install via make or Make.py:
    
-
    make yes-body
-make machine
-
    
-
    
-
    Make.py -p body -a machine
-
    
-
    
-
    To un-install via make or Make.py:
    
-
    make no-body
-make machine
-
    
-
    
-
    Make.py -p ^body -a machine
-
    
-
    
 
    Examples: examples/USER/qtb
    
 
    
 
    
 
    
 
    4.2.21. USER-QUIP package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    Examples: examples/USER/quip
    
 
    
 
    
 
    
 
    4.2.22. USER-REAXC package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
@@ -2528,9 +2813,27 @@ questions.
    
 
    
 
    
 
    4.2.23. USER-SMD package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package implements smoothed Mach dynamics (SMD) in
 LAMMPS.  Currently, the package has the following features:
    
@@ -2557,23 +2860,27 @@ you have questions.
    
 
    
 
    
 
    4.2.24. USER-SMTBQ package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
 potential for the description of ionocovalent bonds in oxides.
    
@@ -2590,23 +2897,27 @@ them directly if you have any questions.
    
 
    
 
    
 
    4.2.25. USER-SPH package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:
    
@@ -2631,33 +2942,54 @@ you have questions.
    
 
    
 
    
 
    4.2.26. USER-TALLY package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
-
    make yes-body
+
    make yes-user-atc
 make machine
 
    
 
    
-
    Make.py -p body -a machine
+
    Make.py -p atc -a machine
 
    
 
    
 
    To un-install via make or Make.py:
    
-
    make no-body
+
    make no-user-atc
 make machine
 
    
 
    
-
    Make.py -p ^body -a machine
+
    Make.py -p ^atc -a machine
 
    
 
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Supporting info:
    
 
    Examples: examples/USER/tally
    
 
    
 
    
 
    
 
    4.2.27. USER-VTK package
    
-
    Contents:
    
+
    Contents: A fix atc command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
    
 
    To install via make or Make.py:
    
+
    make yes-user-atc
+make machine
+
    
+
    
+
    Make.py -p atc -a machine
+
    
+
    
 
    To un-install via make or Make.py:
    
-
    Supporting info:
    
+
    make no-user-atc
+make machine
+
    
+
    
+
    Make.py -p ^atc -a machine
+
    
+
    
+
    Supporting info: fix atc, examples/USER/atc
    
 
    Examples: examples/USER/tally
    
 
    
 
    
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 3bf6585f15..31e5093735 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -34,10 +34,14 @@ has a summary of what the package contains.  It has specific
 instructions on how to install it, build or obtain any auxiliary
 library it requires, and any Makefile.machine changes it requires.  It
 also lists pointers to examples of its use or documentation provided
-in the LAMMPS distribution.
+in the LAMMPS distribution.  If you want to know the complete list of
+commands that a package adds to LAMMPS, simply list the files in its
+directory, e.g. "ls src/GRANULAR".  Source files with names that start
+with compute, fix, pair, bond, etc correspond to command styles with
+the same names.
 
-NOTE: The sub-sections below are still being filled in, as of Feb
-2016.
+NOTE: The USER package sub-sections below are still being filled in,
+as of March 2016.
 
 Unless otherwise noted below, every package is independent of all the
 others.  I.e. any package can be included or excluded in a LAMMPS
@@ -63,15 +67,14 @@ Package, Description, Author(s), Doc page, Example, Library
 "ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
 "BODY"_#BODY, body-style particles, -, "body"_body.html, body, -
 "CLASS2"_#CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_#COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
+"COLLOID"_#COLLOID, colloidal particles, Kumar (1), "atom_style colloid"_atom_style.html, colloid, -
 "COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
 "CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
 "DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"FLD"_#FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
 "GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
 "GRANULAR"_#GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
 "KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
 "KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
 "MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
@@ -94,8 +97,9 @@ Package, Description, Author(s), Doc page, Example, Library
 The "Authors" column lists a name(s) if a specific person is
 responible for creating and maintaining the package.
 
-(1) The FLD package was created by Amit Kumar and Michael Bybee from
-Jonathan Higdon's group at UIUC.
+(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
+which were created by Amit Kumar and Michael Bybee from Jonathan
+Higdon's group at UIUC.
 
 (2) The OPT package was created by James Fischer (High Performance
 Technologies), David Richie, and Vincent Natoli (Stone Ridge
@@ -104,9 +108,9 @@ Technolgy).
 (3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
 and Ellad Tadmor (U Minn).
 
-(4) The KOKKOS package was created primarily by Christian Trott
-(Sandia).  It uses the Kokkos library which was developed by Carter
-Edwards, Christian, and collaborators at Sandia.
+(4) The KOKKOS package was created primarily by Christian Trott and
+Stan Moore (Sandia).  It uses the Kokkos library which was developed
+by Carter Edwards, Christian Trott, and others at Sandia.
 
 The "Doc page" column links to either a sub-section of the
 "Section_howto"_Section_howto.html of the manual, or an input script
@@ -130,8 +134,8 @@ p.s.: are we ever going to get commit messages from you? ;-)
 
 ASPHERE package :link(ASPHERE),h5
 
-Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
-triangles.
+Contents: Several computes, time-integration fixes, and pair styles
+for aspherical particle models: ellipsoids, 2d lines, 3d triangles.
 
 To install via make or Make.py:
 
@@ -147,14 +151,20 @@ make machine :pre
 
 Make.py -p ^asphere -a machine :pre
 
-Supporting info: examples/ASPHERE, examples/ellipse, Section howto
-6.14, pair gayberne
+Supporting info: "Section howto 6.14"_Section_howto.html#howto_14,
+"pair_style gayberne"_pair_gayberne.html, "pair_style
+resquared"_pair_resquared.html,
+"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
+"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf,
+examples/ASPHERE, examples/ellipse
 
 :line
 
 BODY package :link(BODY),h5
 
-Contents:
+Contents: Support for body-style particles.  Computes,
+time-integration fixes, pair styles, as well as the body styles
+themselves.  See the "body"_body.html doc page for an overview.
 
 To install via make or Make.py:
 
@@ -170,13 +180,15 @@ make machine :pre
 
 Make.py -p ^body -a machine :pre
 
-Supporting info: examples/body
+Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
+"pair_style body"_pair_body.html, examples/body
 
 :line
  
 CLASS2 package :link(CLASS2),h5
 
-Contents:
+Contents: Bond, angle, dihedral, improper, and pair styles for the
+COMPASS CLASS2 molecular force field.
 
 To install via make or Make.py:
 
@@ -192,13 +204,20 @@ make machine :pre
 
 Make.py -p ^class2 -a machine :pre
 
-Supporting info: 
+Supporting info: "bond_style class2"_bond_class2.html, "angle_style
+class2"_angle_class2.html, "dihedral_style
+class2"_dihedral_class2.html, "improper_style
+class2"_improper_class2.html, "pair_style lj/class2"_pair_class2.html
  
 :line
  
 COLLOID package :link(COLLOID),h5
 
-Contents:
+Contents: Support for coarse-grained colloidal particles.  Wall fix
+and pair styles that implement colloidal interaction models for
+finite-size particles.  This includes the Fast Lubrication Dynamics
+method for hydrodynamic interactions, which is a simplified
+approximation to Stokesian dynamics.
 
 To install via make or Make.py:
 
@@ -214,13 +233,26 @@ make machine :pre
 
 Make.py -p ^colloid -a machine :pre
 
-Supporting info: examples/colloid, examples/srd
- 
+Supporting info: "fix wall/colloid"_fix_wall.html, "pair_style
+colloid"_pair_colloid.html, "pair_style
+yukawa/colloid"_pair_yukawa_colloid.html, "pair_style
+brownian"_pair_brownian.html, "pair_style
+lubricate"_pair_lubricate.html, "pair_style
+lubricateU"_pair_lubricateU.html, examples/colloid, examples/srd
+
 :line
  
 COMPRESS package :link(COMPRESS),h5
  
-Contents:
+Contents: Support for compressed output of dump files via the zlib
+compression library, using dump styles with a "gz" in their style
+name.
+
+Building with the COMPRESS package assumes you have the zlib
+compression library available on your system.  The build uses the
+lib/compress/Makefile.lammps file in the compile/link process.  You
+should only need to edit this file if the LAMMPS build cannot find the
+zlib info it specifies.
 
 To install via make or Make.py:
 
@@ -236,13 +268,21 @@ make machine :pre
 
 Make.py -p ^compress -a machine :pre
 
-Supporting info: 
+Supporting info: src/COMPRESS/README, lib/compress/README, "dump
+atom/gz"_dump.html, "dump cfg/gz"_dump.html, "dump
+custom/gz"_dump.html, "dump xyz/gz"_dump.html
 
 :line
  
 CORESHELL package :link(CORESHELL),h5
 
-Contents:
+Contents: Compute and pair styles that implement the adiabatic
+core/shell model for polarizability.  The compute temp/cs command
+measures the temperature of a system with core/shell particles.  The
+pair styles augment Born, Buckingham, and Lennard-Jones styles with
+core/shell capabilities.  See "Section howto
+6.26"_Section_howto.html#howto_26 for an overview of how to use the
+package.
 
 To install via make or Make.py:
 
@@ -258,13 +298,18 @@ make machine :pre
 
 Make.py -p ^coreshell -a machine :pre
 
-Supporting info: examples/coreshell, Section howto 6.26
+Supporting info: "Section howto
+6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html,
+"pair_style born/coul/long/cs"_pair_cs.html, "pair_style
+buck/coul/long/cs"_pair_cs.html, pair_style
+lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
 
 :line
  
 DIPOLE package :link(DIPOLE),h5
 
-Contents:
+Contents: An atom style and several pair styles to support point
+dipole models with short-range or long-range interactions.
 
 To install via make or Make.py:
 
@@ -280,42 +325,54 @@ make machine :pre
 
 Make.py -p ^dipole -a machine :pre
 
-Supporting info: examples/dipole
- 
-:line
- 
-FLD package :link(FLD),h5
-
-Contents:
-
-To install via make or Make.py:
-
-make yes-fld
-make machine :pre
-
-Make.py -p fld -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-fld
-make machine :pre
-
-Make.py -p ^fld -a machine :pre
-
-Supporting info: 
+Supporting info: "atom_style dipole"_atom_style.html, "pair_style
+lj/cut/dipole/cut"_pair_dipole.html, "pair_style
+lj/cut/dipole/long"_pair_dipole.html, "pair_style
+lj/long/dipole/long"_pair_dipole.html, examples/dipole
  
 :line
  
 GPU package :link(GPU),h5
 
-Contents:
+Contents: Dozens of pair styles and a version of the PPPM long-range
+Coulombic solver for NVIDIA GPUs.  All of them have a "gpu" in their
+style name.  "Section accelerate gpu"_accelerate_gpu.html gives
+details of what hardware and Cuda software is required on your system,
+and how to build and use this package.  See the KOKKOS and USER-CUDA
+packages, which also have GPU-enabled styles.
+
+Building LAMMPS with the GPU package requires first building the GPU
+library itself, which is a set of C and Cuda files in lib/gpu.
+Details of how to do this are in lib/gpu/README.  As illustrated
+below, perform a "make" using one of the Makefile.machine files in
+lib/gpu which should create a lib/reax/libgpu.a file.
+Makefile.linux.* and Makefile.xk7 are examples for different
+platforms.  There are 3 important settings in the Makefile.machine you
+use:
+
+CUDA_HOME = where NVIDIA Cuda software is installed on your system
+CUDA_ARCH = appropriate to your GPU hardware
+CUDA_PREC = precision (double, mixed, single) you desire :ul
+
+See example Makefile.machine files in lib/gpu for the syntax of these
+settings.  See lib/gpu/Makefile.linux.double for ARCH settings for
+various NVIDIA GPUs.  The "make" also creates a
+lib/gpu/Makefile.lammps file.  This file has settings that enable
+LAMMPS to link with Cuda libraries.  If the settings in
+Makefile.lammps for your machine are not correct, the LAMMPS link will
+fail.  Note that the Make.py script has a "-gpu" option to allow the
+GPU library (with several of its options) and LAMMPS to be built in
+one step, with Type "python src/Make.py -h -gpu" to see the details.
 
 To install via make or Make.py:
 
+cd ~/lammps/lib/gpu
+make -f Makefile.linux.mixed     # for example
+cd ~/lammps/src
 make yes-gpu
 make machine :pre
 
-Make.py -p gpu -a machine :pre
+Make.py -p gpu -gpu mode=mixed arch=35 -a machine :pre
 
 To un-install via make or Make.py:
 
@@ -324,13 +381,20 @@ make machine :pre
 
 Make.py -p ^gpu -a machine :pre
 
-Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
+Supporting info: src/GPU/README, lib/gpu/README, "Section
+acclerate"_Section_accelerate.html, "Section accelerate
+gpu"_accelerate_gpu.html, Pair Styles section of "Section commands
+3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),
+"kspace_style"_kspace_style.html, "package gpu"_package.html,
+examples/accelerate, bench/FERMI, bench/KEPLER
  
 :line
  
 GRANULAR package :link(GRANULAR),h5
 
-Contents:
+Contents: Fixes and pair styles that support models of finite-size
+granular particles, which interact with each other and boundaries via
+frictional and dissipative potentials.
 
 To install via make or Make.py:
 
@@ -346,13 +410,24 @@ make machine :pre
 
 Make.py -p ^granular -a machine :pre
 
-Supporting info: examples/pour, bench/in.chute, Section howto 6.6
+Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix
+pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
+gran/hooke"_pair_gran.html, "pair_style
+gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
  
 :line
  
 KIM package :link(KIM),h5
 
-Contents:
+Contents: A pair style that interfaces to the Knowledge Base for
+Interatomic Models (KIM) repository of interatomic potentials, so that
+KIM potentials can be used in a LAMMPS simulation.
+
+To build LAMMPS with the KIM package you must have previously
+installed the KIM API (library) on your system.  The lib/kim/README
+file explains how to download and install KIM.  Building with the KIM
+package also uses the lib/kim/Makefile.lammps file in the compile/link
+process.  You should not need to edit this file.
 
 To install via make or Make.py:
 
@@ -368,57 +443,85 @@ make machine :pre
 
 Make.py -p ^kim -a machine :pre
 
-Supporting info: examples/kim
+Supporting info: src/KIM/README, lib/kim/README, "pair_style
+kim"_pair_kim.html, examples/kim
  
 :line
  
 KOKKOS package :link(KOKKOS),h5
 
-Contents:
+Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
+which run with the Kokkos library to provide optimization for
+multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
+native mode).  All of them have a "kk" in their style name.  "Section
+accelerate kokkos"_accelerate_kokkos.html gives details of what
+hardware and software is required on your system, and how to build and
+use this package.  See the GPU, OPT, USER-CUDA, USER-INTEL, USER-OMP
+packages, which also provide optimizations for the same range of
+hardware.
 
-To install via make or Make.py:
+Building with the KOKKOS package requires choosing which of 3 hardware
+options you are optimizing for: CPU acceleration via OpenMP, GPU
+acceleration, or Intel Xeon Phi.  (You can build multiple times to
+create LAMMPS executables for different hardware.)  It also requires a
+C++11 compatible compiler.  For GPUs, the NVIDIA "nvcc" compiler is
+used, and an appopriate KOKKOS_ARCH setting should be made in your
+Makefile.machine for your GPU hardware and NVIDIA software.
 
-make yes-kokkow
-make machine :pre
+The simplest way to do this is to use Makefile.kokkos_cuda or
+Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
+"make kokkos_cuda" or "make kokkos_omp" or "make kokkos_phi".  (Check
+the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
+below, you can use the Make.py script with its "-kokkos" option to
+choose which hardware to build for.  Type "python src/Make.py -h
+-kokkos" to see the details.  If these methods do not work on your
+system, you will need to read the "Section accelerate
+kokkos"_accelerate_kokkos.html doc page for details of what
+Makefile.machine settings are needed.
 
-Make.py -p kokkow -a machine :pre
+To install via make or Make.py for each of 3 hardware options:
+
+make yes-kokkos
+make kokkos_omp    # for CPUs with OpenMP
+make kokkos_cuda   # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
+make kokkos_phi    # for Xeon Phis :pre
+
+Make.py -p kokkos -kokkos omp -a machine           # for CPUs with OpenMP
+Make.py -p kokkos -kokkos cuda arch=35 -a machine  # for GPUs of style arch
+Make.py -p kokkos -kokkos phi -a machine           # for Xeon Phis
 
 To un-install via make or Make.py:
 
-make no-kokkow
+make no-kokkos
 make machine :pre
 
-Make.py -p ^kokkow -a machine :pre
+Make.py -p ^kokkos -a machine :pre
 
-Supporting info: 
+Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section
+acclerate"_Section_accelerate.html, "Section accelerate
+kokkos"_accelerate_kokkos.html, Pair Styles section of "Section
+commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
+with a (k), "package kokkos"_package.html,
+examples/accelerate, bench/FERMI, bench/KEPLER
 
-For the KOKKOS package, you have 3 choices when building.  You can
-build with OMP or Cuda or Phi support.  Phi support uses Xeon Phi
-chips in "native" mode.  This can be done by setting the following
-variables in your Makefile.machine:
-
-for OMP support, set OMP = yes
-for Cuda support, set OMP = yes and CUDA = yes
-for Phi support, set OMP = yes and MIC = yes :ul
-
-These can also be set as additional arguments to the make command, e.g.
-
-make g++ OMP=yes MIC=yes :pre
-
-Building the KOKKOS package with CUDA support requires a Makefile
-machine that uses the NVIDIA "nvcc" compiler, as well as an
-appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
-software you have on your machine.  See
-src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
-Makefile.
-
-Examples: examples/accelerate, bench/FERMI, bench/KEPLER
- 
 :line
  
 KSPACE package :link(KSPACE),h5
 
-Contents:
+Contents: A variety of long-range Coulombic solvers, and pair styles
+which compute the corresponding short-range portion of the pairwise
+Coulombic interactions.  These include Ewald, particle-particle
+particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
+
+Building with the KSPACE package requires a 1d FFT library be present
+on your system for use by the PPPM solvers.  This can be the KISS FFT
+library provided with LAMMPS, or 3rd party libraries like FFTW or a
+vendor-supplied FFT library.  See step 6 of "Section start
+2.2.2"_Section_start.html#start_2_2 of the manual for details of how
+to select different FFT options in your machine Makefile.  The Make.py
+tool has an "-fft" option which can insert these settings into your
+machine Makefile automatically.  Type "python src/Make.py -h -fft" to
+see the details.
 
 To install via make or Make.py:
 
@@ -434,17 +537,22 @@ make machine :pre
 
 Make.py -p ^kspace -a machine :pre
 
-Supporting info: 
-
-Examples: examples/peptide, bench/in.rhodo
-
-Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
+Supporting info: "kspace_style"_kspace_style.html,
+"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto
+6.7"_Section_howto.html#howto_7, "Section howto
+6.8"_Section_howto.html#howto_8, "Section howto
+6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,
+other pair style command doc pages which have "long" or "msm" in their
+style name, examples/peptide, bench/in.rhodo
 
 :line
  
 MANYBODY package :link(MANYBODY),h5
 
-Contents:
+Contents: A variety of many-body and bond-order potentials.  These
+include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
+potentials.  Do a directory listing, "ls src/MANYBODY", to see
+the full list.
 
 To install via make or Make.py:
 
@@ -462,13 +570,18 @@ Make.py -p ^manybody -a machine :pre
 
 Supporting info: 
  
-Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
+Examples: Pair Styles section of "Section commands
+3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
+examples/nb3d, examples/vashishta
 
 :line
  
 MC package :link(MC),h5
 
-Contents:
+Contents: Several fixes and a pair style that have Monte Carlo (MC) or
+MC-like attributes.  These include fixes for creating, breaking, and
+swapping bonds, and for performing atomic swaps and grand-canonical MC
+in conjuction with dynamics.
 
 To install via make or Make.py:
 
@@ -484,20 +597,46 @@ make machine :pre
 
 Make.py -p ^mc -a machine :pre
 
-Supporting info: 
+Supporting info: "fix atom/swap"_fix_atom_swap.html, "fix
+bond/break"_fix_bond_break.html, "fix
+bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
+"fix gcmc"_fix_gcmc.html, "pair_style dsmc"_pair_dsmc.html
  
 :line
  
 MEAM package :link(MEAM),h5
 
-Contents:
+Contents: A pair style for the modified embedded atom (MEAM)
+potential.
+
+Building LAMMPS with the MEAM package requires first building the MEAM
+library itself, which is a set of Fortran 95 files in lib/meam.
+Details of how to do this are in lib/meam/README.  As illustrated
+below, perform a "make" using one of the Makefile.machine files in
+lib/meam which should create a lib/meam/libmeam.a file.
+Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
+and Intel Fortran compilers.  The "make" also copies a
+lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps.
+This file has settings that enable the C++ compiler used to build
+LAMMPS to link with a Fortran library (typically the 2 compilers to be
+consistent e.g. both Intel compilers, or both GNU compilers).  If the
+settings in Makefile.lammps for your compilers and machine are not
+correct, the LAMMPS link will fail.  Note that the Make.py script has
+a "-meam" option to allow the MEAM library and LAMMPS to be built in
+one step.  Type "python src/Make.py -h -meam" to see the details.
+
+NOTE: The MEAM potential can run dramatically faster if built with the
+Intel Fortran compiler, rather than the GNU Fortran compiler.
 
 To install via make or Make.py:
 
+cd ~/lammps/lib/meam
+make -f Makefile.gfortran    # for example
+cd ~/lammps/src
 make yes-meam
 make machine :pre
 
-Make.py -p meam -a machine :pre
+Make.py -p meam -meam make=gfortran -a machine :pre
 
 To un-install via make or Make.py:
 
@@ -506,13 +645,16 @@ make machine :pre
 
 Make.py -p ^meam -a machine :pre
 
-Supporting info: examples/meam
+Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
+examples/meam
  
 :line
  
 MISC package :link(MISC),h5
 
-Contents:
+Contents: A variety of computes, fixes, and pair styles that are not
+commonly used, but don't align with other packages.  Do a directory
+listing, "ls src/MISC", to see the list of commands.
 
 To install via make or Make.py:
 
@@ -528,13 +670,18 @@ make machine :pre
 
 Make.py -p ^misc -a machine :pre
 
-Supporting info: examples/misc
+Supporting info: "compute ti"_compute_ti.html, "fix
+evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
+viscosity"_fix_viscosity.html, examples/misc
  
 :line
  
 MOLECULE package :link(MOLECULE),h5
 
-Contents:
+Contents: A large number of atom, pair, bond, angle, dihedral,
+improper styles that are used to model molecular systems with fixed
+covalent bonds.  The pair styles include terms for the Dreiding
+(hydrogen-bonding) and CHARMM force fields, and TIP4P water model.
 
 To install via make or Make.py:
 
@@ -550,13 +697,24 @@ make machine :pre
 
 Make.py -p ^molecule -a machine :pre
 
-Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3
- 
+Supporting info:"atom_style"_atom_style.html,
+"bond_style"_bond_style.html, "angle_style"_angle_style.html,
+"dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html, "pair_style
+hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
+lj/charmm/coul/charmm"_pair_charmm.html, "Section howto
+6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,
+bench/in.chain, bench/in.rhodo
+
 :line
  
 MPIIO package :link(MPIIO),h5
 
-Contents:
+Contents: Support for parallel output/input of dump and restart files
+via the MPIIO library, which is part of the standard message-passing
+interface (MPI) library.  It adds "dump styles"_dump.html with a
+"mpiio" in their style name.  Restart files with an ".mpiio" suffix
+are also written and read in parallel.
 
 To install via make or Make.py:
 
@@ -572,13 +730,26 @@ make machine :pre
 
 Make.py -p ^mpiio -a machine :pre
 
-Supporting info: 
+Supporting info: "dump"_dump.html, "restart"_restart.html,
+"write_restart"_write_restart.html, "read_restart"_read_restart.html
  
 :line
  
 OPT package :link(OPT),h5
 
-Contents:
+Contents: A handful of pair styles with an "opt" in their style name
+which are optimized for improved CPU performance on single or multiple
+cores.  These include EAM, LJ, CHARMM, and Morse potentials.  "Section
+accelerate opt"_accelerate_opt.html gives details of how to build and
+use this package.  See the KOKKOS, USER-INTEL, and USER-OMP packages,
+which also have styles optimized for CPU performance.
+
+Some C++ compilers, like the Intel compiler, require the compile flag
+"-restrict" to build LAMMPS with the OPT package.  It should be added
+to the CCFLAGS line of your Makefile.machine.  Or use Makefile.opt in
+src/MAKE/OPTIONS, via "make opt".  For compilers that use the flag,
+the Make.py command adds it automatically to the Makefile.auto file it
+creates and uses.
 
 To install via make or Make.py:
 
@@ -594,18 +765,19 @@ make machine :pre
 
 Make.py -p ^opt -a machine :pre
 
-Supporting info: examples/accelerate, bench/KEPLER
-
-For the OPT package, your Makefile.machine needs an additional
-settings for CCFLAGS.
-
-CCFLAGS: add -restrict :ul
+Supporting info: "Section acclerate"_Section_accelerate.html, "Section
+accelerate opt"_accelerate_opt.html, Pair Styles section of "Section
+commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
+with an (o), examples/accelerate, bench/KEPLER
 
 :line
  
 PERI package :link(PERI),h5
 
-Contents:
+Contents: Support for the Peridynamics method, a particle-based
+meshless continuum model.  The package includes an atom style, several
+computes which calculate diagnostics, and several Peridynamic pair
+styles which implement different materials models.
 
 To install via make or Make.py:
 
@@ -621,35 +793,74 @@ make machine :pre
 
 Make.py -p ^peri -a machine :pre
 
-Supporting info: examples/peri
+Supporting info:
+"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf,
+"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf,
+"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
+peri"_atom_style.html, "compute damage"_compute_damage.html,
+"pair_style peri/pmb"_pair_peri.html, examples/peri
  
 :line
  
 POEMS package :link(POEMS),h5
 
-Contents:
+Contents: A fix that wraps the Parallelizable Open source Efficient
+Multibody Software (POEMS) librar, which is able to simulate the
+dynamics of articulated body systems.  These are systems with multiple
+rigid bodies (collections of atoms or particles) whose motion is
+coupled by connections at hinge points.
+
+Building LAMMPS with the POEMS package requires first building the
+POEMS library itself, which is a set of C++ files in lib/poems.
+Details of how to do this are in lib/poems/README.  As illustrated
+below, perform a "make" using one of the Makefile.machine files in
+lib/poems which should create a lib/meam/libpoems.a file.
+Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++
+compilers.  The "make" also creates a lib/poems/Makefile.lammps file
+which you should not need to change.  Note the Make.py script has a
+"-poems" option to allow the POEMS library and LAMMPS to be built in
+one step.  Type "python src/Make.py -h -poems" to see the details.
 
 To install via make or Make.py:
 
+cd ~/lammps/lib/poems
+make -f Makefile.g++    # for example
+cd ~/lammps/src
 make yes-poems
 make machine :pre
 
-Make.py -p poems -a machine :pre
+Make.py -p poems -poems make=g++ -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-poems
+make no-meam
 make machine :pre
 
-Make.py -p ^poems -a machine :pre
+Make.py -p ^meam -a machine :pre
 
-Supporting info: examples/rigid
+Supporting info: src/POEMS/README, lib/poems/README,
+"fix_poems"_fix_poems.html, examples/rigid
 
 :line
  
 PYTHON package :link(PYTHON),h5
 
-Contents:
+Contents: A "python"_python.html command which allow you to execute
+Python code from a LAMMPS input script.  The code can be in a separate
+file or embedded in the input script itself.  See "Section python
+11.2"_Section_python.html#py_2" for an overview of using Python from
+LAMMPS and "Section python"_Section_python.html" for other ways to use
+LAMMPS and Python together.
+
+Building with the PYTHON package assumes you have a Python shared
+library available on your system, which needs to be a Python 2
+version, 2.6 or later.  Python 3 is not supported.  The build uses the
+contents of the lib/python/Makefile.lammps file to find all the Python
+files required in the build/link process.  See the lib/python/README
+file if the settings in that file do not work on your system.  Note
+that the Make.py script has a "-python" option to allow an alternate
+lib/python/Makefile.lammps file to be specified and LAMMPS to be built
+in one step.  Type "python src/Make.py -h -python" to see the details.
 
 To install via make or Make.py:
 
@@ -671,7 +882,9 @@ Supporting info: examples/python
  
 QEQ package :link(QEQ),h5
 
-Contents:
+Contents: Several fixes for performing charge equilibration (QEq) via
+severeal different algorithms.  These can be used with pair styles
+that use QEq as part of their formulation.
 
 To install via make or Make.py:
 
@@ -687,20 +900,41 @@ make machine :pre
 
 Make.py -p ^qeq -a machine :pre
 
-Supporting info: examples/qeq
+Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
  
 :line
  
 REAX package :link(REAX),h5
 
-Contents:
+Contents: A pair style for the ReaxFF potential, a universal reactive
+force field, as well as a "fix reax/bonds"_fix_reax_bonds.html command
+for monitoring molecules as bonds are created and destroyed.
+
+Building LAMMPS with the REAX package requires first building the REAX
+library itself, which is a set of Fortran 95 files in lib/reax.
+Details of how to do this are in lib/reax/README.  As illustrated
+below, perform a "make" using one of the Makefile.machine files in
+lib/reax which should create a lib/reax/libreax.a file.
+Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
+and Intel Fortran compilers.  The "make" also copies a
+lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps.
+This file has settings that enable the C++ compiler used to build
+LAMMPS to link with a Fortran library (typically the 2 compilers to be
+consistent e.g. both Intel compilers, or both GNU compilers).  If the
+settings in Makefile.lammps for your compilers and machine are not
+correct, the LAMMPS link will fail.  Note that the Make.py script has
+a "-reax" option to allow the REAX library and LAMMPS to be built in
+one step.  Type "python src/Make.py -h -reax" to see the details.
 
 To install via make or Make.py:
 
+cd ~/lammps/lib/reax
+make -f Makefile.gfortran    # for example
+cd ~/lammps/src
 make yes-reax
 make machine :pre
 
-Make.py -p reax -a machine :pre
+Make.py -p reax -reax make=gfortran -a machine :pre
 
 To un-install via make or Make.py:
 
@@ -709,13 +943,24 @@ make machine :pre
 
 Make.py -p ^reax -a machine :pre
 
-Supporting info: examples/reax
+Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
+"fix reax/bonds"_fix_reax_bonds.html, examples/reax
  
 :line
  
 REPLICA package :link(REPLICA),h5
 
-Contents:
+Contents: A collection of multi-replica methods that are used by
+invoking multiple instances (replicas) of LAMMPS
+simulations. Communication between individual replicas is performed in
+different ways by the different methods.  See "Section howto
+6.5"_Section_howto.html#howto_5 for an overview of how to run
+multi-replica simulations in LAMMPS.  Multi-replica methods included
+in the package are nudged elastic band (NEB), parallel replica
+dynamics (PRD), temperature accelerated dynamics (TAD), parallel
+tempering, and a verlet/split algorithm for performing long-range
+Coulombics on one set of processors, and the remainded of the force
+field calcalation on another set.
 
 To install via make or Make.py:
 
@@ -731,13 +976,19 @@ make machine :pre
 
 Make.py -p ^replica -a machine :pre
 
-Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
+Supporting info: "Section howto 6.5"_Section_howto.html#howto_5,
+"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
+"run_style verlet/split"_run_style.html, examples/neb, examples/prd,
+examples/tad
 
 :line
  
 RIGID package :link(RIGID),h5
 
-Contents:
+Contents: A collection of computes and fixes which enforce rigid
+constraints on collections of atoms or particles.  This includes SHAKE
+and RATTLE, as well as variants of rigid-body time integrators for a
+few large bodies or many small bodies.
 
 To install via make or Make.py:
 
@@ -753,13 +1004,16 @@ make machine :pre
 
 Make.py -p ^rigid -a machine :pre
 
-Supporting info: examples/ASPHERE, examples/rigid
+Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
+"fix shake"_fix_shake.html, "fix rattle"_fix_rattle.html, "fix
+rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
 
 :line
  
 SHOCK package :link(SHOCK),h5
 
-Contents:
+Contents: A small number of fixes useful for running impact
+simulations where a shock-wave passes through a material.
 
 To install via make or Make.py:
 
@@ -775,13 +1029,18 @@ make machine :pre
 
 Make.py -p ^shock -a machine :pre
 
-Supporting info: examples/hugoniostat, examples/msst
+Supporting info: "fix append/atoms"_fix_append_atoms.html, "fix
+msst"_fix_msst.html, "fix nphug"_fix_nphug.html, "fix
+wall/piston"_fix_wall_piston.html, examples/hugoniostat, examples/msst
  
 :line
  
 SNAP package :link(SNAP),h5
 
-Contents:
+Contents: A pair style for the spectral neighbor analysis potential
+(SNAP), which is an empirical potential which can be quantum accurate
+when fit to an archive of DFT data.  Computes useful for analyzing 
+properties of the potential are also included. 
 
 To install via make or Make.py:
 
@@ -797,13 +1056,17 @@ make machine :pre
 
 Make.py -p ^snap -a machine :pre
 
-Supporting info: examples/snap
+Supporting info: "pair snap"_pair_snap.html, "compute
+sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna.html,
+"compute snav/atom"_compute_sna.html, examples/snap
  
 :line
  
 SRD package :link(SRD),h5
 
-Contents:
+Contents: Two fixes which implement the Stochastic Rotation Dynamics
+(SRD) method for coarse-graining of a solvent, typically around large
+colloidal-scale particles.
 
 To install via make or Make.py:
 
@@ -819,20 +1082,47 @@ make machine :pre
 
 Make.py -p ^srd -a machine :pre
 
-Supporting info: 
+Supporting info: "fix srd"_fix_srd.html, "fix
+wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
  
 :line
  
 VORONOI package :link(VORONOI),h5
 
-Contents:
+Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
+which computes the Voronoi tesselation of a collection of atoms or
+particles by wrapping the Voro++ lib
+
+To build LAMMPS with the KIM package you must have previously
+installed the KIM API (library) on your system.  The lib/kim/README
+file explains how to download and install KIM.  Building with the KIM
+package also uses the lib/kim/Makefile.lammps file in the compile/link
+process.  You should not need to edit this file.
+
+
+To build LAMMPS with the VORONOI package you must have previously
+installed the Voro++ library on your system.  The lib/voronoi/README
+file explains how to download and install Voro++.  There is a
+lib/voronoi/install.py script which automates the process.  Type
+"python install.py" to see instructions.  The final step is to create
+soft links in the lib/voronoi directory for "includelink" and
+"liblink" which point to installed Voro++ directories.  Building with
+the VORONOI package uses the contents of the
+lib/voronoi/Makefile.lammps file in the compile/link process.  You
+should not need to edit this file.  Note that the Make.py script has a
+"-voronoi" option to allow the Voro++ library to be downloaded and/or
+installed and LAMMPS to be built in one step.  Type "python
+src/Make.py -h -voronoi" to see the details.
 
 To install via make or Make.py:
 
+cd ~/lammps/lib/voronoi
+python install.py -g -b -l    # download Voro++, build in lib/voronoi, create links
+cd ~/lammps/src
 make yes-voronoi
 make machine :pre
 
-Make.py -p voronoi -a machine :pre
+Make.py -p voronoi -voronoi install="-g -b -l" -a machine :pre
 
 To un-install via make or Make.py:
 
@@ -841,13 +1131,15 @@ make machine :pre
 
 Make.py -p ^voronoi -a machine :pre
 
-Supporting info: examples/voronoi
+Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
+voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
  
 :line
  
 XTC package :link(XTC),h5
 
-Contents:
+Contents: A "dump xtc"_dump.html command for writing snapshots in the
+XTC format used by the GROMACS MD package.
 
 To install via make or Make.py:
 
@@ -863,7 +1155,7 @@ make machine :pre
 
 Make.py -p ^xtc -a machine :pre
 
-Supporting info: 
+Supporting info: "dump xtc"_dump.html
  
 :line
 
@@ -952,184 +1244,164 @@ See details on all of this below for individual packages.
 
 USER-ATC package :link(USER-ATC),h5
 
-Contents:
- 
+Contents: ATC stands for atoms-to-continuum.  This package implements
+a "fix atc"_fix_atc.html command to either couple MD with continuum
+finite element equations or perform on-the-fly post-processing of
+atomic information to continuum fields.  See src/USER-ATC/README for
+more details.
+
+To build LAMMPS with this package ...
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package implements a "fix atc" command which can be used in a
-LAMMPS input script.  This fix can be employed to either do concurrent
-coupling of MD with FE-based physics surrogates or on-the-fly
-post-processing of atomic information to continuum fields.
 
-See the doc page for the fix atc command to get started.  At the
-bottom of the doc page are many links to additional documentation
-contained in the doc/USER/atc directory.
+make no-user-atc
+make machine :pre
 
-There are example scripts for using this package in examples/USER/atc.
+Make.py -p ^atc -a machine :pre
 
-This package uses an external library in lib/atc which must be
-compiled before making LAMMPS.  See the lib/atc/README file and the
-LAMMPS manual for information on building LAMMPS with external
-libraries.
+Supporting info:src/USER-ATC/README, "fix atc"_fix_atc.html,
+examples/USER/atc
 
-The primary people who created this package are Reese Jones (rjones at
-sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
-Zimmerman (jzimmer at sandia.gov) at Sandia.  Contact them directly if
-you have questions.
-
-Examples: examples/USER/atc
+Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
+at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
+Contact them directly if you have questions.
 
 :line
 
 USER-AWPMD package :link(USER-AWPMD),h5
 
-Contents:
- 
+Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular
+Dynamics.  This package implements an atom, pair, and fix style which
+allows electrons to be treated as explicit particles in an MD
+calculation.  See src/USER-AWPMD/README for more details.
+
+To build LAMMPS with this package ...
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package contains a LAMMPS implementation of the Antisymmetrized
-Wave Packet Molecular Dynamics (AWPMD) method.
 
-See the doc page for the pair_style awpmd/cut command to get started.
+make no-user-atc
+make machine :pre
 
-There are example scripts for using this package in examples/USER/awpmd.
+Make.py -p ^atc -a machine :pre
 
-This package uses an external library in lib/awpmd which must be
-compiled before making LAMMPS.  See the lib/awpmd/README file and the
-LAMMPS manual for information on building LAMMPS with external
-libraries.
+Supporting info: src/USER-AWPMD/README, "fix
+awpmd/cut"_pair_awpmd_cut.html, examples/USER/awpmd
 
-The person who created this package is Ilya Valuev at the JIHT in
-Russia (valuev at physik.hu-berlin.de).  Contact him directly if you
-have questions.
-
-Examples: examples/USER/awpmd
+Author: Ilya Valuev at the JIHT in Russia (valuev at
+physik.hu-berlin.de).  Contact him directly if you have questions.
 
 :line
 
 USER-CG-CMM package :link(USER-CG-CMM),h5
 
-Contents:
- 
+Contents: CG-CMM stands for coarse-grained ??.  This package
+implements several pair styles and an angle style using the coarse
+grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
+(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
+lipids and charged amino acids.  See src/USER-CG-CMM/README for more
+details.
+
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
 
-Supporting info: 
- 
-This package implements 3 commands which can be used in a LAMMPS input
-script:
+Supporting info: src/USER-CG-CMM/README, "pair lj/sdk"_pair_sdk.html,
+"pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html,
+examples/USER/cg-cmm
 
-pair_style lj/sdk
-pair_style lj/sdk/coul/long
-angle_style sdk :ul
-
-These styles allow coarse grained MD simulations with the
-parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
-(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
-and charged amino acids.
-
-See the doc pages for these commands for details.
-
-There are example scripts for using this package in
-examples/USER/cg-cmm.
-
-This is the second generation implementation reducing the the clutter
-of the previous version. For many systems with electrostatics, it will
-be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
-instead of the combined lj/sdk/coul/long style.  since the number of
-charged atom types is usually small.  For any other coulomb
-interactions this is now required.  To exploit this property, the use
-of the kspace_style pppm/cg is recommended over regular pppm. For all
-new styles, input file backward compatibility is provided.  The old
-implementation is still available through appending the /old
-suffix. These will be discontinued and removed after the new
-implementation has been fully validated.
-
-The current version of this package should be considered beta
-quality. The CG potentials work correctly for "normal" situations, but
-have not been testing with all kinds of potential parameters and
-simulation systems.
-
-The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com).  Contact him directly if you have questions.
-
-Examples: examples/USER/cg-cmm
+Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com).  Contact
+him directly if you have questions.
 
 :line
 
 USER-COLVARS package :link(USER-COLVARS),h5
 
-Contents:
- 
+Contents: COLVARS stands for collective variables which can be used to
+implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
+Sampling and Restraints.  This package implements a "fix
+colvars"_fix_colvars.html command which wraps a COLVARS library which
+can perform those kinds of simulations.  See src/USER-COLVARS/README
+for more details.
+
+To build LAMMPS with this package ...
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package implements the "fix colvars" command which can be
-used in a LAMMPS input script.
 
-This fix allows to use "collective variables" to implement
-Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
-Sampling and Restraints. This code consists of two parts:
+make no-user-atc
+make machine :pre
 
-A portable collective variable module library written and maintained
-by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
-Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
-the directory lib/colvars and needs to be compiled first.  The colvars
-fix and an interface layer, exchanges information between LAMMPS and
-the collective variable module. :ul
+Make.py -p ^atc -a machine :pre
 
-See the doc page of "fix colvars"_fix_colvars.html for more details.
+Supporting info:
+"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf,
+src/USER-COLVARS/README, lib/colvars/README, "fix
+colvars"_fix_colvars.html, examples/USER/colvars
 
-There are example scripts for using this package in
-examples/USER/colvars
-
-This is a very new interface that does not yet support all
-features in the module and will see future optimizations
-and improvements. The colvars module library is also available
-in NAMD has been thoroughly used and tested there. Bugs and
-problems are likely due to the interface layers code.
-Thus the current version of this package should be considered
-beta quality.
-
-The person who created this package is Axel Kohlmeyer at Temple U
-(akohlmey at gmail.com).  Contact him directly if you have questions.
-
-Examples: examples/USER/colvars
-
-Contents:
- 
-To install via make or Make.py:
- 
-To un-install via make or Make.py:
- 
-Supporting info: 
+Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
+fix.  The COLVARS library itself is written and maintained by Giacomo
+Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
+Henin (LISM, CNRS, Marseille, France).  Contact them directly if you
+have questions.
  
 :line
 
 USER-CUDA package :link(USER-CUDA),h5
 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
+To build LAMMPS with this package ...
+
+To install via make or Make.py:
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
+
 This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
 GPUs.
@@ -1151,301 +1423,249 @@ University of Technology Ilmenau, Germany (christian.trott at
 tu-ilmenau.de).  Contact him directly if you have questions.
 
 Examples: examples/accelerate, bench/FERMI, bench/KEPLER
-
-Contents:
- 
-To install via make or Make.py:
- 
-To un-install via make or Make.py:
- 
-Supporting info: 
  
 :line
 
 USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
 
-This package contains the commands neeed to calculate x-ray and
-electron diffraction intensities based on kinematic diffraction 
-theory.
+Contents: This packages implements two computes and a fix for
+calculating x-ray and electron diffraction intensities based on
+kinematic diffraction theory.  See src/USER-DIFFRACTION/README for
+more details.
 
-See these doc pages and their related commands to get started:
-
-"compute xrd"_compute_xrd.html
-"compute saed"_compute_saed.html
-"fix saed/vtk"_fix_saed_vtk.html :ul
-
-The person who created this package is Shawn P. Coleman 
-(shawn.p.coleman8.ctr at mail.mil) while at the University of 
-Arkansas.  Contact him directly if you have questions.
-
-Examples: examples/USER/diffraction
-
-Contents:
- 
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "compute saed"_compute_saed.html, "compute
+xrd"_compute_xrd.html, "fix saed.vtk"_fix_saed_vtk.html,
+examples/USER/diffraction
+
+Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
+the University of Arkansas.  Contact him directly if you have
+questions.
 
-Supporting info: 
- 
 :line
 
 USER-DPD package :link(USER-DPD),h5
 
-This package implements the dissipative particle dynamics (DPD) method
-under isothermal, isoenergetic, isobaric and isenthalpic conditions.
-The DPD equations of motion are integrated efficiently through the
-Shardlow splitting algorithm.
-
-See these doc pages and their related commands to get started:
-
-"compute dpd"_compute_dpd.html
-"compute dpd/atom"_compute_dpd_atom.html
-"fix_eos/cv"_fix_eos_table.html
-"fix_eos/table"_fix_eos_table.html
-"fix_shardlow"_fix_shardlow.html
-"pair_dpd/conservative"_pair_dpd_conservative.html
-"pair_dpd/fdt"_pair_dpd_fdt.html
-"pair_dpd/fdt/energy"_pair_dpd_fdt.html :ul
-
-There are example scripts for using this package in examples/USER/dpd.
-
-The people who created this package are James Larentzos
-(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
-engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
-Contact them directly if you have questions.
+Contents: DPD stands for dissipative particle dynamics, This package
+implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
+conditions.  The DPD equations of motion are integrated efficiently
+through the Shardlow splitting algorithm.  See src/USER-DPD/README for
+more details.
 
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
 
-Examples: examples/USER/dpd
+Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
+"compute dpd/atom"_compute_dpd_atom.html
+"fix_eos/cv"_fix_eos_table.html "fix_eos/table"_fix_eos_table.html
+"fix_shardlow"_fix_shardlow.html
+"pair_dpd/conservative"_pair_dpd_conservative.html
+"pair_dpd/fdt"_pair_dpd_fdt.html
+"pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd
+
+Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
+Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
+and John Brennan (ARL) (john.k.brennan.civ at mail.mil).  Contact them
+directly if you have questions.
 
 :line
 
 USER-DRUDE package :link(USER-DRUDE),h5
 
-Contents:
- 
-To install via make or Make.py:
- 
-To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package implements methods for simulating polarizable systems
-in LAMMPS using thermalized Drude oscillators.
-
-See these doc pages and their related commands to get started:
-
-"Drude tutorial"_tutorial_drude.html
-"fix drude"_fix_drude.html
-"compute temp/drude"_compute_temp_drude.html
-"fix langevin/drude"_fix_langevin_drude.html
-"fix drude/transform/..."_fix_drude_transform.html
-"pair thole"_pair_thole.html :ul
-
-There are auxiliary tools for using this package in tools/drude.
-
-The person who created this package is Alain Dequidt at Universite
-Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
-Contact him directly if you have questions. Co-authors: Julien Devemy,
-Agilio Padua.
+Contents: This package contains methods for simulating polarizable
+systems using thermalized Drude oscillators.  It has computes, fixes,
+and pair styles for this purpose.  See "Section howto
+6.27"_Section_howto.html#howto_27 for an overview of how to use the
+package.  See src/USER-DRUDE/README for additional details.  There are
+auxiliary tools for using this package in tools/drude.
 
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
 
-Examples: examples/USER/drude
+Supporting info: "Section howto 6.27"_Section_howto.html#howto_27,
+src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
+drude/transform/*"_fix_drude_transform.html, "compute
+temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
+"pair lj/cut/thole/long"_pair_thole.html, examples/USER/drude,
+tools/drude
 
-Doc: Section howto 6.27
+Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand
+(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy,
+Agilio Padua.  Contact them directly if you have questions.
 
 :line
 
 USER-EFF package :link(USER-EFF),h5
 
-Contents:
- 
+Contents: EFF stands for electron force field.  This package contains
+atom, pair, fix and compute styles which implement the eFF as
+described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
+JCC, 2010. The eFF potential was first introduced by Su and Goddard,
+in 2007.  See src/USER-EFF/README for more details.  There are
+auxiliary tools for using this package in tools/eff; see its README
+file.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "atom_style electron"_atom_style.html, "compute
+temp/eff"_compute_temp_eff.html, "fix
+langevin/eff"_fix_langevin_eff.html, "fix nve/eff"_fix_nve_eff.html,
+"pair eff/cut"_pair_eff.html, examples/USER/eff, tools/eff
+
 Supporting info: 
- 
-This package contains a LAMMPS implementation of the electron Force
-Field (eFF) currently under development at Caltech, as described in
-A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
-2010. The eFF potential was first introduced by Su and Goddard, in
-2007.
 
-eFF can be viewed as an approximation to QM wave packet dynamics and
-Fermionic molecular dynamics, combining the ability of electronic
-structure methods to describe atomic structure, bonding, and chemistry
-in materials, and of plasma methods to describe nonequilibrium
-dynamics of large systems with a large number of highly excited
-electrons. We classify it as a mixed QM-classical approach rather than
-a conventional force field method, which introduces QM-based terms (a
-spin-dependent repulsion term to account for the Pauli exclusion
-principle and the electron wavefunction kinetic energy associated with
-the Heisenberg principle) that reduce, along with classical
-electrostatic terms between nuclei and electrons, to the sum of a set
-of effective pairwise potentials.  This makes eFF uniquely suited to
-simulate materials over a wide range of temperatures and pressures
-where electronically excited and ionized states of matter can occur
-and coexist.
-
-The necessary customizations to the LAMMPS core are in place to
-enable the correct handling of explicit electron properties during
-minimization and dynamics.
-
-See the doc page for the pair_style eff/cut command to get started.
-
-There are example scripts for using this package in
-examples/USER/eff.
-
-There are auxiliary tools for using this package in tools/eff.
-
-The person who created this package is Andres Jaramillo-Botero at
-CalTech (ajaramil at wag.caltech.edu).  Contact him directly if you
-have questions.
-
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
-Examples: examples/USER/eff
+Author: Andres Jaramillo-Botero at CalTech (ajaramil at
+wag.caltech.edu).  Contact him directly if you have questions.
 
 :line
 
 USER-FEP package :link(USER-FEP),h5
 
-Contents:
- 
-To install via make or Make.py:
- 
-To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package provides methods for performing free energy perturbation
-simulations with soft-core pair potentials in LAMMPS.
-
-See these doc pages and their related commands to get started:
-
-"fix adapt/fep"_fix_adapt_fep.html
-"compute fep"_compute_fep.html
-"soft pair styles"_pair_lj_soft.html :ul
-
-The person who created this package is Agilio Padua at Universite
-Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
-Contact him directly if you have questions.
+Contents: FEP stands for free energy perturbation.  This package
+provides methods for performing FEP simulations by using a "fix
+adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
+which have a "soft" in their style name.  See src/USER-FEP/README for
+more details.  There are auxiliary tools for using this package in
+tools/fep; see its README file.
 
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
 
-Examples: examples/USER/fep
+Supporting info: src/USER-FEP/README, "fix
+adapt/fep"_fix_adapt_fep.html, "compute fep"_compute_fep.html,
+"pair_style */soft"_pair_lj_soft.html, examples/USER/fep
+
+Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand
+(agilio.padua at univ-bpclermont.fr). Contact him directly if you have
+questions.
 
 :line
 
 USER-H5MD package :link(USER-H5MD),h5
 
-Contents:
- 
-To install via make or Make.py:
- 
-To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package contains a "dump h5md"_dump_h5md.html command for
-performing a dump of atom properties in HDF5 format.  "HDF5
-files"_HDF5 are binary, portable and self-describing and can be
-examined and used by a variety of auxiliary tools.  The output HDF5
-files are structured in a format called H5MD, which was designed to
-store molecular data, and can be used and produced by various MD and
-MD-related codes.  The "dump h5md"_doc/dump_h5md.html command gives a
-citation to a paper describing the format.
+Contents: H5MD stands for HDF5 for MD.  "HDF5"_HDF5 is a binary,
+portable, self-describing file format, used by many scientific
+simulations.  H5MD is a format for molecular simulations, built on top
+of HDF5.  This package implements a "dump h5md"_dump_h5md.html command
+to output LAMMPS snapshots in this format.  See src/USER-H5MD/README
+for more details.
 
 :link(HDF5,http://www.hdfgroup.org/HDF5/)
 
-The person who created this package and the underlying H5MD format is
-Pierre de Buyl at KU Leuven (see http://pdebuyl.be).  Contact him
+To build LAMMPS with this package ...
+
+To install via make or Make.py:
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: src/USER-H5MD/README, lib/h5md/README, "dump
+h5md"_dump_h5md.html
+
+Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created
+this package as well as the H5MD format and library.  Contact him
 directly if you have questions.
 
 :line
 
 USER-INTEL package :link(USER-INTEL),h5
 
-Contents:
- 
+Contents: Dozens of pair, bond, angle, dihedral, and improper styles
+that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
+mode).  All of them have an "intel" in their style name.  "Section
+accelerate intel"_accelerate_intel.html gives details of what hardware
+and compilers are required on your system, and how to build and use
+this package.  Also see src/USER-INTEL/README for more details. See
+the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
+Phi-enabled styles.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
-Supporting info: 
- 
-This package provides options for performing neighbor list and
-non-bonded force calculations in single, mixed, or double precision
-and also a capability for accelerating calculations with an
-Intel(R) Xeon Phi(TM) coprocessor.
- 
-See this section of the manual to get started:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: examples/accelerate, src/USER-INTEL/TEST
 
 "Section_accelerate"_Section_accelerate.html#acc_9
 
-The person who created this package is W. Michael Brown at Intel
-(michael.w.brown at intel.com).  Contact him directly if you have questions.
+Author: Mike Brown at Intel (michael.w.brown at intel.com).  Contact
+him directly if you have questions.
 
 For the USER-INTEL package, you have 2 choices when building.  You can
 build with CPU or Phi support.  The latter uses Xeon Phi chips in
@@ -1466,17 +1686,32 @@ And also add this to CCFLAGS:
 
 -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
 
-Examples: examples/accelerate, bench/KEPLER
+Examples: 
 
 :line
 
 USER-LB package :link(USER-LB),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
  
 Supporting info: 
  
@@ -1492,32 +1727,33 @@ The people who created this package are Frances Mackay (fmackay at
 uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
 Western Ontario.  Contact them directly if you have questions.
 
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
 Examples: examples/USER/lb
 
 :line
 
 USER-MGPT package :link(USER-MGPT),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 This package contains a fast implementation for LAMMPS of
@@ -1544,32 +1780,33 @@ The persons who created the USER-MGPT package are Tomas Oppelstrup
 (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
 Contact them directly if you have any questions.
 
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
 Examples: examples/USER/mgpt
 
 :line
 
 USER-MISC package :link(USER-MISC),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 The files in this package are a potpourri of (mostly) unrelated
@@ -1591,32 +1828,33 @@ src/USER-MISC/README file.
 You should contact the author directly if you have specific questions
 about the feature or its coding.
 
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
 Examples: examples/USER/misc
 
 :line
 
 USER-MOLFILE package :link(USER-MOLFILE),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 This package contains a dump molfile command which uses molfile
@@ -1643,12 +1881,27 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 USER-OMP package :link(USER-OMP),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 This package provides OpenMP multi-threading support and
@@ -1674,6 +1927,27 @@ Examples: examples/accelerate, bench/KEPLER
 
 USER-PHONON package :link(USER-PHONON),h5
 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
+To install via make or Make.py:
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
@@ -1686,32 +1960,33 @@ The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.
 
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
 Examples: examples/USER/phonon
 
 :line
 
 USER-QMMM package :link(USER-QMMM),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 This package provides a fix qmmm command which allows LAMMPS to be
@@ -1738,12 +2013,27 @@ The person who created this package is Axel Kohlmeyer at Temple U
 :line
  
 USER-QTB package :link(USER-QTB),h5
- 
-Contents:
- 
+
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
  
 Supporting info: 
  
@@ -1770,32 +2060,33 @@ The person who created this package is Yuan Shen (sy0302 at
 stanford.edu) at Stanford University.  Contact him directly if you
 have questions.
 
-To install via make or Make.py:
-
-make yes-body
-make machine :pre
-
-Make.py -p body -a machine :pre
-
-To un-install via make or Make.py:
-
-make no-body
-make machine :pre
-
-Make.py -p ^body -a machine :pre
-
 Examples: examples/USER/qtb
 
 :line
 
 USER-QUIP package :link(USER-QUIP),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 Examples: examples/USER/quip
@@ -1804,21 +2095,26 @@ Examples: examples/USER/quip
 
 USER-REAXC package :link(USER-REAXC),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
 
 Supporting info: 
  
@@ -1859,12 +2155,27 @@ Examples: examples/reax
 
 USER-SMD package :link(USER-SMD),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
- 
+
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
- 
+
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
+
 Supporting info: 
  
 This package implements smoothed Mach dynamics (SMD) in
@@ -1900,21 +2211,26 @@ Examples: examples/USER/smd
 
 USER-SMTBQ package :link(USER-SMTBQ),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
 
 Supporting info: 
  
@@ -1939,21 +2255,26 @@ Examples: examples/USER/smtbq
 
 USER-SPH package :link(USER-SPH),h5
 
-Contents:
- 
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
+
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
 
 Supporting info: 
 
@@ -1988,21 +2309,26 @@ Examples: examples/USER/sph
 
 USER-TALLY package :link(USER-TALLY),h5
 
-Contents:
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
 
 To install via make or Make.py:
 
-make yes-body
+make yes-user-atc
 make machine :pre
 
-Make.py -p body -a machine :pre
+Make.py -p atc -a machine :pre
 
 To un-install via make or Make.py:
 
-make no-body
+make no-user-atc
 make machine :pre
 
-Make.py -p ^body -a machine :pre
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
 
 Supporting info: 
 
@@ -2012,12 +2338,25 @@ Examples: examples/USER/tally
 
 USER-VTK package :link(USER-VTK),h5
 
-Contents:
+Contents: A "fix atc"_fix_atc.html command (atoms to continuum) to
+either couple of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.  See
+src/USER-ATC/README for more details.
 
 To install via make or Make.py:
 
+make yes-user-atc
+make machine :pre
+
+Make.py -p atc -a machine :pre
+
 To un-install via make or Make.py:
 
-Supporting info: 
+make no-user-atc
+make machine :pre
+
+Make.py -p ^atc -a machine :pre
+
+Supporting info: "fix atc"_fix_atc.html, examples/USER/atc
 
 Examples: examples/USER/tally
diff --git a/doc/Section_perf.html b/doc/Section_perf.html
index 166caa7357..f21f85c93d 100644
--- a/doc/Section_perf.html
+++ b/doc/Section_perf.html
@@ -137,12 +137,17 @@
             
   
    
 
    8. Performance & scalability
    
-
    LAMMPS performance on several prototypical benchmarks and machines is
-discussed on the Benchmarks page of the LAMMPS WWW Site where
-CPU timings and parallel efficiencies are listed.  Here, the
-benchmarks are described briefly and some useful rules of thumb about
-their performance are highlighted.
    
-
    These are the 5 benchmark problems:
    
+
    Current LAMMPS performance is discussed on the Benchmarks page of the
+LAMMPS WWW Site where CPU timings and parallel efficiencies are
+listed.  The page has several sections, which are briefly described
+below:
    
+
      
+
    • CPU performance on 5 standard problems, strong and weak scaling
      • 
+
    • GPU and Xeon Phi performance on same and related problems
      • 
+
    • Comparison of cost of interatomic potentials
      • 
+
    • Performance of huge, billion-atom problems
      • 
+
    
+
    The 5 standard problems are as follow:
    
 
      
 
    1. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
      2. 
 
    
@@ -161,73 +166,46 @@ field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
 particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
 integration
    • -

    The input files for running the benchmarks are included in the LAMMPS -distribution, as are sample output files. Each of the 5 problems has -32,000 atoms and runs for 100 timesteps. Each can be run as a serial -benchmarks (on one processor) or in parallel. In parallel, each -benchmark can be run as a fixed-size or scaled-size problem. For -fixed-size benchmarking, the same 32K atom problem is run on various -numbers of processors. For scaled-size benchmarking, the model size -is increased with the number of processors. E.g. on 8 processors, a -256K-atom problem is run; on 1024 processors, a 32-million atom -problem is run, etc.

    -

    A useful metric from the benchmarks is the CPU cost per atom per -timestep. Since LAMMPS performance scales roughly linearly with -problem size and timesteps, the run time of any problem using the same -model (atom style, force field, cutoff, etc) can then be estimated. -For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler -under Red Hat Linux), the CPU run-time in seconds/atom/timestep for -the 5 problems is

    - -------- - - - - - - - - - - - - - - - - - - - - - - - -
    Problem:LJChainEAMChuteRhodopsin
    CPU/atom/step:4.55E-62.18E-69.38E-62.18E-61.11E-4
    Ratio to LJ:1.00.482.060.4824.5
    -

    The ratios mean that if the atomic LJ system has a normalized cost of -1.0, the bead-spring chains and granular systems run 2x faster, while -the EAM metal and solvated protein models run 2x and 25x slower -respectively. The bulk of these cost differences is due to the -expense of computing a particular pairwise force field for a given -number of neighbors per atom.

    -

    Performance on a parallel machine can also be predicted from the -one-processor timings if the parallel efficiency can be estimated. -The communication bandwidth and latency of a particular parallel -machine affects the efficiency. On most machines LAMMPS will give -fixed-size parallel efficiencies on these benchmarks above 50% so long -as the atoms/processor count is a few 100 or greater - i.e. on 64 to -128 processors. Likewise, scaled-size parallel efficiencies will -typically be 80% or greater up to very large processor counts. The -benchmark data on the LAMMPS WWW Site gives specific examples on -some different machines, including a run of 3/4 of a billion LJ atoms -on 1500 processors that ran at 85% parallel efficiency.

    +

    Input files for these 5 problems are provided in the bench directory +of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 +timesteps. The size of the problem (number of atoms) can be varied +using command-line switches as described in the bench/README file. +This is an easy way to test performance and either strong or weak +scalability on your machine.

    +

    The bench directory includes a few log.* files that show performance +of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI +and bench/KEPLER dirs have input files and scripts and instructions +for running the same (or similar) problems using OpenMP or GPU or Xeon +Phi acceleration options. See the README files in those dirs and the +Section accelerate doc pages for +instructions on how to build LAMMPS and run on that kind of hardware.

    +

    The bench/POTENTIALS directory has input files which correspond to the +table of results on the +Potentials section of +the Benchmarks web page. So you can also run those test problems on +your machine.

    +

    The billion-atom section +of the Benchmarks web page has performance data for very large +benchmark runs of simple Lennard-Jones (LJ) models, which use the +bench/in.lj input script.

    +
    +

    For all the benchmarks, a useful metric is the CPU cost per atom per +timestep. Since performance scales roughly linearly with problem size +and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained +potentials), the run time of any problem using the same model (atom +style, force field, cutoff, etc) can then be estimated.

    +

    Performance on a parallel machine can also be predicted from one-core +or one-node timings if the parallel efficiency can be estimated. The +communication bandwidth and latency of a particular parallel machine +affects the efficiency. On most machines LAMMPS will give parallel +efficiencies on these benchmarks above 50% so long as the number of +atoms/core is a few 100 or greater, and closer to 100% for large +numbers of atoms/core. This is for all-MPI mode with one MPI task per +core. For nodes with accelerator options or hardware (OpenMP, GPU, +Phi), you should first measure single node performance. Then you can +estimate parallel performance for multi-node runs using the same logic +as for all-MPI mode, except that now you will typically need many more +atoms/node to achieve good scalability.

    diff --git a/doc/Section_perf.txt b/doc/Section_perf.txt index 896d522cac..d1cafa0bda 100644 --- a/doc/Section_perf.txt +++ b/doc/Section_perf.txt @@ -8,13 +8,17 @@ 8. Performance & scalability :h3 -LAMMPS performance on several prototypical benchmarks and machines is -discussed on the Benchmarks page of the "LAMMPS WWW Site"_lws where -CPU timings and parallel efficiencies are listed. Here, the -benchmarks are described briefly and some useful rules of thumb about -their performance are highlighted. +Current LAMMPS performance is discussed on the Benchmarks page of the +"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are +listed. The page has several sections, which are briefly described +below: -These are the 5 benchmark problems: +CPU performance on 5 standard problems, strong and weak scaling +GPU and Xeon Phi performance on same and related problems +Comparison of cost of interatomic potentials +Performance of huge, billion-atom problems :ul + +The 5 standard problems are as follow: LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 neighbors per atom), NVE integration :olb,l @@ -34,44 +38,49 @@ field with a 10 Angstrom LJ cutoff (440 neighbors per atom), particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT integration :ole,l -The input files for running the benchmarks are included in the LAMMPS -distribution, as are sample output files. Each of the 5 problems has -32,000 atoms and runs for 100 timesteps. Each can be run as a serial -benchmarks (on one processor) or in parallel. In parallel, each -benchmark can be run as a fixed-size or scaled-size problem. For -fixed-size benchmarking, the same 32K atom problem is run on various -numbers of processors. For scaled-size benchmarking, the model size -is increased with the number of processors. E.g. on 8 processors, a -256K-atom problem is run; on 1024 processors, a 32-million atom -problem is run, etc. +Input files for these 5 problems are provided in the bench directory +of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 +timesteps. The size of the problem (number of atoms) can be varied +using command-line switches as described in the bench/README file. +This is an easy way to test performance and either strong or weak +scalability on your machine. -A useful metric from the benchmarks is the CPU cost per atom per -timestep. Since LAMMPS performance scales roughly linearly with -problem size and timesteps, the run time of any problem using the same -model (atom style, force field, cutoff, etc) can then be estimated. -For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler -under Red Hat Linux), the CPU run-time in seconds/atom/timestep for -the 5 problems is +The bench directory includes a few log.* files that show performance +of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI +and bench/KEPLER dirs have input files and scripts and instructions +for running the same (or similar) problems using OpenMP or GPU or Xeon +Phi acceleration options. See the README files in those dirs and the +"Section accelerate"_Section_accelerate.html doc pages for +instructions on how to build LAMMPS and run on that kind of hardware. -Problem:, LJ, Chain, EAM, Chute, Rhodopsin -CPU/atom/step:, 4.55E-6, 2.18E-6, 9.38E-6, 2.18E-6, 1.11E-4 -Ratio to LJ:, 1.0, 0.48, 2.06, 0.48, 24.5 :tb(ea=c,ca1=r) +The bench/POTENTIALS directory has input files which correspond to the +table of results on the +"Potentials"_http://lammps.sandia.gov/bench.html#potentials section of +the Benchmarks web page. So you can also run those test problems on +your machine. -The ratios mean that if the atomic LJ system has a normalized cost of -1.0, the bead-spring chains and granular systems run 2x faster, while -the EAM metal and solvated protein models run 2x and 25x slower -respectively. The bulk of these cost differences is due to the -expense of computing a particular pairwise force field for a given -number of neighbors per atom. +The "billion-atom"_http://lammps.sandia.gov/bench.html#billion section +of the Benchmarks web page has performance data for very large +benchmark runs of simple Lennard-Jones (LJ) models, which use the +bench/in.lj input script. -Performance on a parallel machine can also be predicted from the -one-processor timings if the parallel efficiency can be estimated. -The communication bandwidth and latency of a particular parallel -machine affects the efficiency. On most machines LAMMPS will give -fixed-size parallel efficiencies on these benchmarks above 50% so long -as the atoms/processor count is a few 100 or greater - i.e. on 64 to -128 processors. Likewise, scaled-size parallel efficiencies will -typically be 80% or greater up to very large processor counts. The -benchmark data on the "LAMMPS WWW Site"_lws gives specific examples on -some different machines, including a run of 3/4 of a billion LJ atoms -on 1500 processors that ran at 85% parallel efficiency. +:line + +For all the benchmarks, a useful metric is the CPU cost per atom per +timestep. Since performance scales roughly linearly with problem size +and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained +potentials), the run time of any problem using the same model (atom +style, force field, cutoff, etc) can then be estimated. + +Performance on a parallel machine can also be predicted from one-core +or one-node timings if the parallel efficiency can be estimated. The +communication bandwidth and latency of a particular parallel machine +affects the efficiency. On most machines LAMMPS will give parallel +efficiencies on these benchmarks above 50% so long as the number of +atoms/core is a few 100 or greater, and closer to 100% for large +numbers of atoms/core. This is for all-MPI mode with one MPI task per +core. For nodes with accelerator options or hardware (OpenMP, GPU, +Phi), you should first measure single node performance. Then you can +estimate parallel performance for multi-node runs using the same logic +as for all-MPI mode, except that now you will typically need many more +atoms/node to achieve good scalability. diff --git a/doc/_sources/Section_example.txt b/doc/_sources/Section_example.txt index d5f6744d5c..2e44b4fc95 100644 --- a/doc/_sources/Section_example.txt +++ b/doc/_sources/Section_example.txt @@ -1,21 +1,20 @@ Example problems ================ -The LAMMPS distribution includes an examples sub-directory with -several sample problems. Each problem is in a sub-directory of its -own. Most are 2d models so that they run quickly, requiring at most a -couple of minutes to run on a desktop machine. Each problem has an -input script (in.*) and produces a log file (log.*) and dump file -(dump.*) when it runs. Some use a data file (data.*) of initial -coordinates as additional input. A few sample log file outputs on -different machines and different numbers of processors are included in -the directories to compare your answers to. E.g. a log file like -log.crack.foo.P means it ran on P processors of machine "foo". +The LAMMPS distribution includes an examples sub-directory with many +sample problems. Many are 2d models that run quickly are are +straightforward to visualize, requiring at most a couple of minutes to +run on a desktop machine. Each problem has an input script (in.*) and +produces a log file (log.*) when it runs. Some use a data file +(data.*) of initial coordinates as additional input. A few sample log +file run on different machines and different numbers of processors are +included in the directories to compare your answers to. E.g. a log +file like log.date.crack.foo.P means the "crack" example was run on P +processors of machine "foo" on that date (i.e. with that version of +LAMMPS). -For examples that use input data files, many of them were produced by -`Pizza.py `_ or setup tools described in the -:doc:`Additional Tools ` section of the LAMMPS -documentation and provided with the LAMMPS distribution. +Many of the input files have commented-out lines for creating dump +files and image files. If you uncomment the :doc:`dump ` command in the input script, a text dump file will be produced, which can be animated by various @@ -28,94 +27,109 @@ snapshot images will be produced when the simulation runs. They can be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. -Animations of many of these examples can be viewed on the Movies -section of the `LAMMPS WWW Site `_. +Animations of many of the examples can be viewed on the Movies section +of the `LAMMPS web site `_. -These are the sample problems in the examples sub-directories: +There are two kinds of sub-directories in the examples dir. Lowercase +dirs contain one or a few simple, quick-to-run problems. Uppercase +dirs contain up to several complex scripts that illustrate a +particular kind of simulation method or model. Some of these run for +longer times, e.g. to measure a particular quantity. -+-------------+----------------------------------------------------------------------------+ -| balance | dynamic load balancing, 2d system | -+-------------+----------------------------------------------------------------------------+ -| body | body particles, 2d system | -+-------------+----------------------------------------------------------------------------+ -| colloid | big colloid particles in a small particle solvent, 2d system | -+-------------+----------------------------------------------------------------------------+ -| comb | models using the COMB potential | -+-------------+----------------------------------------------------------------------------+ -| crack | crack propagation in a 2d solid | -+-------------+----------------------------------------------------------------------------+ -| cuda | use of the USER-CUDA package for GPU acceleration | -+-------------+----------------------------------------------------------------------------+ -| dipole | point dipolar particles, 2d system | -+-------------+----------------------------------------------------------------------------+ -| dreiding | methanol via Dreiding FF | -+-------------+----------------------------------------------------------------------------+ -| eim | NaCl using the EIM potential | -+-------------+----------------------------------------------------------------------------+ -| ellipse | ellipsoidal particles in spherical solvent, 2d system | -+-------------+----------------------------------------------------------------------------+ -| flow | Couette and Poiseuille flow in a 2d channel | -+-------------+----------------------------------------------------------------------------+ -| friction | frictional contact of spherical asperities between 2d surfaces | -+-------------+----------------------------------------------------------------------------+ -| gpu | use of the GPU package for GPU acceleration | -+-------------+----------------------------------------------------------------------------+ -| hugoniostat | Hugoniostat shock dynamics | -+-------------+----------------------------------------------------------------------------+ -| indent | spherical indenter into a 2d solid | -+-------------+----------------------------------------------------------------------------+ -| intel | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor | -+-------------+----------------------------------------------------------------------------+ -| kim | use of potentials in Knowledge Base for Interatomic Models (KIM) | -+-------------+----------------------------------------------------------------------------+ -| line | line segment particles in 2d rigid bodies | -+-------------+----------------------------------------------------------------------------+ -| meam | MEAM test for SiC and shear (same as shear examples) | -+-------------+----------------------------------------------------------------------------+ -| melt | rapid melt of 3d LJ system | -+-------------+----------------------------------------------------------------------------+ -| micelle | self-assembly of small lipid-like molecules into 2d bilayers | -+-------------+----------------------------------------------------------------------------+ -| min | energy minimization of 2d LJ melt | -+-------------+----------------------------------------------------------------------------+ -| msst | MSST shock dynamics | -+-------------+----------------------------------------------------------------------------+ -| nb3b | use of nonbonded 3-body harmonic pair style | -+-------------+----------------------------------------------------------------------------+ -| neb | nudged elastic band (NEB) calculation for barrier finding | -+-------------+----------------------------------------------------------------------------+ -| nemd | non-equilibrium MD of 2d sheared system | -+-------------+----------------------------------------------------------------------------+ -| obstacle | flow around two voids in a 2d channel | -+-------------+----------------------------------------------------------------------------+ -| peptide | dynamics of a small solvated peptide chain (5-mer) | -+-------------+----------------------------------------------------------------------------+ -| peri | Peridynamic model of cylinder impacted by indenter | -+-------------+----------------------------------------------------------------------------+ -| pour | pouring of granular particles into a 3d box, then chute flow | -+-------------+----------------------------------------------------------------------------+ -| prd | parallel replica dynamics of vacancy diffusion in bulk Si | -+-------------+----------------------------------------------------------------------------+ -| qeq | use of the QEQ package for charge equilibration | -+-------------+----------------------------------------------------------------------------+ -| reax | RDX and TATB models using the ReaxFF | -+-------------+----------------------------------------------------------------------------+ -| rigid | rigid bodies modeled as independent or coupled | -+-------------+----------------------------------------------------------------------------+ -| shear | sideways shear applied to 2d solid, with and without a void | -+-------------+----------------------------------------------------------------------------+ -| snap | NVE dynamics for BCC tantalum crystal using SNAP potential | -+-------------+----------------------------------------------------------------------------+ -| srd | stochastic rotation dynamics (SRD) particles as solvent | -+-------------+----------------------------------------------------------------------------+ -| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si | -+-------------+----------------------------------------------------------------------------+ -| tri | triangular particles in rigid bodies | -+-------------+----------------------------------------------------------------------------+ +Lists of both kinds of directories are given below. -vashishta: models using the Vashishta potential -Here is how you might run and visualize one of the sample problems: +---------- + + +Lowercase directories +--------------------- + ++-------------+------------------------------------------------------------------+ +| accelerate | run with various acceleration options (OpenMP, GPU, Phi) | ++-------------+------------------------------------------------------------------+ +| balance | dynamic load balancing, 2d system | ++-------------+------------------------------------------------------------------+ +| body | body particles, 2d system | ++-------------+------------------------------------------------------------------+ +| colloid | big colloid particles in a small particle solvent, 2d system | ++-------------+------------------------------------------------------------------+ +| comb | models using the COMB potential | ++-------------+------------------------------------------------------------------+ +| coreshell | core/shell model using CORESHELL package | ++-------------+------------------------------------------------------------------+ +| crack | crack propagation in a 2d solid | ++-------------+------------------------------------------------------------------+ +| cuda | use of the USER-CUDA package for GPU acceleration | ++-------------+------------------------------------------------------------------+ +| deposit | deposit atoms and molecules on a surface | ++-------------+------------------------------------------------------------------+ +| dipole | point dipolar particles, 2d system | ++-------------+------------------------------------------------------------------+ +| dreiding | methanol via Dreiding FF | ++-------------+------------------------------------------------------------------+ +| eim | NaCl using the EIM potential | ++-------------+------------------------------------------------------------------+ +| ellipse | ellipsoidal particles in spherical solvent, 2d system | ++-------------+------------------------------------------------------------------+ +| flow | Couette and Poiseuille flow in a 2d channel | ++-------------+------------------------------------------------------------------+ +| friction | frictional contact of spherical asperities between 2d surfaces | ++-------------+------------------------------------------------------------------+ +| hugoniostat | Hugoniostat shock dynamics | ++-------------+------------------------------------------------------------------+ +| indent | spherical indenter into a 2d solid | ++-------------+------------------------------------------------------------------+ +| kim | use of potentials in Knowledge Base for Interatomic Models (KIM) | ++-------------+------------------------------------------------------------------+ +| meam | MEAM test for SiC and shear (same as shear examples) | ++-------------+------------------------------------------------------------------+ +| melt | rapid melt of 3d LJ system | ++-------------+------------------------------------------------------------------+ +| micelle | self-assembly of small lipid-like molecules into 2d bilayers | ++-------------+------------------------------------------------------------------+ +| min | energy minimization of 2d LJ melt | ++-------------+------------------------------------------------------------------+ +| msst | MSST shock dynamics | ++-------------+------------------------------------------------------------------+ +| nb3b | use of nonbonded 3-body harmonic pair style | ++-------------+------------------------------------------------------------------+ +| neb | nudged elastic band (NEB) calculation for barrier finding | ++-------------+------------------------------------------------------------------+ +| nemd | non-equilibrium MD of 2d sheared system | ++-------------+------------------------------------------------------------------+ +| obstacle | flow around two voids in a 2d channel | ++-------------+------------------------------------------------------------------+ +| peptide | dynamics of a small solvated peptide chain (5-mer) | ++-------------+------------------------------------------------------------------+ +| peri | Peridynamic model of cylinder impacted by indenter | ++-------------+------------------------------------------------------------------+ +| pour | pouring of granular particles into a 3d box, then chute flow | ++-------------+------------------------------------------------------------------+ +| prd | parallel replica dynamics of vacancy diffusion in bulk Si | ++-------------+------------------------------------------------------------------+ +| python | using embedded Python in a LAMMPS input script | ++-------------+------------------------------------------------------------------+ +| qeq | use of the QEQ package for charge equilibration | ++-------------+------------------------------------------------------------------+ +| reax | RDX and TATB models using the ReaxFF | ++-------------+------------------------------------------------------------------+ +| rigid | rigid bodies modeled as independent or coupled | ++-------------+------------------------------------------------------------------+ +| shear | sideways shear applied to 2d solid, with and without a void | ++-------------+------------------------------------------------------------------+ +| snap | NVE dynamics for BCC tantalum crystal using SNAP potential | ++-------------+------------------------------------------------------------------+ +| srd | stochastic rotation dynamics (SRD) particles as solvent | ++-------------+------------------------------------------------------------------+ +| streitz | use of Streitz/Mintmire potential with charge equilibration | ++-------------+------------------------------------------------------------------+ +| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si | ++-------------+------------------------------------------------------------------+ +| vashishta | use of the Vashishta potential | ++-------------+------------------------------------------------------------------+ + +Here is how you can run and visualize one of the sample problems: .. parsed-literal:: @@ -124,16 +138,16 @@ Here is how you might run and visualize one of the sample problems: lmp_linux -in in.indent # run the problem Running the simulation produces the files *dump.indent* and -*log.lammps*. You can visualize the dump file as follows: - -.. parsed-literal:: - - ../../tools/xmovie/xmovie -scale dump.indent +*log.lammps*. You can visualize the dump file of snapshots with a +variety of 3rd-party tools highlighted on the +`Visualization `_ page of the LAMMPS +web site. If you uncomment the :doc:`dump image ` line(s) in the input -script a series of JPG images will be produced by the run. These can -be viewed individually or turned into a movie or animated by tools -like ImageMagick or QuickTime or various Windows-based tools. See the +script a series of JPG images will be produced by the run (assuming +you built LAMMPS with JPG support; see :doc:`Section start 2.2 ` for details). These can be viewed +individually or turned into a movie or animated by tools like +ImageMagick or QuickTime or various Windows-based tools. See the :doc:`dump image ` doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. @@ -146,23 +160,38 @@ browser. ---------- -There is also a COUPLE directory with examples of how to use LAMMPS as -a library, either by itself or in tandem with another code or library. -See the COUPLE/README file to get started. +Uppercase directories +--------------------- -There is also an ELASTIC directory with an example script for -computing elastic constants at zero temperature, using an Si example. See -the ELASTIC/in.elastic file for more info. ++-----------+--------------------------------------------------------------------------------------------------+ +| ASPHERE | various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc | ++-----------+--------------------------------------------------------------------------------------------------+ +| COUPLE | examples of how to use LAMMPS as a library | ++-----------+--------------------------------------------------------------------------------------------------+ +| DIFFUSE | compute diffusion coefficients via several methods | ++-----------+--------------------------------------------------------------------------------------------------+ +| ELASTIC | compute elastic constants at zero temperature | ++-----------+--------------------------------------------------------------------------------------------------+ +| ELASTIC_T | compute elastic constants at finite temperature | ++-----------+--------------------------------------------------------------------------------------------------+ +| KAPPA | compute thermal conductivity via several methods | ++-----------+--------------------------------------------------------------------------------------------------+ +| MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system | ++-----------+--------------------------------------------------------------------------------------------------+ +| USER | examples for USER packages and USER-contributed commands | ++-----------+--------------------------------------------------------------------------------------------------+ +| VISCOSITY | compute viscosity via several methods | ++-----------+--------------------------------------------------------------------------------------------------+ -There is also an ELASTIC_T directory with an example script for -computing elastic constants at finite temperature, using an Si example. See -the ELASTIC_T/in.elastic file for more info. +Nearly all of these directories have README files which give more +details on how to understand and use their contents. -There is also a USER directory which contains subdirectories of -user-provided examples for user packages. See the README files in -those directories for more info. See the -:doc:`Section_start.html ` file for more info about user -packages. +The USER directory has a large number of sub-directories which +correspond by name to a USER package. They contain scripts that +illustrate how to use the command(s) provided in that package. Many +of the sub-directories have their own README files which give further +instructions. See the :doc:`Section packages ` doc +page for more info on specific USER packages. .. _lws: http://lammps.sandia.gov diff --git a/doc/_sources/Section_packages.txt b/doc/_sources/Section_packages.txt index c7d06c676c..d9b5137ec5 100644 --- a/doc/_sources/Section_packages.txt +++ b/doc/_sources/Section_packages.txt @@ -26,12 +26,16 @@ has a summary of what the package contains. It has specific instructions on how to install it, build or obtain any auxiliary library it requires, and any Makefile.machine changes it requires. It also lists pointers to examples of its use or documentation provided -in the LAMMPS distribution. +in the LAMMPS distribution. If you want to know the complete list of +commands that a package adds to LAMMPS, simply list the files in its +directory, e.g. "ls src/GRANULAR". Source files with names that start +with compute, fix, pair, bond, etc correspond to command styles with +the same names. .. note:: - The sub-sections below are still being filled in, as of Feb - 2016. + The USER package sub-sections below are still being filled in, + as of March 2016. Unless otherwise noted below, every package is independent of all the others. I.e. any package can be included or excluded in a LAMMPS @@ -67,7 +71,7 @@ name links to a sub-section below with more details. +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`CLASS2 ` | class 2 force fields | - | :doc:`pair_style lj/class2 ` | - | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ -| :ref:`COLLOID ` | colloidal particles | - | :doc:`atom_style colloid ` | colloid | - | +| :ref:`COLLOID ` | colloidal particles | Kumar (1) | :doc:`atom_style colloid ` | colloid | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`COMPRESS ` | I/O compression | Axel Kohlmeyer (Temple U) | :doc:`dump */gz ` | - | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ @@ -75,15 +79,13 @@ name links to a sub-section below with more details. +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`DIPOLE ` | point dipole particles | - | :doc:`pair_style dipole/cut ` | dipole | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ -| :ref:`FLD ` | Fast Lubrication Dynamics | Kumar & Bybee & Higdon (1) | :doc:`pair_style lubricateU ` | - | - | -+------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`GPU ` | GPU-enabled styles | Mike Brown (ORNL) | :doc:`Section accelerate ` | gpu | lib/gpu | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`GRANULAR ` | granular systems | - | :ref:`Section_howto 6.6 ` | pour | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`KIM ` | openKIM potentials | Smirichinski & Elliot & Tadmor (3) | :doc:`pair_style kim ` | kim | KIM | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ -| :ref:`KOKKOS ` | Kokkos-enabled styles | Trott & Edwards (4) | :doc:`Section_accelerate ` | kokkos | lib/kokkos | +| :ref:`KOKKOS ` | Kokkos-enabled styles | Trott & Moore (4) | :doc:`Section_accelerate ` | kokkos | lib/kokkos | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ | :ref:`KSPACE ` | long-range Coulombic solvers | - | :doc:`kspace_style ` | peptide | - | +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ @@ -125,8 +127,9 @@ name links to a sub-section below with more details. The "Authors" column lists a name(s) if a specific person is responible for creating and maintaining the package. -(1) The FLD package was created by Amit Kumar and Michael Bybee from -Jonathan Higdon's group at UIUC. +(1) The COLLOID package includes Fast Lubrication Dynamics pair styles +which were created by Amit Kumar and Michael Bybee from Jonathan +Higdon's group at UIUC. (2) The OPT package was created by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -135,9 +138,9 @@ Technolgy). (3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, and Ellad Tadmor (U Minn). -(4) The KOKKOS package was created primarily by Christian Trott -(Sandia). It uses the Kokkos library which was developed by Carter -Edwards, Christian, and collaborators at Sandia. +(4) The KOKKOS package was created primarily by Christian Trott and +Stan Moore (Sandia). It uses the Kokkos library which was developed +by Carter Edwards, Christian Trott, and others at Sandia. The "Doc page" column links to either a sub-section of the :doc:`Section_howto ` of the manual, or an input script @@ -166,8 +169,8 @@ p.s.: are we ever going to get commit messages from you? ;-) ASPHERE package ^^^^^^^^^^^^^^^ -Contents: Aspherical particle models for ellipsoids, 2d lines, 3d -triangles. +Contents: Several computes, time-integration fixes, and pair styles +for aspherical particle models: ellipsoids, 2d lines, 3d triangles. To install via make or Make.py: @@ -191,8 +194,11 @@ To un-install via make or Make.py: Make.py -p ^asphere -a machine -Supporting info: examples/ASPHERE, examples/ellipse, Section howto -6.14, pair gayberne +Supporting info: :ref:`Section howto 6.14 `, +:doc:`pair_style gayberne `, :doc:`pair_style resquared `, +`doc/PDF/pair_gayberne_extra.pdf `_, +`doc/PDF/pair_resquared_extra.pdf `_, +examples/ASPHERE, examples/ellipse ---------- @@ -203,7 +209,9 @@ Supporting info: examples/ASPHERE, examples/ellipse, Section howto BODY package ^^^^^^^^^^^^ -Contents: +Contents: Support for body-style particles. Computes, +time-integration fixes, pair styles, as well as the body styles +themselves. See the :doc:`body ` doc page for an overview. To install via make or Make.py: @@ -227,7 +235,8 @@ To un-install via make or Make.py: Make.py -p ^body -a machine -Supporting info: examples/body +Supporting info: :doc:`atom_style body `, :doc:`body `, +:doc:`pair_style body `, examples/body ---------- @@ -238,7 +247,8 @@ Supporting info: examples/body CLASS2 package ^^^^^^^^^^^^^^ -Contents: +Contents: Bond, angle, dihedral, improper, and pair styles for the +COMPASS CLASS2 molecular force field. To install via make or Make.py: @@ -262,7 +272,7 @@ To un-install via make or Make.py: Make.py -p ^class2 -a machine -Supporting info: +Supporting info: :doc:`bond_style class2 `, :doc:`angle_style class2 `, :doc:`dihedral_style class2 `, :doc:`improper_style class2 `, :doc:`pair_style lj/class2 ` ---------- @@ -273,7 +283,11 @@ Supporting info: COLLOID package ^^^^^^^^^^^^^^^ -Contents: +Contents: Support for coarse-grained colloidal particles. Wall fix +and pair styles that implement colloidal interaction models for +finite-size particles. This includes the Fast Lubrication Dynamics +method for hydrodynamic interactions, which is a simplified +approximation to Stokesian dynamics. To install via make or Make.py: @@ -297,7 +311,7 @@ To un-install via make or Make.py: Make.py -p ^colloid -a machine -Supporting info: examples/colloid, examples/srd +Supporting info: :doc:`fix wall/colloid `, :doc:`pair_style colloid `, :doc:`pair_style yukawa/colloid `, :doc:`pair_style brownian `, :doc:`pair_style lubricate `, :doc:`pair_style lubricateU `, examples/colloid, examples/srd ---------- @@ -308,7 +322,15 @@ Supporting info: examples/colloid, examples/srd COMPRESS package ^^^^^^^^^^^^^^^^ -Contents: +Contents: Support for compressed output of dump files via the zlib +compression library, using dump styles with a "gz" in their style +name. + +Building with the COMPRESS package assumes you have the zlib +compression library available on your system. The build uses the +lib/compress/Makefile.lammps file in the compile/link process. You +should only need to edit this file if the LAMMPS build cannot find the +zlib info it specifies. To install via make or Make.py: @@ -332,7 +354,7 @@ To un-install via make or Make.py: Make.py -p ^compress -a machine -Supporting info: +Supporting info: src/COMPRESS/README, lib/compress/README, :doc:`dump atom/gz `, :doc:`dump cfg/gz `, :doc:`dump custom/gz `, :doc:`dump xyz/gz ` ---------- @@ -343,7 +365,12 @@ Supporting info: CORESHELL package ^^^^^^^^^^^^^^^^^ -Contents: +Contents: Compute and pair styles that implement the adiabatic +core/shell model for polarizability. The compute temp/cs command +measures the temperature of a system with core/shell particles. The +pair styles augment Born, Buckingham, and Lennard-Jones styles with +core/shell capabilities. See :ref:`Section howto 6.26 ` for an overview of how to use the +package. To install via make or Make.py: @@ -367,7 +394,9 @@ To un-install via make or Make.py: Make.py -p ^coreshell -a machine -Supporting info: examples/coreshell, Section howto 6.26 +Supporting info: :ref:`Section howto 6.26 `, :doc:`compute temp/cs `, +:doc:`pair_style born/coul/long/cs `, :doc:`pair_style buck/coul/long/cs `, pair_style +lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell ---------- @@ -378,7 +407,8 @@ Supporting info: examples/coreshell, Section howto 6.26 DIPOLE package ^^^^^^^^^^^^^^ -Contents: +Contents: An atom style and several pair styles to support point +dipole models with short-range or long-range interactions. To install via make or Make.py: @@ -402,42 +432,7 @@ To un-install via make or Make.py: Make.py -p ^dipole -a machine -Supporting info: examples/dipole - - ----------- - - -.. _FLD: - -FLD package -^^^^^^^^^^^ - -Contents: - -To install via make or Make.py: - -.. parsed-literal:: - - make yes-fld - make machine - -.. parsed-literal:: - - Make.py -p fld -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-fld - make machine - -.. parsed-literal:: - - Make.py -p ^fld -a machine - -Supporting info: +Supporting info: :doc:`atom_style dipole `, :doc:`pair_style lj/cut/dipole/cut `, :doc:`pair_style lj/cut/dipole/long `, :doc:`pair_style lj/long/dipole/long `, examples/dipole ---------- @@ -448,18 +443,49 @@ Supporting info: GPU package ^^^^^^^^^^^ -Contents: +Contents: Dozens of pair styles and a version of the PPPM long-range +Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their +style name. :doc:`Section accelerate gpu ` gives +details of what hardware and Cuda software is required on your system, +and how to build and use this package. See the KOKKOS and USER-CUDA +packages, which also have GPU-enabled styles. + +Building LAMMPS with the GPU package requires first building the GPU +library itself, which is a set of C and Cuda files in lib/gpu. +Details of how to do this are in lib/gpu/README. As illustrated +below, perform a "make" using one of the Makefile.machine files in +lib/gpu which should create a lib/reax/libgpu.a file. +Makefile.linux.* and Makefile.xk7 are examples for different +platforms. There are 3 important settings in the Makefile.machine you +use: + +* CUDA_HOME = where NVIDIA Cuda software is installed on your system +* CUDA_ARCH = appropriate to your GPU hardware +* CUDA_PREC = precision (double, mixed, single) you desire + +See example Makefile.machine files in lib/gpu for the syntax of these +settings. See lib/gpu/Makefile.linux.double for ARCH settings for +various NVIDIA GPUs. The "make" also creates a +lib/gpu/Makefile.lammps file. This file has settings that enable +LAMMPS to link with Cuda libraries. If the settings in +Makefile.lammps for your machine are not correct, the LAMMPS link will +fail. Note that the Make.py script has a "-gpu" option to allow the +GPU library (with several of its options) and LAMMPS to be built in +one step, with Type "python src/Make.py -h -gpu" to see the details. To install via make or Make.py: .. parsed-literal:: + cd ~/lammps/lib/gpu + make -f Makefile.linux.mixed # for example + cd ~/lammps/src make yes-gpu make machine .. parsed-literal:: - Make.py -p gpu -a machine + Make.py -p gpu -gpu mode=mixed arch=35 -a machine To un-install via make or Make.py: @@ -472,7 +498,9 @@ To un-install via make or Make.py: Make.py -p ^gpu -a machine -Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER +Supporting info: src/GPU/README, lib/gpu/README, :doc:`Section acclerate `, :doc:`Section accelerate gpu `, Pair Styles section of :ref:`Section commands 3.5 ` for any pair style listed with a (g), +:doc:`kspace_style `, :doc:`package gpu `, +examples/accelerate, bench/FERMI, bench/KEPLER ---------- @@ -483,7 +511,9 @@ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER GRANULAR package ^^^^^^^^^^^^^^^^ -Contents: +Contents: Fixes and pair styles that support models of finite-size +granular particles, which interact with each other and boundaries via +frictional and dissipative potentials. To install via make or Make.py: @@ -507,7 +537,7 @@ To un-install via make or Make.py: Make.py -p ^granular -a machine -Supporting info: examples/pour, bench/in.chute, Section howto 6.6 +Supporting info: :ref:`Section howto 6.6 `, :doc:`fix pour `, :doc:`fix wall/gran `, :doc:`pair_style gran/hooke `, :doc:`pair_style gran/hertz/history `, examples/pour, bench/in.chute ---------- @@ -518,7 +548,15 @@ Supporting info: examples/pour, bench/in.chute, Section howto 6.6 KIM package ^^^^^^^^^^^ -Contents: +Contents: A pair style that interfaces to the Knowledge Base for +Interatomic Models (KIM) repository of interatomic potentials, so that +KIM potentials can be used in a LAMMPS simulation. + +To build LAMMPS with the KIM package you must have previously +installed the KIM API (library) on your system. The lib/kim/README +file explains how to download and install KIM. Building with the KIM +package also uses the lib/kim/Makefile.lammps file in the compile/link +process. You should not need to edit this file. To install via make or Make.py: @@ -542,7 +580,7 @@ To un-install via make or Make.py: Make.py -p ^kim -a machine -Supporting info: examples/kim +Supporting info: src/KIM/README, lib/kim/README, :doc:`pair_style kim `, examples/kim ---------- @@ -553,55 +591,60 @@ Supporting info: examples/kim KOKKOS package ^^^^^^^^^^^^^^ -Contents: +Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles +which run with the Kokkos library to provide optimization for +multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in +native mode). All of them have a "kk" in their style name. :doc:`Section accelerate kokkos ` gives details of what +hardware and software is required on your system, and how to build and +use this package. See the GPU, OPT, USER-CUDA, USER-INTEL, USER-OMP +packages, which also provide optimizations for the same range of +hardware. -To install via make or Make.py: +Building with the KOKKOS package requires choosing which of 3 hardware +options you are optimizing for: CPU acceleration via OpenMP, GPU +acceleration, or Intel Xeon Phi. (You can build multiple times to +create LAMMPS executables for different hardware.) It also requires a +C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is +used, and an appopriate KOKKOS_ARCH setting should be made in your +Makefile.machine for your GPU hardware and NVIDIA software. + +The simplest way to do this is to use Makefile.kokkos_cuda or +Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via +"make kokkos_cuda" or "make kokkos_omp" or "make kokkos_phi". (Check +the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated +below, you can use the Make.py script with its "-kokkos" option to +choose which hardware to build for. Type "python src/Make.py -h +-kokkos" to see the details. If these methods do not work on your +system, you will need to read the :doc:`Section accelerate kokkos ` doc page for details of what +Makefile.machine settings are needed. + +To install via make or Make.py for each of 3 hardware options: .. parsed-literal:: - make yes-kokkow - make machine + make yes-kokkos + make kokkos_omp # for CPUs with OpenMP + make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda + make kokkos_phi # for Xeon Phis -.. parsed-literal:: - - Make.py -p kokkow -a machine +Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP +Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch +Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis To un-install via make or Make.py: .. parsed-literal:: - make no-kokkow + make no-kokkos make machine .. parsed-literal:: - Make.py -p ^kokkow -a machine + Make.py -p ^kokkos -a machine -Supporting info: - -For the KOKKOS package, you have 3 choices when building. You can -build with OMP or Cuda or Phi support. Phi support uses Xeon Phi -chips in "native" mode. This can be done by setting the following -variables in your Makefile.machine: - -* for OMP support, set OMP = yes -* for Cuda support, set OMP = yes and CUDA = yes -* for Phi support, set OMP = yes and MIC = yes - -These can also be set as additional arguments to the make command, e.g. - -.. parsed-literal:: - - make g++ OMP=yes MIC=yes - -Building the KOKKOS package with CUDA support requires a Makefile -machine that uses the NVIDIA "nvcc" compiler, as well as an -appropriate "arch" setting appropriate to the GPU hardware and NVIDIA -software you have on your machine. See -src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine -Makefile. - -Examples: examples/accelerate, bench/FERMI, bench/KEPLER +Supporting info: src/KOKKOS/README, lib/kokkos/README, :doc:`Section acclerate `, :doc:`Section accelerate kokkos `, Pair Styles section of :ref:`Section commands 3.5 ` for any pair style listed +with a (k), :doc:`package kokkos `, +examples/accelerate, bench/FERMI, bench/KEPLER ---------- @@ -612,7 +655,19 @@ Examples: examples/accelerate, bench/FERMI, bench/KEPLER KSPACE package ^^^^^^^^^^^^^^ -Contents: +Contents: A variety of long-range Coulombic solvers, and pair styles +which compute the corresponding short-range portion of the pairwise +Coulombic interactions. These include Ewald, particle-particle +particle-mesh (PPPM), and multilevel summation method (MSM) solvers. + +Building with the KSPACE package requires a 1d FFT library be present +on your system for use by the PPPM solvers. This can be the KISS FFT +library provided with LAMMPS, or 3rd party libraries like FFTW or a +vendor-supplied FFT library. See step 6 of :ref:`Section start 2.2.2 ` of the manual for details of how +to select different FFT options in your machine Makefile. The Make.py +tool has an "-fft" option which can insert these settings into your +machine Makefile automatically. Type "python src/Make.py -h -fft" to +see the details. To install via make or Make.py: @@ -636,11 +691,10 @@ To un-install via make or Make.py: Make.py -p ^kspace -a machine -Supporting info: - -Examples: examples/peptide, bench/in.rhodo - -Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9 +Supporting info: :doc:`kspace_style `, +`doc/PDF/kspace.pdf `_, :ref:`Section howto 6.7 `, :ref:`Section howto 6.8 `, :ref:`Section howto 6.9 `, :doc:`pair_style coul `, +other pair style command doc pages which have "long" or "msm" in their +style name, examples/peptide, bench/in.rhodo ---------- @@ -651,7 +705,10 @@ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9 MANYBODY package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A variety of many-body and bond-order potentials. These +include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff +potentials. Do a directory listing, "ls src/MANYBODY", to see +the full list. To install via make or Make.py: @@ -677,7 +734,8 @@ To un-install via make or Make.py: Supporting info: -Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta +Examples: Pair Styles section of :ref:`Section commands 3.5 `, examples/comb, examples/eim, +examples/nb3d, examples/vashishta ---------- @@ -688,7 +746,10 @@ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta MC package ^^^^^^^^^^ -Contents: +Contents: Several fixes and a pair style that have Monte Carlo (MC) or +MC-like attributes. These include fixes for creating, breaking, and +swapping bonds, and for performing atomic swaps and grand-canonical MC +in conjuction with dynamics. To install via make or Make.py: @@ -712,7 +773,8 @@ To un-install via make or Make.py: Make.py -p ^mc -a machine -Supporting info: +Supporting info: :doc:`fix atom/swap `, :doc:`fix bond/break `, :doc:`fix bond/create `, :doc:`fix bond/swap `, +:doc:`fix gcmc `, :doc:`pair_style dsmc ` ---------- @@ -723,18 +785,43 @@ Supporting info: MEAM package ^^^^^^^^^^^^ -Contents: +Contents: A pair style for the modified embedded atom (MEAM) +potential. + +Building LAMMPS with the MEAM package requires first building the MEAM +library itself, which is a set of Fortran 95 files in lib/meam. +Details of how to do this are in lib/meam/README. As illustrated +below, perform a "make" using one of the Makefile.machine files in +lib/meam which should create a lib/meam/libmeam.a file. +Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran +and Intel Fortran compilers. The "make" also copies a +lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps. +This file has settings that enable the C++ compiler used to build +LAMMPS to link with a Fortran library (typically the 2 compilers to be +consistent e.g. both Intel compilers, or both GNU compilers). If the +settings in Makefile.lammps for your compilers and machine are not +correct, the LAMMPS link will fail. Note that the Make.py script has +a "-meam" option to allow the MEAM library and LAMMPS to be built in +one step. Type "python src/Make.py -h -meam" to see the details. + +.. note:: + + The MEAM potential can run dramatically faster if built with the + Intel Fortran compiler, rather than the GNU Fortran compiler. To install via make or Make.py: .. parsed-literal:: + cd ~/lammps/lib/meam + make -f Makefile.gfortran # for example + cd ~/lammps/src make yes-meam make machine .. parsed-literal:: - Make.py -p meam -a machine + Make.py -p meam -meam make=gfortran -a machine To un-install via make or Make.py: @@ -747,7 +834,8 @@ To un-install via make or Make.py: Make.py -p ^meam -a machine -Supporting info: examples/meam +Supporting info: lib/meam/README, :doc:`pair_style meam `, +examples/meam ---------- @@ -758,7 +846,9 @@ Supporting info: examples/meam MISC package ^^^^^^^^^^^^ -Contents: +Contents: A variety of computes, fixes, and pair styles that are not +commonly used, but don't align with other packages. Do a directory +listing, "ls src/MISC", to see the list of commands. To install via make or Make.py: @@ -782,7 +872,7 @@ To un-install via make or Make.py: Make.py -p ^misc -a machine -Supporting info: examples/misc +Supporting info: :doc:`compute ti `, :doc:`fix evaporate `, :doc:`fix tmm `, :doc:`fix viscosity `, examples/misc ---------- @@ -793,7 +883,10 @@ Supporting info: examples/misc MOLECULE package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A large number of atom, pair, bond, angle, dihedral, +improper styles that are used to model molecular systems with fixed +covalent bonds. The pair styles include terms for the Dreiding +(hydrogen-bonding) and CHARMM force fields, and TIP4P water model. To install via make or Make.py: @@ -817,7 +910,11 @@ To un-install via make or Make.py: Make.py -p ^molecule -a machine -Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3 +Supporting info::doc:`atom_style `, +:doc:`bond_style `, :doc:`angle_style `, +:doc:`dihedral_style `, +:doc:`improper_style `, :doc:`pair_style hbond/dreiding/lj `, :doc:`pair_style lj/charmm/coul/charmm `, :ref:`Section howto 6.3 `, examples/micelle, examples/peptide, +bench/in.chain, bench/in.rhodo ---------- @@ -828,7 +925,11 @@ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rh MPIIO package ^^^^^^^^^^^^^ -Contents: +Contents: Support for parallel output/input of dump and restart files +via the MPIIO library, which is part of the standard message-passing +interface (MPI) library. It adds :doc:`dump styles ` with a +"mpiio" in their style name. Restart files with an ".mpiio" suffix +are also written and read in parallel. To install via make or Make.py: @@ -852,7 +953,8 @@ To un-install via make or Make.py: Make.py -p ^mpiio -a machine -Supporting info: +Supporting info: :doc:`dump `, :doc:`restart `, +:doc:`write_restart `, :doc:`read_restart ` ---------- @@ -863,7 +965,18 @@ Supporting info: OPT package ^^^^^^^^^^^ -Contents: +Contents: A handful of pair styles with an "opt" in their style name +which are optimized for improved CPU performance on single or multiple +cores. These include EAM, LJ, CHARMM, and Morse potentials. :doc:`Section accelerate opt ` gives details of how to build and +use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages, +which also have styles optimized for CPU performance. + +Some C++ compilers, like the Intel compiler, require the compile flag +"-restrict" to build LAMMPS with the OPT package. It should be added +to the CCFLAGS line of your Makefile.machine. Or use Makefile.opt in +src/MAKE/OPTIONS, via "make opt". For compilers that use the flag, +the Make.py command adds it automatically to the Makefile.auto file it +creates and uses. To install via make or Make.py: @@ -887,12 +1000,8 @@ To un-install via make or Make.py: Make.py -p ^opt -a machine -Supporting info: examples/accelerate, bench/KEPLER - -For the OPT package, your Makefile.machine needs an additional -settings for CCFLAGS. - -* CCFLAGS: add -restrict +Supporting info: :doc:`Section acclerate `, :doc:`Section accelerate opt `, Pair Styles section of :ref:`Section commands 3.5 ` for any pair style listed +with an (o), examples/accelerate, bench/KEPLER ---------- @@ -903,7 +1012,10 @@ settings for CCFLAGS. PERI package ^^^^^^^^^^^^ -Contents: +Contents: Support for the Peridynamics method, a particle-based +meshless continuum model. The package includes an atom style, several +computes which calculate diagnostics, and several Peridynamic pair +styles which implement different materials models. To install via make or Make.py: @@ -927,7 +1039,11 @@ To un-install via make or Make.py: Make.py -p ^peri -a machine -Supporting info: examples/peri +Supporting info: +`doc/PDF/PDLammps_overview.pdf `_, +`doc/PDF/PDLammps_EPS.pdf `_, +`doc/PDF/PDLammps_VES.pdf `_, :doc:`atom_style peri `, :doc:`compute damage `, +:doc:`pair_style peri/pmb `, examples/peri ---------- @@ -938,31 +1054,50 @@ Supporting info: examples/peri POEMS package ^^^^^^^^^^^^^ -Contents: +Contents: A fix that wraps the Parallelizable Open source Efficient +Multibody Software (POEMS) librar, which is able to simulate the +dynamics of articulated body systems. These are systems with multiple +rigid bodies (collections of atoms or particles) whose motion is +coupled by connections at hinge points. + +Building LAMMPS with the POEMS package requires first building the +POEMS library itself, which is a set of C++ files in lib/poems. +Details of how to do this are in lib/poems/README. As illustrated +below, perform a "make" using one of the Makefile.machine files in +lib/poems which should create a lib/meam/libpoems.a file. +Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++ +compilers. The "make" also creates a lib/poems/Makefile.lammps file +which you should not need to change. Note the Make.py script has a +"-poems" option to allow the POEMS library and LAMMPS to be built in +one step. Type "python src/Make.py -h -poems" to see the details. To install via make or Make.py: .. parsed-literal:: + cd ~/lammps/lib/poems + make -f Makefile.g++ # for example + cd ~/lammps/src make yes-poems make machine .. parsed-literal:: - Make.py -p poems -a machine + Make.py -p poems -poems make=g++ -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-poems + make no-meam make machine .. parsed-literal:: - Make.py -p ^poems -a machine + Make.py -p ^meam -a machine -Supporting info: examples/rigid +Supporting info: src/POEMS/README, lib/poems/README, +:doc:`fix_poems `, examples/rigid ---------- @@ -973,7 +1108,21 @@ Supporting info: examples/rigid PYTHON package ^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`python ` command which allow you to execute +Python code from a LAMMPS input script. The code can be in a separate +file or embedded in the input script itself. See :ref:`Section python 11.2 ` for an overview of using Python from +LAMMPS and `Section python `_ for other ways to use +LAMMPS and Python together. + +Building with the PYTHON package assumes you have a Python shared +library available on your system, which needs to be a Python 2 +version, 2.6 or later. Python 3 is not supported. The build uses the +contents of the lib/python/Makefile.lammps file to find all the Python +files required in the build/link process. See the lib/python/README +file if the settings in that file do not work on your system. Note +that the Make.py script has a "-python" option to allow an alternate +lib/python/Makefile.lammps file to be specified and LAMMPS to be built +in one step. Type "python src/Make.py -h -python" to see the details. To install via make or Make.py: @@ -1008,7 +1157,9 @@ Supporting info: examples/python QEQ package ^^^^^^^^^^^ -Contents: +Contents: Several fixes for performing charge equilibration (QEq) via +severeal different algorithms. These can be used with pair styles +that use QEq as part of their formulation. To install via make or Make.py: @@ -1032,7 +1183,7 @@ To un-install via make or Make.py: Make.py -p ^qeq -a machine -Supporting info: examples/qeq +Supporting info: :doc:`fix qeq/* `, examples/qeq ---------- @@ -1043,18 +1194,39 @@ Supporting info: examples/qeq REAX package ^^^^^^^^^^^^ -Contents: +Contents: A pair style for the ReaxFF potential, a universal reactive +force field, as well as a :doc:`fix reax/bonds ` command +for monitoring molecules as bonds are created and destroyed. + +Building LAMMPS with the REAX package requires first building the REAX +library itself, which is a set of Fortran 95 files in lib/reax. +Details of how to do this are in lib/reax/README. As illustrated +below, perform a "make" using one of the Makefile.machine files in +lib/reax which should create a lib/reax/libreax.a file. +Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran +and Intel Fortran compilers. The "make" also copies a +lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps. +This file has settings that enable the C++ compiler used to build +LAMMPS to link with a Fortran library (typically the 2 compilers to be +consistent e.g. both Intel compilers, or both GNU compilers). If the +settings in Makefile.lammps for your compilers and machine are not +correct, the LAMMPS link will fail. Note that the Make.py script has +a "-reax" option to allow the REAX library and LAMMPS to be built in +one step. Type "python src/Make.py -h -reax" to see the details. To install via make or Make.py: .. parsed-literal:: + cd ~/lammps/lib/reax + make -f Makefile.gfortran # for example + cd ~/lammps/src make yes-reax make machine .. parsed-literal:: - Make.py -p reax -a machine + Make.py -p reax -reax make=gfortran -a machine To un-install via make or Make.py: @@ -1067,7 +1239,8 @@ To un-install via make or Make.py: Make.py -p ^reax -a machine -Supporting info: examples/reax +Supporting info: lib/reax/README, :doc:`pair_style reax `, +:doc:`fix reax/bonds `, examples/reax ---------- @@ -1078,7 +1251,16 @@ Supporting info: examples/reax REPLICA package ^^^^^^^^^^^^^^^ -Contents: +Contents: A collection of multi-replica methods that are used by +invoking multiple instances (replicas) of LAMMPS +simulations. Communication between individual replicas is performed in +different ways by the different methods. See :ref:`Section howto 6.5 ` for an overview of how to run +multi-replica simulations in LAMMPS. Multi-replica methods included +in the package are nudged elastic band (NEB), parallel replica +dynamics (PRD), temperature accelerated dynamics (TAD), parallel +tempering, and a verlet/split algorithm for performing long-range +Coulombics on one set of processors, and the remainded of the force +field calcalation on another set. To install via make or Make.py: @@ -1102,7 +1284,10 @@ To un-install via make or Make.py: Make.py -p ^replica -a machine -Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5 +Supporting info: :ref:`Section howto 6.5 `, +:doc:`neb `, :doc:`prd `, :doc:`tad `, :doc:`temper `, +:doc:`run_style verlet/split `, examples/neb, examples/prd, +examples/tad ---------- @@ -1113,7 +1298,10 @@ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5 RIGID package ^^^^^^^^^^^^^ -Contents: +Contents: A collection of computes and fixes which enforce rigid +constraints on collections of atoms or particles. This includes SHAKE +and RATTLE, as well as variants of rigid-body time integrators for a +few large bodies or many small bodies. To install via make or Make.py: @@ -1137,7 +1325,8 @@ To un-install via make or Make.py: Make.py -p ^rigid -a machine -Supporting info: examples/ASPHERE, examples/rigid +Supporting info: :doc:`compute erotate/rigid `, +:doc:`fix shake `, :doc:`fix rattle `, :doc:`fix rigid/* `, examples/ASPHERE, examples/rigid ---------- @@ -1148,7 +1337,8 @@ Supporting info: examples/ASPHERE, examples/rigid SHOCK package ^^^^^^^^^^^^^ -Contents: +Contents: A small number of fixes useful for running impact +simulations where a shock-wave passes through a material. To install via make or Make.py: @@ -1172,7 +1362,7 @@ To un-install via make or Make.py: Make.py -p ^shock -a machine -Supporting info: examples/hugoniostat, examples/msst +Supporting info: :doc:`fix append/atoms `, :doc:`fix msst `, :doc:`fix nphug `, :doc:`fix wall/piston `, examples/hugoniostat, examples/msst ---------- @@ -1183,7 +1373,10 @@ Supporting info: examples/hugoniostat, examples/msst SNAP package ^^^^^^^^^^^^ -Contents: +Contents: A pair style for the spectral neighbor analysis potential +(SNAP), which is an empirical potential which can be quantum accurate +when fit to an archive of DFT data. Computes useful for analyzing +properties of the potential are also included. To install via make or Make.py: @@ -1207,7 +1400,8 @@ To un-install via make or Make.py: Make.py -p ^snap -a machine -Supporting info: examples/snap +Supporting info: :doc:`pair snap `, :doc:`compute sna/atom `, :doc:`compute snad/atom `, +:doc:`compute snav/atom `, examples/snap ---------- @@ -1218,7 +1412,9 @@ Supporting info: examples/snap SRD package ^^^^^^^^^^^ -Contents: +Contents: Two fixes which implement the Stochastic Rotation Dynamics +(SRD) method for coarse-graining of a solvent, typically around large +colloidal-scale particles. To install via make or Make.py: @@ -1242,7 +1438,7 @@ To un-install via make or Make.py: Make.py -p ^srd -a machine -Supporting info: +Supporting info: :doc:`fix srd `, :doc:`fix wall/srd `, examples/srd, examples/ASPHERE ---------- @@ -1253,18 +1449,43 @@ Supporting info: VORONOI package ^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`compute voronoi/atom ` command +which computes the Voronoi tesselation of a collection of atoms or +particles by wrapping the Voro++ lib + +To build LAMMPS with the KIM package you must have previously +installed the KIM API (library) on your system. The lib/kim/README +file explains how to download and install KIM. Building with the KIM +package also uses the lib/kim/Makefile.lammps file in the compile/link +process. You should not need to edit this file. + +To build LAMMPS with the VORONOI package you must have previously +installed the Voro++ library on your system. The lib/voronoi/README +file explains how to download and install Voro++. There is a +lib/voronoi/install.py script which automates the process. Type +"python install.py" to see instructions. The final step is to create +soft links in the lib/voronoi directory for "includelink" and +"liblink" which point to installed Voro++ directories. Building with +the VORONOI package uses the contents of the +lib/voronoi/Makefile.lammps file in the compile/link process. You +should not need to edit this file. Note that the Make.py script has a +"-voronoi" option to allow the Voro++ library to be downloaded and/or +installed and LAMMPS to be built in one step. Type "python +src/Make.py -h -voronoi" to see the details. To install via make or Make.py: .. parsed-literal:: + cd ~/lammps/lib/voronoi + python install.py -g -b -l # download Voro++, build in lib/voronoi, create links + cd ~/lammps/src make yes-voronoi make machine .. parsed-literal:: - Make.py -p voronoi -a machine + Make.py -p voronoi -voronoi install="-g -b -l" -a machine To un-install via make or Make.py: @@ -1277,7 +1498,7 @@ To un-install via make or Make.py: Make.py -p ^voronoi -a machine -Supporting info: examples/voronoi +Supporting info: src/VORONOI/README, lib/voronoi/README, :doc:`compute voronoi/atom `, examples/voronoi ---------- @@ -1288,7 +1509,8 @@ Supporting info: examples/voronoi XTC package ^^^^^^^^^^^ -Contents: +Contents: A :doc:`dump xtc ` command for writing snapshots in the +XTC format used by the GROMACS MD package. To install via make or Make.py: @@ -1312,7 +1534,7 @@ To un-install via make or Make.py: Make.py -p ^xtc -a machine -Supporting info: +Supporting info: :doc:`dump xtc ` ---------- @@ -1455,36 +1677,42 @@ See details on all of this below for individual packages. USER-ATC package ^^^^^^^^^^^^^^^^ -Contents: +Contents: ATC stands for atoms-to-continuum. This package implements +a :doc:`fix atc ` command to either couple MD with continuum +finite element equations or perform on-the-fly post-processing of +atomic information to continuum fields. See src/USER-ATC/README for +more details. + +To build LAMMPS with this package ... To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: -Supporting info: +.. parsed-literal:: -This package implements a "fix atc" command which can be used in a -LAMMPS input script. This fix can be employed to either do concurrent -coupling of MD with FE-based physics surrogates or on-the-fly -post-processing of atomic information to continuum fields. + make no-user-atc + make machine -See the doc page for the fix atc command to get started. At the -bottom of the doc page are many links to additional documentation -contained in the doc/USER/atc directory. +.. parsed-literal:: -There are example scripts for using this package in examples/USER/atc. + Make.py -p ^atc -a machine -This package uses an external library in lib/atc which must be -compiled before making LAMMPS. See the lib/atc/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. +Supporting info:src/USER-ATC/README, :doc:`fix atc `, +examples/USER/atc -The primary people who created this package are Reese Jones (rjones at -sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon -Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if -you have questions. - -Examples: examples/USER/atc +Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl +at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia. +Contact them directly if you have questions. ---------- @@ -1495,31 +1723,39 @@ Examples: examples/USER/atc USER-AWPMD package ^^^^^^^^^^^^^^^^^^ -Contents: +Contents: AWPMD stands for Antisymmetrized Wave Packet Molecular +Dynamics. This package implements an atom, pair, and fix style which +allows electrons to be treated as explicit particles in an MD +calculation. See src/USER-AWPMD/README for more details. + +To build LAMMPS with this package ... To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: -Supporting info: +.. parsed-literal:: -This package contains a LAMMPS implementation of the Antisymmetrized -Wave Packet Molecular Dynamics (AWPMD) method. + make no-user-atc + make machine -See the doc page for the pair_style awpmd/cut command to get started. +.. parsed-literal:: -There are example scripts for using this package in examples/USER/awpmd. + Make.py -p ^atc -a machine -This package uses an external library in lib/awpmd which must be -compiled before making LAMMPS. See the lib/awpmd/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. +Supporting info: src/USER-AWPMD/README, :doc:`fix awpmd/cut `, examples/USER/awpmd -The person who created this package is Ilya Valuev at the JIHT in -Russia (valuev at physik.hu-berlin.de). Contact him directly if you -have questions. - -Examples: examples/USER/awpmd +Author: Ilya Valuev at the JIHT in Russia (valuev at +physik.hu-berlin.de). Contact him directly if you have questions. ---------- @@ -1530,70 +1766,41 @@ Examples: examples/USER/awpmd USER-CG-CMM package ^^^^^^^^^^^^^^^^^^^ -Contents: +Contents: CG-CMM stands for coarse-grained ??. This package +implements several pair styles and an angle style using the coarse +grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 +(2007) (SDK), with extensions to simulate ionic liquids, electrolytes, +lipids and charged amino acids. See src/USER-CG-CMM/README for more +details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine -Supporting info: +Supporting info: src/USER-CG-CMM/README, :doc:`pair lj/sdk `, +:doc:`pair lj/sdk/coul/long `, :doc:`angle sdk `, +examples/USER/cg-cmm -This package implements 3 commands which can be used in a LAMMPS input -script: - -* pair_style lj/sdk -* pair_style lj/sdk/coul/long -* angle_style sdk - -These styles allow coarse grained MD simulations with the -parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) -(SDK), with extensions to simulate ionic liquids, electrolytes, lipids -and charged amino acids. - -See the doc pages for these commands for details. - -There are example scripts for using this package in -examples/USER/cg-cmm. - -This is the second generation implementation reducing the the clutter -of the previous version. For many systems with electrostatics, it will -be faster to use pair_style hybrid/overlay with lj/sdk and coul/long -instead of the combined lj/sdk/coul/long style. since the number of -charged atom types is usually small. For any other coulomb -interactions this is now required. To exploit this property, the use -of the kspace_style pppm/cg is recommended over regular pppm. For all -new styles, input file backward compatibility is provided. The old -implementation is still available through appending the /old -suffix. These will be discontinued and removed after the new -implementation has been fully validated. - -The current version of this package should be considered beta -quality. The CG potentials work correctly for "normal" situations, but -have not been testing with all kinds of potential parameters and -simulation systems. - -The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. - -Examples: examples/USER/cg-cmm +Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact +him directly if you have questions. ---------- @@ -1604,53 +1811,45 @@ Examples: examples/USER/cg-cmm USER-COLVARS package ^^^^^^^^^^^^^^^^^^^^ -Contents: +Contents: COLVARS stands for collective variables which can be used to +implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella +Sampling and Restraints. This package implements a :doc:`fix colvars ` command which wraps a COLVARS library which +can perform those kinds of simulations. See src/USER-COLVARS/README +for more details. + +To build LAMMPS with this package ... To install via make or Make.py: -To un-install via make or Make.py: +.. parsed-literal:: -Supporting info: + make yes-user-atc + make machine -This package implements the "fix colvars" command which can be -used in a LAMMPS input script. +.. parsed-literal:: -This fix allows to use "collective variables" to implement -Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella -Sampling and Restraints. This code consists of two parts: - -* A portable collective variable module library written and maintained -* by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and -* Jerome Henin (LISM, CNRS, Marseille, France). This code is located in -* the directory lib/colvars and needs to be compiled first. The colvars -* fix and an interface layer, exchanges information between LAMMPS and -* the collective variable module. - -See the doc page of :doc:`fix colvars ` for more details. - -There are example scripts for using this package in -examples/USER/colvars - -This is a very new interface that does not yet support all -features in the module and will see future optimizations -and improvements. The colvars module library is also available -in NAMD has been thoroughly used and tested there. Bugs and -problems are likely due to the interface layers code. -Thus the current version of this package should be considered -beta quality. - -The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. - -Examples: examples/USER/colvars - -Contents: - -To install via make or Make.py: + Make.py -p atc -a machine To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + Supporting info: +`doc/PDF/colvars-refman-lammps.pdf `_, +src/USER-COLVARS/README, lib/colvars/README, :doc:`fix colvars `, examples/USER/colvars + +Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the +fix. The COLVARS library itself is written and maintained by Giacomo +Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome +Henin (LISM, CNRS, Marseille, France). Contact them directly if you +have questions. ---------- @@ -1661,6 +1860,37 @@ Supporting info: USER-CUDA package ^^^^^^^^^^^^^^^^^ +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. + +To build LAMMPS with this package ... + +To install via make or Make.py: + +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + +To un-install via make or Make.py: + +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + This package provides acceleration of various LAMMPS pair styles, fix styles, compute styles, and long-range Coulombics via PPPM for NVIDIA GPUs. @@ -1683,14 +1913,6 @@ tu-ilmenau.de). Contact him directly if you have questions. Examples: examples/accelerate, bench/FERMI, bench/KEPLER -Contents: - -To install via make or Make.py: - -To un-install via make or Make.py: - -Supporting info: - ---------- @@ -1700,47 +1922,39 @@ Supporting info: USER-DIFFRACTION package ^^^^^^^^^^^^^^^^^^^^^^^^ -This package contains the commands neeed to calculate x-ray and -electron diffraction intensities based on kinematic diffraction -theory. - -See these doc pages and their related commands to get started: - -* :doc:`compute xrd ` -* :doc:`compute saed ` -* :doc:`fix saed/vtk ` - -The person who created this package is Shawn P. Coleman -(shawn.p.coleman8.ctr at mail.mil) while at the University of -Arkansas. Contact him directly if you have questions. - -Examples: examples/USER/diffraction - -Contents: +Contents: This packages implements two computes and a fix for +calculating x-ray and electron diffraction intensities based on +kinematic diffraction theory. See src/USER-DIFFRACTION/README for +more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine -Supporting info: +Supporting info: :doc:`compute saed `, :doc:`compute xrd `, :doc:`fix saed.vtk `, +examples/USER/diffraction + +Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at +the University of Arkansas. Contact him directly if you have +questions. ---------- @@ -1751,52 +1965,46 @@ Supporting info: USER-DPD package ^^^^^^^^^^^^^^^^ -This package implements the dissipative particle dynamics (DPD) method -under isothermal, isoenergetic, isobaric and isenthalpic conditions. -The DPD equations of motion are integrated efficiently through the -Shardlow splitting algorithm. - -See these doc pages and their related commands to get started: - -* :doc:`compute dpd ` -* :doc:`compute dpd/atom ` -* :doc:`fix_eos/cv ` -* :doc:`fix_eos/table ` -* :doc:`fix_shardlow ` -* :doc:`pair_dpd/conservative ` -* :doc:`pair_dpd/fdt ` -* :doc:`pair_dpd/fdt/energy ` - -There are example scripts for using this package in examples/USER/dpd. - -The people who created this package are James Larentzos -(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at -engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil). -Contact them directly if you have questions. +Contents: DPD stands for dissipative particle dynamics, This package +implements DPD for isothermal, isoenergetic, isobaric and isenthalpic +conditions. The DPD equations of motion are integrated efficiently +through the Shardlow splitting algorithm. See src/USER-DPD/README for +more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine -Examples: examples/USER/dpd +Supporting info: /src/USER-DPD/README, :doc:`compute dpd ` +:doc:`compute dpd/atom ` +:doc:`fix_eos/cv ` :doc:`fix_eos/table ` +:doc:`fix_shardlow ` +:doc:`pair_dpd/conservative ` +:doc:`pair_dpd/fdt ` +:doc:`pair_dpd/fdt/energy `, examples/USER/dpd + +Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil), +Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com) +and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them +directly if you have questions. ---------- @@ -1807,58 +2015,42 @@ Examples: examples/USER/dpd USER-DRUDE package ^^^^^^^^^^^^^^^^^^ -Contents: - -To install via make or Make.py: - -To un-install via make or Make.py: - -Supporting info: - -This package implements methods for simulating polarizable systems -in LAMMPS using thermalized Drude oscillators. - -See these doc pages and their related commands to get started: - -* :doc:`Drude tutorial ` -* :doc:`fix drude ` -* :doc:`compute temp/drude ` -* :doc:`fix langevin/drude ` -* :doc:`fix drude/transform/... ` -* :doc:`pair thole ` - -There are auxiliary tools for using this package in tools/drude. - -The person who created this package is Alain Dequidt at Universite -Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr) -Contact him directly if you have questions. Co-authors: Julien Devemy, -Agilio Padua. +Contents: This package contains methods for simulating polarizable +systems using thermalized Drude oscillators. It has computes, fixes, +and pair styles for this purpose. See :ref:`Section howto 6.27 ` for an overview of how to use the +package. See src/USER-DRUDE/README for additional details. There are +auxiliary tools for using this package in tools/drude. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine -Examples: examples/USER/drude +Supporting info: :ref:`Section howto 6.27 `, +src/USER-DRUDE/README, :doc:`fix drude `, :doc:`fix drude/transform/* `, :doc:`compute temp/drude `, :doc:`pair thole `, +:doc:`pair lj/cut/thole/long `, examples/USER/drude, +tools/drude -Doc: Section howto 6.27 +Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand +(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy, +Agilio Padua. Contact them directly if you have questions. ---------- @@ -1869,74 +2061,43 @@ Doc: Section howto 6.27 USER-EFF package ^^^^^^^^^^^^^^^^ -Contents: +Contents: EFF stands for electron force field. This package contains +atom, pair, fix and compute styles which implement the eFF as +described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, +JCC, 2010. The eFF potential was first introduced by Su and Goddard, +in 2007. See src/USER-EFF/README for more details. There are +auxiliary tools for using this package in tools/eff; see its README +file. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`atom_style electron `, :doc:`compute temp/eff `, :doc:`fix langevin/eff `, :doc:`fix nve/eff `, +:doc:`pair eff/cut `, examples/USER/eff, tools/eff + Supporting info: -This package contains a LAMMPS implementation of the electron Force -Field (eFF) currently under development at Caltech, as described in -A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, -2010. The eFF potential was first introduced by Su and Goddard, in -2007. - -eFF can be viewed as an approximation to QM wave packet dynamics and -Fermionic molecular dynamics, combining the ability of electronic -structure methods to describe atomic structure, bonding, and chemistry -in materials, and of plasma methods to describe nonequilibrium -dynamics of large systems with a large number of highly excited -electrons. We classify it as a mixed QM-classical approach rather than -a conventional force field method, which introduces QM-based terms (a -spin-dependent repulsion term to account for the Pauli exclusion -principle and the electron wavefunction kinetic energy associated with -the Heisenberg principle) that reduce, along with classical -electrostatic terms between nuclei and electrons, to the sum of a set -of effective pairwise potentials. This makes eFF uniquely suited to -simulate materials over a wide range of temperatures and pressures -where electronically excited and ionized states of matter can occur -and coexist. - -The necessary customizations to the LAMMPS core are in place to -enable the correct handling of explicit electron properties during -minimization and dynamics. - -See the doc page for the pair_style eff/cut command to get started. - -There are example scripts for using this package in -examples/USER/eff. - -There are auxiliary tools for using this package in tools/eff. - -The person who created this package is Andres Jaramillo-Botero at -CalTech (ajaramil at wag.caltech.edu). Contact him directly if you -have questions. - -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - -Examples: examples/USER/eff +Author: Andres Jaramillo-Botero at CalTech (ajaramil at +wag.caltech.edu). Contact him directly if you have questions. ---------- @@ -1947,50 +2108,40 @@ Examples: examples/USER/eff USER-FEP package ^^^^^^^^^^^^^^^^ -Contents: - -To install via make or Make.py: - -To un-install via make or Make.py: - -Supporting info: - -This package provides methods for performing free energy perturbation -simulations with soft-core pair potentials in LAMMPS. - -See these doc pages and their related commands to get started: - -* :doc:`fix adapt/fep ` -* :doc:`compute fep ` -* :doc:`soft pair styles ` - -The person who created this package is Agilio Padua at Universite -Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr) -Contact him directly if you have questions. +Contents: FEP stands for free energy perturbation. This package +provides methods for performing FEP simulations by using a :doc:`fix adapt/fep ` command with soft-core pair potentials, +which have a "soft" in their style name. See src/USER-FEP/README for +more details. There are auxiliary tools for using this package in +tools/fep; see its README file. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine -Examples: examples/USER/fep +Supporting info: src/USER-FEP/README, :doc:`fix adapt/fep `, :doc:`compute fep `, +:doc:`pair_style */soft `, examples/USER/fep + +Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand +(agilio.padua at univ-bpclermont.fr). Contact him directly if you have +questions. ---------- @@ -2001,28 +2152,45 @@ Examples: examples/USER/fep USER-H5MD package ^^^^^^^^^^^^^^^^^ -Contents: - -To install via make or Make.py: - -To un-install via make or Make.py: - -Supporting info: - -This package contains a :doc:`dump h5md ` command for -performing a dump of atom properties in HDF5 format. `HDF5 files `_ are binary, portable and self-describing and can be -examined and used by a variety of auxiliary tools. The output HDF5 -files are structured in a format called H5MD, which was designed to -store molecular data, and can be used and produced by various MD and -MD-related codes. The :doc:`dump h5md ` command gives a -citation to a paper describing the format. +Contents: H5MD stands for HDF5 for MD. `HDF5 `_ is a binary, +portable, self-describing file format, used by many scientific +simulations. H5MD is a format for molecular simulations, built on top +of HDF5. This package implements a :doc:`dump h5md ` command +to output LAMMPS snapshots in this format. See src/USER-H5MD/README +for more details. .. _HDF5: http://www.hdfgroup.org/HDF5/ -The person who created this package and the underlying H5MD format is -Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him +To build LAMMPS with this package ... + +To install via make or Make.py: + +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + +To un-install via make or Make.py: + +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: src/USER-H5MD/README, lib/h5md/README, :doc:`dump h5md ` + +Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created +this package as well as the H5MD format and library. Contact him directly if you have questions. @@ -2034,25 +2202,42 @@ directly if you have questions. USER-INTEL package ^^^^^^^^^^^^^^^^^^ -Contents: +Contents: Dozens of pair, bond, angle, dihedral, and improper styles +that are optimized for Intel CPUs and the Intel Xeon Phi (in offload +mode). All of them have an "intel" in their style name. :doc:`Section accelerate intel ` gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Also see src/USER-INTEL/README for more details. See +the KOKKOS, OPT, and USER-OMP packages, which also have CPU and +Phi-enabled styles. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: -Supporting info: +.. parsed-literal:: -This package provides options for performing neighbor list and -non-bonded force calculations in single, mixed, or double precision -and also a capability for accelerating calculations with an -Intel(R) Xeon Phi(TM) coprocessor. + make no-user-atc + make machine -See this section of the manual to get started: +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: examples/accelerate, src/USER-INTEL/TEST :ref:`Section_accelerate ` -The person who created this package is W. Michael Brown at Intel -(michael.w.brown at intel.com). Contact him directly if you have questions. +Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact +him directly if you have questions. For the USER-INTEL package, you have 2 choices when building. You can build with CPU or Phi support. The latter uses Xeon Phi chips in @@ -2075,7 +2260,7 @@ And also add this to CCFLAGS: -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" -Examples: examples/accelerate, bench/KEPLER +Examples: ---------- @@ -2086,12 +2271,35 @@ Examples: examples/accelerate, bench/KEPLER USER-LB package ^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package contains a LAMMPS implementation of a background @@ -2106,28 +2314,6 @@ The people who created this package are Frances Mackay (fmackay at uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of Western Ontario. Contact them directly if you have questions. -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - Examples: examples/USER/lb @@ -2139,12 +2325,35 @@ Examples: examples/USER/lb USER-MGPT package ^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package contains a fast implementation for LAMMPS of @@ -2171,28 +2380,6 @@ The persons who created the USER-MGPT package are Tomas Oppelstrup (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) Contact them directly if you have any questions. -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - Examples: examples/USER/mgpt @@ -2204,12 +2391,35 @@ Examples: examples/USER/mgpt USER-MISC package ^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: The files in this package are a potpourri of (mostly) unrelated @@ -2231,28 +2441,6 @@ src/USER-MISC/README file. You should contact the author directly if you have specific questions about the feature or its coding. -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - Examples: examples/USER/misc @@ -2264,12 +2452,35 @@ Examples: examples/USER/misc USER-MOLFILE package ^^^^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package contains a dump molfile command which uses molfile @@ -2301,12 +2512,35 @@ The person who created this package is Axel Kohlmeyer at Temple U USER-OMP package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package provides OpenMP multi-threading support and @@ -2337,6 +2571,35 @@ Examples: examples/accelerate, bench/KEPLER USER-PHONON package ^^^^^^^^^^^^^^^^^^^ +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. + +To install via make or Make.py: + +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + +To un-install via make or Make.py: + +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + This package contains a fix phonon command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. @@ -2349,28 +2612,6 @@ The person who created this package is Ling-Ti Kong (konglt at sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly if you have questions. -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - Examples: examples/USER/phonon @@ -2382,12 +2623,35 @@ Examples: examples/USER/phonon USER-QMMM package ^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package provides a fix qmmm command which allows LAMMPS to be @@ -2422,12 +2686,35 @@ The person who created this package is Axel Kohlmeyer at Temple U USER-QTB package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package provides a self-consistent quantum treatment of the @@ -2453,28 +2740,6 @@ The person who created this package is Yuan Shen (sy0302 at stanford.edu) at Stanford University. Contact him directly if you have questions. -To install via make or Make.py: - -.. parsed-literal:: - - make yes-body - make machine - -.. parsed-literal:: - - Make.py -p body -a machine - -To un-install via make or Make.py: - -.. parsed-literal:: - - make no-body - make machine - -.. parsed-literal:: - - Make.py -p ^body -a machine - Examples: examples/USER/qtb @@ -2486,12 +2751,35 @@ Examples: examples/USER/qtb USER-QUIP package ^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: Examples: examples/USER/quip @@ -2505,29 +2793,34 @@ Examples: examples/USER/quip USER-REAXC package ^^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc Supporting info: @@ -2573,12 +2866,35 @@ Examples: examples/reax USER-SMD package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc + Supporting info: This package implements smoothed Mach dynamics (SMD) in @@ -2619,29 +2935,34 @@ Examples: examples/USER/smd USER-SMTBQ package ^^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc Supporting info: @@ -2671,29 +2992,34 @@ Examples: examples/USER/smtbq USER-SPH package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc Supporting info: @@ -2733,29 +3059,34 @@ Examples: examples/USER/sph USER-TALLY package ^^^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: .. parsed-literal:: - make yes-body + make yes-user-atc make machine .. parsed-literal:: - Make.py -p body -a machine + Make.py -p atc -a machine To un-install via make or Make.py: .. parsed-literal:: - make no-body + make no-user-atc make machine .. parsed-literal:: - Make.py -p ^body -a machine + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc Supporting info: @@ -2770,13 +3101,34 @@ Examples: examples/USER/tally USER-VTK package ^^^^^^^^^^^^^^^^ -Contents: +Contents: A :doc:`fix atc ` command (atoms to continuum) to +either couple of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. See +src/USER-ATC/README for more details. To install via make or Make.py: +.. parsed-literal:: + + make yes-user-atc + make machine + +.. parsed-literal:: + + Make.py -p atc -a machine + To un-install via make or Make.py: -Supporting info: +.. parsed-literal:: + + make no-user-atc + make machine + +.. parsed-literal:: + + Make.py -p ^atc -a machine + +Supporting info: :doc:`fix atc `, examples/USER/atc Examples: examples/USER/tally diff --git a/doc/_sources/Section_perf.txt b/doc/_sources/Section_perf.txt index 65f761c120..fa44adb3b0 100644 --- a/doc/_sources/Section_perf.txt +++ b/doc/_sources/Section_perf.txt @@ -1,13 +1,17 @@ Performance & scalability ========================= -LAMMPS performance on several prototypical benchmarks and machines is -discussed on the Benchmarks page of the `LAMMPS WWW Site `_ where -CPU timings and parallel efficiencies are listed. Here, the -benchmarks are described briefly and some useful rules of thumb about -their performance are highlighted. +Current LAMMPS performance is discussed on the Benchmarks page of the +`LAMMPS WWW Site `_ where CPU timings and parallel efficiencies are +listed. The page has several sections, which are briefly described +below: -These are the 5 benchmark problems: +* CPU performance on 5 standard problems, strong and weak scaling +* GPU and Xeon Phi performance on same and related problems +* Comparison of cost of interatomic potentials +* Performance of huge, billion-atom problems + +The 5 standard problems are as follow: #. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 neighbors per atom), NVE integration @@ -22,51 +26,54 @@ These are the 5 benchmark problems: field with a 10 Angstrom LJ cutoff (440 neighbors per atom), particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT integration -The input files for running the benchmarks are included in the LAMMPS -distribution, as are sample output files. Each of the 5 problems has -32,000 atoms and runs for 100 timesteps. Each can be run as a serial -benchmarks (on one processor) or in parallel. In parallel, each -benchmark can be run as a fixed-size or scaled-size problem. For -fixed-size benchmarking, the same 32K atom problem is run on various -numbers of processors. For scaled-size benchmarking, the model size -is increased with the number of processors. E.g. on 8 processors, a -256K-atom problem is run; on 1024 processors, a 32-million atom -problem is run, etc. +Input files for these 5 problems are provided in the bench directory +of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 +timesteps. The size of the problem (number of atoms) can be varied +using command-line switches as described in the bench/README file. +This is an easy way to test performance and either strong or weak +scalability on your machine. -A useful metric from the benchmarks is the CPU cost per atom per -timestep. Since LAMMPS performance scales roughly linearly with -problem size and timesteps, the run time of any problem using the same -model (atom style, force field, cutoff, etc) can then be estimated. -For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler -under Red Hat Linux), the CPU run-time in seconds/atom/timestep for -the 5 problems is +The bench directory includes a few log.* files that show performance +of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI +and bench/KEPLER dirs have input files and scripts and instructions +for running the same (or similar) problems using OpenMP or GPU or Xeon +Phi acceleration options. See the README files in those dirs and the +:doc:`Section accelerate ` doc pages for +instructions on how to build LAMMPS and run on that kind of hardware. -+----------------+---------+---------+---------+---------+-----------+ -| Problem: | LJ | Chain | EAM | Chute | Rhodopsin | -+----------------+---------+---------+---------+---------+-----------+ -| CPU/atom/step: | 4.55E-6 | 2.18E-6 | 9.38E-6 | 2.18E-6 | 1.11E-4 | -+----------------+---------+---------+---------+---------+-----------+ -| Ratio to LJ: | 1.0 | 0.48 | 2.06 | 0.48 | 24.5 | -+----------------+---------+---------+---------+---------+-----------+ +The bench/POTENTIALS directory has input files which correspond to the +table of results on the +:ref:`Potentials ` section of +the Benchmarks web page. So you can also run those test problems on +your machine. -The ratios mean that if the atomic LJ system has a normalized cost of -1.0, the bead-spring chains and granular systems run 2x faster, while -the EAM metal and solvated protein models run 2x and 25x slower -respectively. The bulk of these cost differences is due to the -expense of computing a particular pairwise force field for a given -number of neighbors per atom. +The :ref:`billion-atom ` section +of the Benchmarks web page has performance data for very large +benchmark runs of simple Lennard-Jones (LJ) models, which use the +bench/in.lj input script. -Performance on a parallel machine can also be predicted from the -one-processor timings if the parallel efficiency can be estimated. -The communication bandwidth and latency of a particular parallel -machine affects the efficiency. On most machines LAMMPS will give -fixed-size parallel efficiencies on these benchmarks above 50% so long -as the atoms/processor count is a few 100 or greater - i.e. on 64 to -128 processors. Likewise, scaled-size parallel efficiencies will -typically be 80% or greater up to very large processor counts. The -benchmark data on the `LAMMPS WWW Site `_ gives specific examples on -some different machines, including a run of 3/4 of a billion LJ atoms -on 1500 processors that ran at 85% parallel efficiency. + +---------- + + +For all the benchmarks, a useful metric is the CPU cost per atom per +timestep. Since performance scales roughly linearly with problem size +and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained +potentials), the run time of any problem using the same model (atom +style, force field, cutoff, etc) can then be estimated. + +Performance on a parallel machine can also be predicted from one-core +or one-node timings if the parallel efficiency can be estimated. The +communication bandwidth and latency of a particular parallel machine +affects the efficiency. On most machines LAMMPS will give parallel +efficiencies on these benchmarks above 50% so long as the number of +atoms/core is a few 100 or greater, and closer to 100% for large +numbers of atoms/core. This is for all-MPI mode with one MPI task per +core. For nodes with accelerator options or hardware (OpenMP, GPU, +Phi), you should first measure single node performance. Then you can +estimate parallel performance for multi-node runs using the same logic +as for all-MPI mode, except that now you will typically need many more +atoms/node to achieve good scalability. .. _lws: http://lammps.sandia.gov diff --git a/doc/_sources/accelerate_kokkos.txt b/doc/_sources/accelerate_kokkos.txt index 7f137b42ab..943d9c4e8a 100644 --- a/doc/_sources/accelerate_kokkos.txt +++ b/doc/_sources/accelerate_kokkos.txt @@ -49,11 +49,13 @@ Here is a quick overview of how to use the KOKKOS package for CPU acceleration, assuming one or more 16-core nodes. More details follow. -use a C++11 compatible compiler -make yes-kokkos -make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package -make kokkos_omp # or Makefile.kokkos_omp already has variable set -Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py +.. parsed-literal:: + + use a C++11 compatible compiler + make yes-kokkos + make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package + make kokkos_omp # or Makefile.kokkos_omp already has variable set + Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py .. parsed-literal:: @@ -72,12 +74,14 @@ details follow. discuss use of NVCC, which Makefiles to examine -use a C++11 compatible compiler -KOKKOS_DEVICES = Cuda, OpenMP -KOKKOS_ARCH = Kepler35 -make yes-kokkos -make machine -Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda +.. parsed-literal:: + + use a C++11 compatible compiler + KOKKOS_DEVICES = Cuda, OpenMP + KOKKOS_ARCH = Kepler35 + make yes-kokkos + make machine + Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda .. parsed-literal:: @@ -101,11 +105,13 @@ for the Intel Phi: make machine Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi -host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): -mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 -mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240 -mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240 -mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis +.. parsed-literal:: + + host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): + mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 + mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240 + mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240 + mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis **Required hardware/software:** diff --git a/doc/_sources/pair_brownian.txt b/doc/_sources/pair_brownian.txt index 02f4e245a1..a6447aaae5 100644 --- a/doc/_sources/pair_brownian.txt +++ b/doc/_sources/pair_brownian.txt @@ -43,9 +43,9 @@ Description """"""""""" Styles *brownian* and *brownain/poly* compute Brownian forces and -torques on finite-size particles. The former requires monodisperse -spherical particles; the latter allows for polydisperse spherical -particles. +torques on finite-size spherical particles. The former requires +monodisperse spherical particles; the latter allows for polydisperse +spherical particles. These pair styles are designed to be used with either the :doc:`pair_style lubricate ` or :doc:`pair_style lubricateU ` commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters @@ -134,8 +134,8 @@ Restrictions """""""""""" -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. Only spherical monodisperse particles are allowed for pair_style brownian. diff --git a/doc/_sources/pair_lubricate.txt b/doc/_sources/pair_lubricate.txt index f50b5e80ec..4e80116456 100644 --- a/doc/_sources/pair_lubricate.txt +++ b/doc/_sources/pair_lubricate.txt @@ -47,8 +47,8 @@ Description """"""""""" Styles *lubricate* and *lubricate/poly* compute hydrodynamic -interactions between mono-disperse spherical particles in a pairwise -fashion. The interactions have 2 components. The first is +interactions between mono-disperse finite-size spherical particles in +a pairwise fashion. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) ` .. image:: Eqs/pair_lubricate.jpg @@ -207,8 +207,8 @@ Restrictions """""""""""" -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. Only spherical monodisperse particles are allowed for pair_style lubricate. diff --git a/doc/_sources/pair_lubricateU.txt b/doc/_sources/pair_lubricateU.txt index b6396cd31e..95e99dd42d 100644 --- a/doc/_sources/pair_lubricateU.txt +++ b/doc/_sources/pair_lubricateU.txt @@ -34,8 +34,9 @@ Description """"""""""" Styles *lubricateU* and *lubricateU/poly* compute velocities and -angular velocities such that the hydrodynamic interaction balances the -force and torque due to all other types of interactions. +angular velocities for finite-size spherical particles such that the +hydrodynamic interaction balances the force and torque due to all +other types of interactions. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in :ref:`(Ball and Melrose) ` @@ -187,8 +188,8 @@ Restrictions """""""""""" -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the :ref:`Making LAMMPS <2_3>` section for more info. Currently, these pair styles assume that all other types of forces/torques on the particles have been already been computed when diff --git a/doc/_sources/pair_peri.txt b/doc/_sources/pair_peri.txt index e00112e016..ab46a44455 100644 --- a/doc/_sources/pair_peri.txt +++ b/doc/_sources/pair_peri.txt @@ -25,7 +25,7 @@ Syntax pair_style style -style = *peri/pmb* or *peri/lps* or *peri/ves* or *peri/eps*:ul +* style = *peri/pmb* or *peri/lps* or *peri/ves* or *peri/eps* Examples """""""" diff --git a/doc/accelerate_kokkos.html b/doc/accelerate_kokkos.html index 8e3499dc35..e50a83f48e 100644 --- a/doc/accelerate_kokkos.html +++ b/doc/accelerate_kokkos.html @@ -166,11 +166,13 @@ produce an executable compatible with specific hardware.

    Here is a quick overview of how to use the KOKKOS package for CPU acceleration, assuming one or more 16-core nodes. More details follow.

    -

    use a C++11 compatible compiler +

    use a C++11 compatible compiler
 make yes-kokkos
 make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
 make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py
    
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py
+
    +
    mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
 mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
 mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
@@ -186,12 +188,14 @@ mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks
 assuming one or more nodes, each with 16 cores and a GPU.  More
 details follow.
    
 
    discuss use of NVCC, which Makefiles to examine
    
-
    use a C++11 compatible compiler
+
    use a C++11 compatible compiler
 KOKKOS_DEVICES = Cuda, OpenMP
 KOKKOS_ARCH = Kepler35
 make yes-kokkos
 make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
    
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+
    
+
    
 
    mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
 mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes
 
    
@@ -210,11 +214,13 @@ make machine
 Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
    -

    host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): +

    host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
 mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
 mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
 mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis
    
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis
+
    +

    Required hardware/software:

    Kokkos support within LAMMPS must be built with a C++11 compatible compiler. If using gcc, version 4.8.1 or later is required.

    diff --git a/doc/accelerate_kokkos.txt b/doc/accelerate_kokkos.txt index fa3f811e69..8d67606377 100644 --- a/doc/accelerate_kokkos.txt +++ b/doc/accelerate_kokkos.txt @@ -61,16 +61,13 @@ use a C++11 compatible compiler make yes-kokkos make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package make kokkos_omp # or Makefile.kokkos_omp already has variable set -Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py +Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py :pre mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre - - - specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support include the KOKKOS package and build LAMMPS enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script :ul @@ -86,7 +83,7 @@ KOKKOS_DEVICES = Cuda, OpenMP KOKKOS_ARCH = Kepler35 make yes-kokkos make machine -Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda +Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes :pre @@ -108,8 +105,7 @@ host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240 mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240 -mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis - +mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis :pre [Required hardware/software:] diff --git a/doc/pair_brownian.html b/doc/pair_brownian.html index 253de974b0..53447f642b 100644 --- a/doc/pair_brownian.html +++ b/doc/pair_brownian.html @@ -164,9 +164,9 @@ pair_coeff * *

    Description

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

    +torques on finite-size spherical particles. The former requires +monodisperse spherical particles; the latter allows for polydisperse +spherical particles.

    These pair styles are designed to be used with either the pair_style lubricate or pair_style lubricateU commands to provide thermostatting when dissipative lubrication forces are acting. Thus the parameters mu, flaglog, flagfld, cutinner, and cutoff should be @@ -226,8 +226,8 @@ to be specified in an input script that reads a restart file.

    Restrictions

    -

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

    +

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

    Only spherical monodisperse particles are allowed for pair_style brownian.

    Only spherical particles are allowed for pair_style brownian/poly.

    diff --git a/doc/pair_brownian.txt b/doc/pair_brownian.txt index c4f5a8ed9f..b79a11040c 100644 --- a/doc/pair_brownian.txt +++ b/doc/pair_brownian.txt @@ -35,9 +35,9 @@ pair_coeff * * :pre [Description:] Styles {brownian} and {brownain/poly} compute Brownian forces and -torques on finite-size particles. The former requires monodisperse -spherical particles; the latter allows for polydisperse spherical -particles. +torques on finite-size spherical particles. The former requires +monodisperse spherical particles; the latter allows for polydisperse +spherical particles. These pair styles are designed to be used with either the "pair_style lubricate"_pair_lubricate.html or "pair_style @@ -121,8 +121,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the "Making +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. Only spherical monodisperse particles are allowed for pair_style diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html index 6d5a22af44..dec98e2f9f 100644 --- a/doc/pair_lubricate.html +++ b/doc/pair_lubricate.html @@ -166,8 +166,8 @@ fix 1 all adapt 1 pair lubricate mu * * v_mu

    Description

    Styles lubricate and lubricate/poly compute hydrodynamic -interactions between mono-disperse spherical particles in a pairwise -fashion. The interactions have 2 components. The first is +interactions between mono-disperse finite-size spherical particles in +a pairwise fashion. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in (Ball and Melrose)

    _images/pair_lubricate.jpg

    which represents the dissipation W between two nearby particles due to @@ -285,8 +285,8 @@ to be specified in an input script that reads a restart file.

    Restrictions

    -

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

    +

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

    Only spherical monodisperse particles are allowed for pair_style lubricate.

    Only spherical particles are allowed for pair_style lubricate/poly.

    diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt index 81b8521c7d..f70e6359ff 100644 --- a/doc/pair_lubricate.txt +++ b/doc/pair_lubricate.txt @@ -38,8 +38,8 @@ fix 1 all adapt 1 pair lubricate mu * * v_mu :pre [Description:] Styles {lubricate} and {lubricate/poly} compute hydrodynamic -interactions between mono-disperse spherical particles in a pairwise -fashion. The interactions have 2 components. The first is +interactions between mono-disperse finite-size spherical particles in +a pairwise fashion. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in "(Ball and Melrose)"_#Ball @@ -190,8 +190,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the "Making +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. Only spherical monodisperse particles are allowed for pair_style diff --git a/doc/pair_lubricateU.html b/doc/pair_lubricateU.html index 629a4ed102..43e79577f3 100644 --- a/doc/pair_lubricateU.html +++ b/doc/pair_lubricateU.html @@ -154,8 +154,9 @@ pair_coeff * *

    Description

    Styles lubricateU and lubricateU/poly compute velocities and -angular velocities such that the hydrodynamic interaction balances the -force and torque due to all other types of interactions.

    +angular velocities for finite-size spherical particles such that the +hydrodynamic interaction balances the force and torque due to all +other types of interactions.

    The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in (Ball and Melrose)

    _images/pair_lubricate.jpg @@ -272,8 +273,8 @@ to be specified in an input script that reads a restart file.

    Restrictions

    -

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

    +

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

    Currently, these pair styles assume that all other types of forces/torques on the particles have been already been computed when it is invoked. This requires this style to be defined as the last of diff --git a/doc/pair_lubricateU.txt b/doc/pair_lubricateU.txt index 446d246ef1..f55c73a72d 100644 --- a/doc/pair_lubricateU.txt +++ b/doc/pair_lubricateU.txt @@ -31,8 +31,9 @@ pair_coeff * * :pre [Description:] Styles {lubricateU} and {lubricateU/poly} compute velocities and -angular velocities such that the hydrodynamic interaction balances the -force and torque due to all other types of interactions. +angular velocities for finite-size spherical particles such that the +hydrodynamic interaction balances the force and torque due to all +other types of interactions. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in "(Ball and @@ -177,8 +178,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -These styles are part of the FLD package. They are only enabled if -LAMMPS was built with that package. See the "Making +These styles are part of the COLLOID package. They are only enabled +if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. Currently, these pair styles assume that all other types of diff --git a/doc/pair_peri.html b/doc/pair_peri.html index a0ff1ce47e..2f2580d90e 100644 --- a/doc/pair_peri.html +++ b/doc/pair_peri.html @@ -146,7 +146,9 @@ 

    pair_style style
    -

    style = peri/pmb or peri/lps or peri/ves or peri/eps:ul

    +
      +
    • style = peri/pmb or peri/lps or peri/ves or peri/eps
      • +

    Examples

    diff --git a/doc/pair_peri.txt b/doc/pair_peri.txt index fe3af00f5f..fa79bbbcbd 100644 --- a/doc/pair_peri.txt +++ b/doc/pair_peri.txt @@ -17,7 +17,7 @@ pair_style peri/eps command :h3 pair_style style :pre -style = {peri/pmb} or {peri/lps} or {peri/ves} or {peri/eps}:ul +style = {peri/pmb} or {peri/lps} or {peri/ves} or {peri/eps} :ul [Examples:] diff --git a/doc/searchindex.js b/doc/searchindex.js index 9cb67c2ae2..d428ba9ac0 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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303,443,444],adust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,507],afshar:400,after:[2,3,5,6,8,9,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,9,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,465,467,499,502],alpha_:[],alpha_c:426,alpha_i:452,alpha_ialpha_j:[],alpha_lj:426,alphabet:[2,3,22,37,45,56,65,180,191,203,350,359,374,393,461,481],alphanumer:[3,65,203,296,304,348,374,507],alreadi:[3,7,8,9,12,16,17,18,43,172,173,175,198,208,212,216,217,220,222,226,254,295,297,323,346,347,374,375,400,411,413,420,428,460,470,473,477,481,482,486,491,507],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,60,61,63,65,68,73,74,75,77,79,83,91,93,94,96,98,108,109,110,111,112,113,118,120,122,123,125,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,164,165,166,167,168,169,172,173,174,175,176,178,180,191,192,194,195,196,197,198,199,200,201,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,232,237,238,239,240,241,243,244,247,248,249,250,260,261,263,264,265,266,267,268,269,270,271,276,279,280,282,283,284,285,286,288,289,290,292,293,294,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,316,317,320,321,323,326,327,328,329,330,334,335,336,337,339,341,344,346,347,348,350,356,359,363,365,366,368,369,370,373,374,375,376,377,379,380,386,390,391,393,397,398,399,400,404,405,406,409,410,412,413,414,422,426,427,430,433,435,437,439,440,441,442,445,446,448,455,456,458,459,461,462,463,464,465,466,467,469,476,478,479,480,481,482,483,484,485,486,488,489,490,491,493,494,495,496,499,500,501,502,503,505,506,507,508,509,511],alter:[3,6,8,9,11,12,42,61,149,150,151,152,153,155,158,159,160,161,164,165,172,176,196,197,199,201,204,205,212,221,222,223,224,226,262,263,302,305,307,309,317,323,331,338,345,372,375,413,481,486,488,491,507,508,511],altern:[1,6,8,11,12,17,18,95,172,196,203,213,226,234,244,248,263,296,307,330,331,338,351,355,365,372,373,381,382,396,401,402,404,405,407,415,418,426,430,431,432,437,441,442,452,462,464,466,469,479,481,482,494,496,499],although:[29,43,192,253,263,294,298,307,330,364,488,502,511],aluminum:473,alwai:[0,6,11,12,17,18,55,59,65,73,170,200,212,213,214,216,217,218,222,225,239,241,245,299,302,307,323,340,344,345,349,365,366,371,373,374,376,377,380,389,392,404,421,433,443,444,451,453,463,464,466,473,476,481,482,484,486,493,495,498,502,507,508],amap:200,amatrix:241,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:199,ambigu:[3,65,203,507],amd:[17,380,433],amend:[],amino:9,amit:9,among:[16,147,210,250],amorph:[172,465],amount:[1,3,6,12,61,92,121,170,174,195,199,210,214,224,225,239,243,247,263,288,294,307,315,323,328,331,336,338,346,365,380,400,439,481,484],amplitud:[226,260,316,341,358,484,507],amu:239,amzallag:451,analag:[6,507],analalog:6,analog:[6,112,146,174,192,410],analys:[7,486],analysi:[7,9,13,65,66,75,201,303,304,313,347,433,452,481,491],analyt:[1,3,9,13,124,166,171,310,365,386,414,415,420,433,441,463],analyz:[6,8,13,375,433],andersen:310,anderson:[292,400],andr:[7,9,13],andrew:13,andzelm:460,ang:288,angl:[],angle1:306,angle2:306,angle_coeff:[],angle_cosineshift:27,angle_cosineshiftexp:[26,181],angle_cutof:412,angle_cutoff:412,angle_hybrid:29,angle_info:444,angle_styl:[],angle_typ:41,angleangl:[3,349,356,481],angleangletors:[3,179,481],anglecoeff:3,angletors:[3,179,185,481],angletyp:222,angmom:[],angmomi:[119,196,197,325],angmomx:[119,196,197,325],angmomz:[119,196,197,325],angstrom:[6,10,61,73,124,161,171,172,195,196,197,199,200,208,216,217,226,227,239,244,245,260,300,305,340,342,343,345,366,368,371,377,381,382,391,404,426,430,437,442,443,444,466,473,484,490,506,508],angular:[6,29,41,63,65,68,86,87,88,89,111,119,146,150,151,164,165,172,196,197,203,247,253,259,260,265,266,267,269,270,271,273,274,275,278,280,281,282,283,286,305,307,310,316,325,381,386,395,410,427,428,430,433,441,461,464,465,481,491,507,508],angularm:274,anharmon:[27,54,181,302,495],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,40,41,42,43,45,56,57,60,61,63,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,175,176,178,180,192,195,196,197,198,199,200,203,206,207,208,210,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,236,239,242,243,245,247,250,253,259,260,263,268,288,290,292,293,294,296,298,299,300,302,304,305,307,309,310,312,316,317,320,322,323,324,325,334,335,340,341,342,343,344,345,346,347,348,350,364,365,366,368,370,371,373,374,375,377,378,379,380,382,386,390,391,395,396,399,400,404,405,407,409,413,414,415,422,433,435,441,443,444,445,452,460,461,462,463,464,465,466,467,468,469,474,475,476,478,479,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,499,500,502,503,505,506,507,508,509,510,511],anihil:426,anim:[2,4,7,11,13,199,375],anion:[407,451],aniso:[3,224,226,263,264,265,266,267,268,269,270,271,294,307],anisotrop:[247,409,445],ann:434,annot:[7,462,464,465,466,469,481],annual:[476,495],anoth:[1,3,4,6,7,8,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1,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,510],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[9,16,366,507],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:400,conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,9,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,9,29,183,190,191,197,200,306,320,347,404,406,507],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,213,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,4,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481],cornflowerblu:200,cornsilk:200,corp:[],corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502],correction_max_iter:209,correctli:[3,8,9,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,4,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,6,12,13,195,443,444,507],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,9,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamon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_j_a:[409,445],epsilon_j_b:[409,445],epsilon_j_c:[409,445],epsilon_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,511],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:506,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,125,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,9,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,9,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:[9,406],exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,9,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,10,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502],explictli:[16,494],exploit:[9,15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_foo:507,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,507],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,12,15,158,380,466],fermion:[9,406],fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,509],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:507,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,125,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,289,330,336,348,364,376,393,396,399,476,482,483,498],four:[6,11,55,83,108,109,146,168,261,335,358,374,375,433,476],fourier: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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","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/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 dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<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 distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<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":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,airebo:382,alloi:404,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:[6,507],constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:[],fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,507],fix_modifi:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],fld:9,flow:6,fluid:250,flux:[95,148],forc:[6,7,148,324],fourier:[30,31,182,354],freez:238,from:[6,11],futur:5,gauss:408,gaybern:409,gcmc:239,gener:[1,6,7,13],get:12,gld:240,gle:241,global:6,gpu:[9,15,384,387,389,391,392,394,396,399,400,404,408,409,411,418,419,420,421,434,436,445,446,453,462,463,464,471,472,473],gran:[341,410],granular:[6,9],graviti:242,gromac:411,group2ndx:347,group:[92,346,507],gyrat:[93,94],h5md:[9,196,198],harmon:[32,48,49,50,183,186,340,355,437],hbond:412,heat:[95,148,243],heatconduct:454,helix:184,hertz:[410,447],hexord:96,histo:215,histori:[5,410],hook:410,hourglass:128,hourglass_error:[],how:6,hybrid:[33,51,185,356,413],idealga:455,imag:[196,199],imd:244,implicit:391,improp:[8,97],improper_coeff:350,improper_styl:[2,349,351,352,353,354,355,356,357,358,359,360,361],includ:362,inclus:8,indent:245,indic:0,individu:2,induc:6,inertia:98,info:[0,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,363],input:[2,6,8],instal:11,instruct:[],integr:[6,7],integrate_tlsph:314,integrate_ulsph:315,intel:[9,16,20,32,48,178,183,189,263,272,273,284,352,355,389,391,409,418,462,464],interfac:[6,11],intern:129,internal_energi:[],introduct:7,invers:230,ipi:246,ipp:13,jan:[],jul:[],jump:364,kate:13,keyword:[435,507],kim:[9,414],kokko:[9,17],kspace:[2,8,9,336],kspace_modifi:365,kspace_styl:[6,366],label:367,lammp:[0,1,2,6,7,8,11,12],langevin:[247,248,249],lattic:368,lcbop:415,lennard:429,librari:[6,11,12],limit:[277,328],line:[12,278,416],linear:[425,436],lineforc:255,list:[2,417],lj1043:340,lj126:340,lj93:340,lj96:419,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,67,70,71,81,97,114,121],log:369,lubric:427,lubricateu:428,make:12,manybodi:9,mar:0,mass:370,math:507,matlab:13,mdf:429,meam:[9,430,431,432],measur:1,mesh:140,meso:[104,105,106,256,257],meso_:[],meso_rho:[],meso_t:[],messag:3,mgpt:[9,433],micelle2d:13,mie:434,min_modifi:371,min_styl:372,minim:[8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,373],misc:9,mod:[335,465],model:[6,7],modifi:8,molecul:[9,374],molfil:[9,196,201],moltempl:13,momentum:[251,259],morri:459,mors:[52,412,436],move:260,move_tri_surf:316,movi:[196,199],mpi:11,mpiio:9,msd:[108,109,110],msi2lmp:13,msm:[387,389,391,396,418],msst:261,multi:[6,7,186],multipl:6,nb3b:437,ndx2group:347,neb:[262,375],neigh:[135,141],neigh_modifi:376,neighbor:377,nemd:6,newton:378,next:379,nharmon:187,noforc:[274,279],non:[6,7],none:[34,53,188,357,439],nongauss:110,nonlinear:54,nph:[263,264,265,266,267,307],nphug:268,npt:[263,264,269,270,271,307],num:[135,141],numer:507,nve:[272,273,274,275,276,277,278,279,280,281,307],nvt:[263,264,282,283,284,285,286,307],omega:111,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,44,46,47,48,49,50,52,54,55,57,178,179,181,182,183,184,186,187,189,190,192,242,263,265,267,268,269,271,272,280,282,284,286,299,349,351,352,354,355,358,360,381,382,384,387,388,389,390,391,392,394,395,396,397,399,400,404,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,432,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473],onewai:287,open:7,oper:507,opl:189,opt:[9,19,391,404,418,422,436],optim:1,option:[6,8,12],orient:288,orientord:112,orthogon:6,other:6,output:[6,7,8,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231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[306,502],adp:[],adri:[9,303,443,444],adust:166,advanc:[3,244,386,476,487],advantag:[1,6,8,11,14,18,40,41,42,220,380,405,490,495],advect:[3,6,323],advertis:8,advis:[375,442],afer:3,affect:[1,6,10,14,15,16,17,41,62,63,73,92,123,147,156,170,176,199,200,205,212,213,215,216,217,218,221,222,223,224,226,227,237,243,245,247,253,260,264,265,266,267,269,270,271,277,282,283,284,286,307,308,321,335,345,358,365,371,372,373,375,376,377,380,406,427,428,435,478,479,481,483,484,486,489,491],affin:[16,17,18,226,380,395],afil:241,aforement:18,afresh:[295,489,507],afshar:400,after:[2,3,5,6,8,11,12,15,21,22,33,40,41,42,45,51,59,60,61,63,65,73,150,151,152,153,154,155,156,159,160,161,162,164,165,172,173,175,176,179,180,185,195,196,197,198,199,200,201,203,204,205,209,210,212,213,220,221,222,223,224,226,230,239,250,251,252,253,254,259,260,261,263,269,270,271,277,282,283,284,286,289,293,297,305,307,310,319,324,326,327,328,330,331,332,333,334,338,340,342,346,349,350,356,364,370,371,373,374,376,378,379,380,381,382,386,393,395,404,405,406,407,413,414,415,426,427,428,430,431,432,433,437,441,443,444,451,452,461,462,464,465,466,469,476,478,480,481,482,483,484,486,487,489,491,493,495,498,499,502,506,507,508,509,510,511],afterrun:489,afterward:3,afterword:42,ag1:171,ag2:171,again:[6,11,12,16,17,64,146,152,158,166,196,200,226,243,293,349,364,375,427,428,476,478,479,481,483,488,495,497,507,509],against:[11,12,13,66,227,375,443,444],aggreg:[6,12,67,70,71,81,97,114,121,243,259,305,307,321,476,508],aggress:[243,495],agilio:[9,13],agre:[3,8,192,373,382,415,444],agreement:[5,7],ahd:412,ahead:342,aidan:[0,5,7,9,13,368],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:199,akohlmei:[7,9,13,201,244],aktulga:[7,9,300,444],al2o3:451,al2o3_001:[124,308],al3:171,ala:[250,451],alain:9,alat:[288,430],alb:[441,464,466],albeit:306,albert:9,alchem:[91,166],alcohol:338,alcu:[381,386],alcu_eam:441,alderton:399,alejandr:[263,264],alessandro:13,algebra:433,algorithm:[0,1,6,7,8,9,42,63,200,209,220,223,226,250,252,253,277,290,298,307,310,311,330,331,335,338,343,371,372,373,377,380,402,406,428,433,448,450,476,478,495],alia:[9,12,16],alias:[1,366],aliceblu:200,align:[6,9,12,29,42,73,174,192,216,220,245,368,481,484,502],alkali:406,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,165,166,167,168,169,170,171,172,173,174,175,176,178,180,185,191,192,193,196,197,198,199,200,201,203,204,205,206,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,256,258,259,261,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,311,312,313,314,315,319,320,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,340,341,342,343,344,345,346,347,348,349,350,354,359,361,363,364,365,366,367,368,370,373,374,375,376,377,379,380,381,382,383,385,386,387,389,390,391,392,393,395,396,399,400,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,422,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,482,483,484,485,486,488,489,490,491,492,493,494,495,496,498,499,500,502,506,507,508,509,510,511],allen:[29,91,399,409],allentildeslei:91,allign:3,allindex:347,alloc:[3,5,6,8,9,11,12,62,237,337,374,376,380,439,444,481,489],allocat:3,alloi:[],allosw:73,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,56,59,60,61,63,64,65,79,96,112,114,148,150,151,152,165,170,171,172,174,180,191,192,196,197,199,200,201,203,204,206,208,209,210,212,213,214,215,216,217,218,220,222,223,224,225,226,227,231,232,237,239,240,241,242,244,247,250,253,254,258,260,263,264,288,292,293,294,295,296,297,301,307,308,310,312,314,315,319,323,330,331,332,333,335,336,337,338,339,340,346,348,350,359,365,366,368,373,374,375,376,379,380,383,386,387,388,389,390,391,396,404,406,410,411,412,413,418,422,427,428,433,435,441,444,445,448,450,451,460,470,472,476,479,481,483,484,485,486,487,488,491,493,494,495,498,499,507,508],almost:[2,3,12,62,245,297,335,366,377,380,460],alo:396,alon:[6,7,223,303,443,444,479],alond:13,along:[6,8,12,29,41,73,91,124,170,171,172,195,196,199,212,223,245,250,251,255,260,262,297,307,310,312,316,320,321,330,334,335,341,344,346,368,371,372,373,375,396,399,410,413,416,418,422,430,443,444,463,481,484,491,492,507],alonso:[431,432],alpha:[6,12,52,204,250,289,297,298,302,373,381,384,387,396,400,402,404,405,407,412,417,418,430,436,440,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al:[476,495],anoth:[1,3,6,7,8,9,11,12,17,29,41,65,73,74,91,122,125,198,199,203,204,210,212,215,216,217,218,223,226,227,240,243,247,248,253,263,264,268,293,296,307,308,326,327,328,335,345,348,371,373,375,376,379,396,400,406,407,409,412,413,417,418,426,443,445,453,460,463,464,465,466,475,476,479,482,488,490,496,502,507,511],ansi:[9,12,16],answer:[3,4,8,12,307,377,378],anthoni:333,antiquewhit:200,antisymmetr:[9,41,383],antisymmetri:406,antonelli:[332,333],antonio:440,anymor:333,anyon:7,anyparticl:90,anyth:[8,11,172,226,246,462,464,466,492],anywai:[175,380,502,509],anywher:[12,172,393,430,452,507],aoff:[374,481],aparam:[91,204,205],apart:[3,173,253,320,376,385,453,481,490],aperiod:289,api:[9,11,12,201,414,479],appar:3,appear:[2,3,6,11,12,13,40,41,42,74,79,91,96,112,114,121,122,146,155,172,173,175,196,197,199,200,212,216,217,220,224,227,230,239,244,293,304,305,334,346,348,349,365,373,374,375,394,404,430,435,451,463,469,477,478,479,481,482,483,486,488,502,507,511],append:[],appendix:[29,399,451],appl:[224,263,264,469],appli:[2,3,4,5,6,8,9,12,17,18,29,33,42,51,59,61,63,65,73,74,91,92,110,122,146,147,152,158,160,162,166,171,172,174,178,180,185,191,195,196,197,199,200,203,204,205,206,207,209,212,219,220,224,225,226,228,231,232,234,235,237,238,239,240,241,242,244,245,247,248,249,250,254,263,264,268,269,270,271,277,282,283,286,287,288,290,294,297,305,306,307,309,310,312,313,316,320,321,322,324,326,327,328,329,331,333,334,335,338,346,365,368,373,374,375,385,387,389,391,396,399,406,410,411,412,413,415,416,418,424,428,433,435,438,443,446,447,448,449,450,460,467,472,481,482,484,485,486,490,491,493,498,502,507,508,509,510],applic:[1,6,9,12,17,201,209,223,227,228,237,239,241,244,288,293,306,312,320,331,338,365,380,466,491,502],applyt:3,appopri:[9,17],approach:[6,7,14,196,209,240,289,290,302,307,330,331,333,335,338,365,386,396,398,402,403,409,413,433,445,447,449,460,470],appropri:[1,2,3,6,8,9,11,12,13,15,17,33,38,43,51,57,63,75,92,95,122,123,150,151,152,180,185,191,192,195,196,197,200,212,213,216,217,218,223,224,226,237,238,241,250,258,260,261,263,265,266,267,268,269,270,271,282,283,284,286,290,293,294,297,302,307,311,323,326,327,328,331,338,340,341,343,344,345,356,366,375,382,386,390,394,395,396,405,410,413,415,422,426,433,442,443,444,462,463,464,465,466,469,470,481,482,483,485,486,494,495,498,507,508],approri:242,approxim:[6,9,124,128,171,239,241,250,290,308,310,330,365,371,372,373,388,398,406,409,427,428,433,435,442,445,451,472,495,502],april:11,aprpopri:476,apu:[427,428],aqua:[199,200],aquamarin:200,ar_therm:209,ar_ttm:209,ara:13,arbitrari:[6,41,60,122,196,197,199,201,225,226,242,263,290,298,462,479,492,507],arbitrarili:[11,61,122,146,195,224,263,396,507],arcco:3,arch:[1,9,12,14,15,17],architect:363,architectur:[16,380,433],archiv:[6,7,9,11,12,325,393,488],arcsin:3,area:[6,42,95,118,122,170,220,226,250,331,338,403,410,440,468,478,491],aren:[122,296,348],arflag:12,arg:[3,11,12,22,41,42,45,56,61,65,73,91,123,160,166,170,172,175,176,180,195,196,197,198,200,203,204,205,206,208,210,212,213,214,215,216,217,218,219,220,221,222,225,226,227,232,237,239,242,243,244,245,253,260,265,266,267,293,306,307,308,309,313,316,317,319,330,333,340,341,342,343,345,346,350,363,375,380,387,388,389,391,392,393,398,399,402,406,411,413,418,422,426,427,428,429,438,446,448,450,461,478,479,481,484,486,488,490,492,494,499,500,507,508,510,511],argon:239,argonn:12,argument:[2,3,6,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,42,43,44,45,46,47,48,49,50,52,54,55,57,61,65,75,91,95,112,115,118,122,146,147,149,154,159,160,161,166,170,172,173,174,176,178,179,180,181,182,183,184,186,187,189,190,192,196,197,200,203,204,205,206,208,211,212,213,214,215,216,217,218,219,220,224,225,226,233,235,237,238,239,241,242,246,247,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,292,293,295,299,304,307,308,309,310,323,326,328,335,337,339,341,343,346,348,349,350,351,352,354,355,356,358,360,363,364,366,367,368,370,375,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,402,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,429,430,431,432,435,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,475,476,477,478,479,480,481,482,484,486,489,490,491,492,496,498,499,507,508,510],aris:[12,472],arithmet:[3,6,108,365,391,394,421,435,467,468],arkansa:9,arl:[9,84,85,234,311],armi:[84,85,234,311],armv8:17,arnold:365,around:[1,3,4,6,9,12,43,59,60,61,68,72,73,74,75,79,122,146,150,167,170,172,174,195,199,200,207,208,224,226,227,245,260,263,296,298,302,307,316,320,323,340,341,344,364,374,451,481,484,491,492,502,507],aroung:3,arrai:[],arrang:146,arrheniu:495,art:[9,476,495],artefact:241,articl:[6,451],articul:[7,9,292],artifact:[92,170,502],artifici:[261,297,455,456,458],arun:13,arxiv:[146,198,452],ascend:[42,200,244,253,307,486],asci:7,ascii:[13,197,308,334,375,404,407,430,481],ash:[427,428],asid:[8,172,430],asin:507,ask:[3,11],askari:440,askoos:13,asoci:199,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172,196,197,201,203,204,205,210,227,232,239,296,298,299,300,304,325,338,365,366,374,387,389,395,396,398,399,404,406,407,413,418,422,426,438,443,444,451,461,466,467,469,470,472,473,481,482,486,491,493,502,506,507],charmm2lammp:13,charmm:[],chartreus:200,cheap:323,cheaper:[231,409,445],check:[3,6,8,9,11,12,15,17,40,42,73,95,192,210,216,220,221,222,227,236,239,245,246,293,306,310,323,331,333,338,346,348,364,373,374,375,376,377,380,403,414,417,435,444,476,478,479,481,489,495,498,499,507],checkf:192,checkqeq:444,checku:192,chem:[6,13,20,21,25,40,41,44,46,47,91,92,112,118,147,178,179,189,214,225,230,240,241,248,250,262,263,264,284,285,290,294,297,299,307,311,312,323,326,327,330,331,332,333,340,349,358,360,365,366,372,375,382,387,391,392,395,396,397,399,400,402,406,408,409,411,412,418,422,423,426,430,434,435,438,451,460,467,490,493,495,502],chemic:[9,124,166,171,196,197,209,210,239,298,303,304,330,366,443,444,456],chemistri:[297,298,300,386,406,443,444],chen:335,cheng:395,chenoweth:[443,444],chenoweth_2008:[443,444],chi:[97,161,195,288,298,300,361,407,409,508],chiefli:442,child:8,chip:[7,9,12,17,18,380,494],chipot:225,chiral:358,chmod:[11,12],cho:430,chocol:[7,200],choic:[3,6,9,12,15,16,18,41,42,55,91,147,150,151,165,176,192,212,216,217,220,223,226,227,241,247,250,261,263,290,298,307,330,359,366,371,372,375,377,380,413,426,435,439,481,490,491,494,495,501,502,506],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,91,123,162,163,199,221,222,223,224,227,236,247,250,261,263,265,266,267,268,269,270,271,293,294,311,323,327,341,365,366,372,470,476,478,490,496],chose:[464,466],chosen:[2,3,6,12,17,146,172,175,184,192,199,205,210,224,227,236,239,240,248,250,261,263,268,290,293,304,323,327,330,331,336,338,339,345,366,367,372,380,401,402,406,410,417,420,446,464,476,490,495,502],chri:170,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[68,77,94,98,109,111,120,152,167,169,212],chute:[4,9,10,242],ciccotti:310,cieplak:[6,178,493],cii:213,cij:213,ciko:2,circl:[43,73,319],circular:[3,6,150,194],circumst:18,circumv:[96,112,302],citat:[],cite:[3,7,8,12,247,451],civ:9,ckio:2,cko:2,cl1:171,clarendon:[29,399],clarifi:[7,464,466],clariti:348,clark:438,class2:[],classic:[0,3,5,6,7,8,9,237,290,297,302,335,360,406],classifi:[461,469],claus:479,clean:[6,12,14,15,17,489],cleanli:[480,510],clear:[],clearli:7,clebsch:146,clermont:[9,13],clever:485,click:[2,11,22,37,45,56,172,180,191,199,244,350,359,375,393,461],client:[244,246],climb:[262,375,495],clinic:[7,13],clo:[161,195,508],clock:[12,476,495],clockwis:341,close:[3,6,11,12,13,40,42,69,73,147,175,196,222,223,224,241,248,250,263,284,307,310,341,344,364,366,369,371,372,375,380,382,386,396,397,416,430,435,447,449,463,466,485,491,502,504],closer:[3,10,42,122,170,195,196,220,224,228,332,375],closest:[222,288,307,338,409,445,460,470],cloud:[451,502],clovertown:18,clsuter:74,clump1:[292,307],clump2:[292,307],clump3:[292,307],clump:307,cluster:[],clutter:3,cmap:481,cmatrix:241,cmax:430,cmd:[11,12,290,492],cmdarg:11,cmin:430,cmm:[],cmoput:139,cn1:213,cn2:213,cna:[],cnn:213,cnr:[9,13],cnt:[413,485],co2:[41,171,310,374],coars:[7,9,10,29,36,41,55,184,292,307,323,411,446,490,493],coarser:[366,507],coarsest:146,code:[],coeff:[3,7,8,12,21,22,33,45,51,178,179,180,185,349,350,356,393,413,417,435,448,450,453,481],coeffcient:481,coeffici:[],coefficienct:400,coefficient0:404,coefficient1:404,coeffieci:[6,384,416],coeffincientn:404,coexist:[239,406],cohes:[6,407,430],coincid:[128,344,391,427,428,476],colberg:198,cold:[6,157,239,243,376,502],coldest:331,coleman8:9,coleman:[9,124,171,308],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,68,77,87,94,98,103,109,111,120,152,160,167,169,172,196,197,200,212,225,253,259,292,302,305,307,346,365,374,376,394,481,488,494,500,511],collid:[231,323,345],colliex:171,collinear:[3,292],collis:[3,250,323,341,345,403,410,473],colllis:323,colloid:[],colombo:40,colon:[201,346,482],color1:200,color2:200,color:[3,9,42,196,199,200,220,240,297,302],column:[3,6,9,12,13,43,65,67,68,69,70,71,73,77,79,81,83,85,94,96,97,98,109,111,112,114,116,119,120,121,122,123,125,146,147,152,160,167,169,170,171,192,196,197,200,203,211,212,213,215,216,217,218,253,260,261,297,307,324,325,335,345,408,412,443,444,482,496,498,507],columnar:170,colvar:[],colvarmodul:12,com:[],comamnd:226,comand:223,comannd:380,comb3:[],comb:[],comb_1:299,comb_2:299,combiant:397,combin:[3,6,7,9,11,13,36,41,65,67,71,81,91,97,108,114,121,150,151,165,196,199,209,215,244,253,263,290,296,311,327,336,344,347,349,365,366,368,372,380,394,396,397,402,406,407,413,425,426,452,462,464,466,469,472,484,489,494,502,507],come:[],comfort:[12,13],comm:[0,3,11,12,63,75,198,244,246,247,366,375,380,400,435,440,463,483],comm_modifi:[],comm_modift:63,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,178,192,196,235,248,307,335,374,375,381,404,405,407,417,430,437,444,451,452,462,463,464,465,466,469,478,479,481,502,507],commerci:7,commit:9,commmand:[3,6,12,61,113,285,416,475,476,478,495,510],common:[],commonli:[3,6,9,12,17,25,59,61,110,112,174,196,199,201,360,411,420,452,464,466,481,484,493],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,60,63,64,73,170,175,176,199,200,220,221,222,224,225,226,244,246,250,252,253,254,263,289,296,298,299,300,307,311,323,335,346,363,365,376,377,378,380,402,403,439,474,478,479,490,491,507,509,511],communc:365,comp:[7,198,246,247,310,366,375,406,435,440,445,459,463,465],compact:[65,203,393,461],compani:[5,7],compar:[1,3,4,6,8,12,17,40,90,116,124,155,171,180,191,200,230,298,346,348,365,366,373,375,430,451,476,495,496,502,506],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,179,180,191,349,350,359,392,461],compat:[3,5,7,8,9,11,12,13,17,18,42,73,123,125,183,196,201,205,211,212,213,215,216,217,218,220,289,301,327,330,337,340,343,365,380,414,433,435,463,478,479,507],compens:[6,221,222,305,376,406],compet:334,competit:366,compil:[3,7,8,9,12,13,14,15,16,17,18,19,170,196,198,199,201,244,334,366,380,433,481,482,486,507],compl:17,complain:[11,12,17],complement:430,complementari:[7,396,418],complet:[3,6,9,11,12,15,42,61,73,200,216,220,225,253,290,293,296,323,334,336,347,348,364,375,380,407,448,450,468,476,481,486,489,493,495,498,502,507],complex:[4,6,8,11,12,13,25,41,43,64,96,112,146,148,160,172,173,250,319,344,363,375,406,433,463,479,481,484,507],compli:[330,334],complic:[6,7,9,12,13,210,239,479],complier:12,compon:[3,6,8,12,63,65,68,69,75,83,92,93,94,95,96,98,99,102,109,110,111,112,113,114,115,116,118,119,123,133,136,137,138,139,142,143,144,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,167,168,169,195,196,197,199,200,206,207,211,212,213,214,215,216,217,218,219,223,224,226,227,232,237,242,246,247,250,253,255,259,260,262,263,264,268,269,270,271,282,283,284,286,287,289,290,291,294,305,307,309,310,312,316,317,320,323,326,327,328,330,337,338,343,344,345,365,368,372,373,374,375,380,400,406,410,427,428,448,450,451,452,481,482,491,499,507,508],componenet:6,composit:[6,210,250,404],compound:[395,406,407,469],compres:[73,120,212],compress:[],compris:[41,344,445,468],compton:[124,171],comptu:3,compuat:366,comput:[],computation:[3,6,221,222,335,386],computational:502,compute_arrai:8,compute_fep:[205,426],compute_group_group:239,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[124,308],compute_scalar:8,compute_temp:8,compute_ti:205,compute_vector:8,compute_xrd:171,concaten:[2,3,510],concav:344,concentr:[73,404],concept:[6,152,162,212,490],conceptu:[3,6,73,160,224,226,375,396,413,430,486],concern:[6,75,91,198,240],concetr:73,concis:[11,334],conclud:12,concret:8,concurr:[16,366,507],conden:[335,464,466],condens:[6,154,335,382,398,404,418,469],condit:[],conducit:6,conduct:[],cone:484,confer:433,confid:[3,495],config:[12,196,478],configfil:225,configur:[1,2,6,12,15,17,38,61,128,174,192,195,196,199,203,224,225,226,227,231,239,246,247,277,290,298,334,363,373,375,382,386,405,430,433,462,464,466,469,476,481,483,484,495],confin:[481,495],conflict:[3,12,41,197,435,479],conform:[3,6,13,61,223,224,262,306,312,334,358,375,406,493],confus:[3,469],conjuct:[9,400],conjug:[7,8,247,372,406,443,444],conjunct:[6,7,73,90,91,120,155,160,166,172,176,200,204,205,247,250,254,277,293,294,298,299,300,302,307,311,323,331,338,343,365,366,375,387,389,393,396,400,406,412,418,435,438,446,467,481,484,488,502,511],connect:[3,6,9,91,157,175,223,244,292,307,310,320,375,397,410,460,466,478,479,481,485,502],conput:3,consecut:[3,11,12,40,73,172,200,204,205,227,244,245,396,418,422,476,482,484],consequ:[1,6,210,335,417,495],conserv:[],consid:[6,72,73,80,91,121,154,157,158,175,196,197,200,204,205,211,213,216,220,222,223,227,251,264,289,307,330,331,334,335,338,366,393,406,413,444,445,451,460,476,477,479,482,483,484,486,489,491,499,502,507],consider:[6,8,247,248,326,327,328,380,490],consist:[3,6,8,9,11,12,41,43,67,71,81,97,109,114,117,118,121,152,155,157,172,184,195,201,206,207,212,226,227,230,232,237,240,247,248,249,260,263,265,266,267,268,269,270,271,272,273,275,276,277,278,280,281,282,283,284,285,286,294,297,302,304,306,307,326,327,328,329,339,365,366,368,374,375,380,382,386,388,394,396,406,409,413,416,427,428,430,433,435,445,448,450,451,463,470,479,481,482,483,484,485,486,493,502,507],consistent_fe_initi:209,consit:307,constant:[],constitu:[3,6,253,307,340,344,394,445],constitut:[448,450],constrain:[3,6,8,149,150,151,152,153,155,158,159,160,161,162,164,165,203,212,227,239,240,245,253,257,292,293,305,307,310,321,331,338,373,374,406,486,493,502],constraint:[],construct:[6,8,12,14,38,55,57,63,66,69,72,74,75,79,96,112,124,146,171,224,263,289,306,344,376,380,399,433,435,460,462,463,484,485,500,507],constructor:[8,11],consult:444,consum:[1,302,439,507],consumpt:363,contact:[],contact_stiff:[447,449],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,65,91,95,122,124,146,152,160,170,171,172,174,178,180,191,192,196,197,199,200,201,203,204,205,209,211,212,213,215,216,217,218,220,225,227,232,235,241,245,246,247,250,261,277,288,289,292,293,295,297,300,304,307,308,313,323,330,334,335,344,345,348,364,366,374,375,378,379,381,382,383,386,395,396,399,404,405,406,413,414,430,433,437,441,442,443,444,452,462,463,464,465,466,467,469,476,477,478,479,481,482,483,484,486,488,490,493,495,496,498,499,502,507,509,511],content:[4,9,12,18,444,497,499],context:[3,6,8,12,17,122,123,200,221,222,227,292,304,339,372,472,481,488,497,506,507,508],contibut:72,contigu:478,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,73,83,108,109,168,200,203,204,205,210,212,213,214,215,216,217,218,220,223,224,225,226,227,239,240,241,243,244,245,247,248,249,255,260,261,263,265,266,267,268,269,270,271,282,283,284,285,286,291,293,296,297,307,308,312,322,323,325,332,333,335,341,344,348,364,379,380,386,400,403,420,423,443,444,445,448,450,465,476,479,481,483,484,489,495,496,498,499,507,509],continuum:[6,7,9,209,335,448,450],contour_integr:209,contract:[61,224,226,263,294,307],contradictori:3,contrain:310,contraint:277,contrari:[241,248],contrast:[1,6,43,56,66,154,157,197,226,346,448,450,472,510],contrib:335,contribut:[3,4,5,6,7,8,9,12,13,17,65,68,70,72,73,76,77,79,82,88,91,92,93,94,95,98,107,109,111,113,114,115,116,118,120,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,205,210,211,212,213,215,216,217,218,224,239,247,250,253,254,258,264,284,285,292,293,301,304,307,308,310,337,365,373,375,383,400,403,404,406,413,427,428,433,435,443,444,451,493,499,502],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,91,95,128,146,181,196,197,199,203,209,210,220,224,225,226,243,244,247,248,263,265,266,267,268,269,270,271,294,299,307,314,315,326,327,328,335,339,363,365,377,406,409,433,443,444,447,449,462,466,476,478,490,496,497],control_typ:209,controlfil:444,convect:95,conveni:[6,12,29,196,201,218,308,368,452,507],convent:[3,8,29,183,190,191,197,200,306,320,347,404,406,507],converg:[3,6,42,92,196,197,199,201,206,220,223,224,232,237,268,297,299,302,306,310,371,372,373,375,395,396,418,451,476,488,495],convers:[3,8,146,199,200,210,213,294,365,396,397,398,406,418,422,426,438,479,495,506],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,61,65,73,95,172,179,196,199,200,213,218,261,293,346,349,351,355,358,368,375,381,404,433,464,466,473,479,481,482,483,488,498,502,506,507,509,511],convex:[43,344],convinc:[7,12],cook:9,cooki:7,cool:[7,162,243,305],cooordin:[196,197],cooper:[5,7],coord123:120,coord1:[3,120,212,216,217],coord2:[3,120,212,216,217],coord3:[3,120,212,216,217],coord:[],coordb:451,coordbb:451,coordiat:373,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,61,63,64,65,68,70,73,76,77,79,83,91,93,94,98,108,109,111,119,120,122,140,146,155,161,167,169,170,172,176,195,196,197,198,199,200,201,203,206,211,212,215,216,217,220,221,222,223,224,225,226,227,230,232,233,237,239,242,243,244,245,246,247,248,260,262,263,265,266,267,269,270,271,284,287,288,289,292,293,294,304,305,307,309,310,312,317,320,321,322,323,325,333,334,335,342,343,345,346,368,373,374,375,380,381,382,385,405,451,476,481,482,483,484,486,489,491,495,502,507,508],coordn:[120,212],coorind:[],copi:[0,3,4,8,9,11,12,15,17,41,125,199,335,375,393,443,479],copper:473,coproccesor:16,coprocessor:[1,7,9,16,17,380,494],coproprocessor:17,copy_arrai:8,copyright:[7,8,292],coral:200,core:[],core_shel:154,coreshel:[],cornel:[6,178,493],corner123i:119,corner123x:119,corner123z:119,corner1i:119,corner1x:119,corner1z:119,corner2i:119,corner2x:119,corner2z:119,corner3i:119,corner3x:119,corner3z:119,corner:[3,6,41,119,199,344,345,368,468,481],cornflowerblu:200,cornsilk:200,corp:9,corpor:16,corr:395,correct:[3,6,9,11,12,16,17,61,91,92,107,108,113,116,122,154,159,166,197,199,226,239,241,247,263,264,284,292,294,297,334,340,344,365,375,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,471,472,473,474,481,496,499,502],correction_max_iter:209,correctli:[3,8,11,17,73,83,107,108,109,149,150,151,153,155,157,158,159,160,161,164,165,168,196,200,206,227,232,237,248,257,263,264,300,307,310,320,322,341,344,375,376,380,398,428,433,478,479,481,491,506,508],correl:[],correpond:235,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,72,73,91,101,102,115,118,119,120,121,124,125,133,136,137,138,139,140,142,143,144,146,149,150,159,166,170,171,178,179,180,181,182,183,184,186,187,189,190,192,195,196,197,199,200,204,205,206,212,214,215,216,217,219,222,224,226,233,237,238,242,247,250,251,259,260,261,263,265,266,267,268,269,270,271,272,273,277,280,282,283,284,286,289,290,294,299,307,309,310,326,328,330,339,340,341,343,344,345,347,349,350,351,352,354,355,358,360,366,370,372,374,375,381,382,384,387,388,389,390,391,392,393,394,395,396,399,400,404,405,406,407,408,409,410,411,412,413,416,418,419,420,421,422,423,424,425,426,427,430,431,433,435,436,437,438,440,441,443,444,445,446,451,452,453,462,463,464,465,466,469,471,472,473,476,478,479,481,482,484,494,495,496,498,499,502,507],correspondingli:[427,428,490],corrupt:3,cosin:[],cosineshift:27,cosmo:[241,246],cossq:[],cost:[1,6,10,11,12,17,40,42,73,115,124,147,171,199,200,212,216,217,220,221,222,236,263,299,335,365,366,378,396,418,422,433,435,462,478,490],costheta0:[462,464,466,469],costheta:441,costli:[11,92,241,376],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,61,68,73,77,91,94,98,109,111,115,118,120,152,162,167,169,185,196,197,199,200,204,205,212,213,216,220,226,237,246,296,297,298,302,305,307,309,323,324,330,334,335,336,340,344,346,348,356,362,364,371,373,376,380,383,408,412,413,416,443,444,477,478,479,481,483,485,488,489,496,497,502,507,508],coulomb:[3,5,6,7,8,9,10,12,14,15,18,74,92,113,114,122,147,173,177,298,300,336,365,366,373,380,387,389,390,391,392,395,396,397,398,399,406,410,411,413,418,422,426,429,435,438,443,444,446,451,461,466,467,469,472,486,493,499,502,506],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,65,70,79,95,120,122,123,160,170,176,206,207,210,212,215,216,217,219,220,227,232,236,239,245,263,277,293,310,326,327,344,366,373,374,375,377,380,408,412,435,499,507],counter:[3,341,476,487,489,495],counteract:239,counterbal:243,counterbalanc:29,counterpart:[196,307,476],counterproduct:18,coupl:[],courant:313,cours:[3,8,132,134,166,196,204,205,240,306,320,334,340,342,343,345,346,366,427,453,478,481,494,502,507,509],courtesi:368,cov:451,coval:[6,9,29,406,430,451,502],covari:241,cover:[6,73,192,200,209,250,406,468],coverag:[73,216],cpc:246,cpp:[1,3,6,8,9,11,12,13,91,196,204,205,237,310],cpu:[1,3,9,10,12,14,15,16,17,18,65,73,200,214,230,248,336,363,366,380,393,461,476,494,495,498,499,500,507],cpuremain:499,cr2:171,cr3:171,crack:[4,376],crada:[5,7],crai:[5,7,13,18,196],crash:[3,12,376,502],craympi:380,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:209,create_faceset:209,create_group:198,create_nodeset:209,createatom:[],creation:[],crimson:200,critchlei:292,criteria:[3,122,173,199,200,221,222,223,258,373,440,468,483,486,507],criterion:[12,42,127,172,175,210,220,223,239,277,299,313,341,346,373,375,395,406,410,451,486,495,496],criterioni:495,critic:[6,49,50,261,330,335,373],crmax:73,crmin:73,cross:[3,12,22,73,93,150,170,180,196,197,199,211,216,222,226,260,262,284,307,316,320,322,331,338,350,368,375,391,400,403,404,411,412,413,418,420,422,441,446,448,450,464,466,473,481,485,491,509],crossov:1,crossterm:481,crozier:[0,7,13],crucial:297,crystal:[3,4,6,13,75,112,288,289,333,368,376,481,485,499,502],crystallin:[6,108,289,368,465,502],crystallis:330,crystallogr:[124,171],crystallograph:[368,499],crystallographi:[124,171,368],cs1:171,cs_chunk:6,cs_im:[41,481],cs_re:[41,481],csanyi:[146,442,452],cscl:430,csequ:6,csh:[11,12,393],cshrc:[11,12],csic:[405,462,464,466,469],csinfo:6,csisi:[405,462,464,466,469],csld:[],cst:404,cstherm:6,cstyle:478,csvr:[],ctcm:[381,404],ctemp_cor:230,cterm:312,ctr:9,ctype:11,cu1:171,cu2:171,cu3au:430,cube:[6,42,170,175,220,230,344,368,502],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:386,cummul:[3,6,218,221,222,223,225,236,241,247,249,323,326,327,328,329,331,338,412,499],cumul:[6,210,212,215,216,217,231,239,247,261,263,268,277,307,308,375],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,61,63,65,73,75,83,91,107,108,114,122,123,136,147,152,160,162,168,170,173,176,195,196,197,198,199,200,201,204,205,209,212,216,217,218,220,221,222,223,224,225,226,227,231,232,237,239,241,244,245,247,253,260,263,264,269,270,271,277,282,283,284,286,292,293,298,299,301,304,305,306,307,310,311,312,313,314,315,316,317,319,321,322,323,326,327,328,334,335,338,339,340,341,342,343,345,346,348,363,364,365,366,369,370,372,373,374,375,380,386,393,395,399,404,406,407,410,413,414,417,427,428,430,431,432,435,441,443,444,447,448,449,450,453,464,466,467,470,476,477,478,479,481,482,483,484,485,487,488,489,491,493,495,496,498,499,507,508,509,510,511],curv:[6,172,239,289],curvatur:[409,445,473],custom:[],cut0:479,cut1:490,cut2:490,cut:[],cuthi:[288,300],cutinn:[388,427,428],cutlo:[288,300],cutmax:441,cutoff1:[392,399,418,422,426,429,438,446],cutoff2:[387,389,390,392,398,399,418,422,426,429,438,446],cutoff:[3,6,8,10,16,18,40,46,47,55,56,63,72,74,75,79,91,96,112,114,121,122,146,170,173,175,176,222,223,228,235,288,297,298,300,302,304,307,311,323,336,340,344,346,363,365,366,373,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,479,483,486,490,502,507],cutoff_glob:[],cutoff_inn:[],cutoffa:405,cutoffc:405,cuu3:404,cval:171,cvd:330,cvel:312,cvff:[],cwiggl:[3,260,340,343,345,507],cyan:[2,199,200],cycl:[3,239,261,263,264,268],cyclic:[3,192],cygwin:12,cylind:[3,4,73,199,212,245,293,341,344,484],cylindr:[6,245,320,341],cypress:380,cyrot:386,cyrstal:289,d3q15:250,d3q19:250,d_double_doubl:15,d_e:335,d_flag2:296,d_flag:296,d_name:[119,196,296,325,491],d_single_doubl:15,d_single_singl:15,d_sx:296,d_sy:296,d_sz:296,daan:333,dai:12,daili:12,daivi:284,damag:[],dammak:302,damp:[3,6,203,208,247,248,249,254,263,264,268,294,297,298,302,307,326,327,339,341,342,372,373,375,387,389,391,396,399,406,410,418,426,438,446,461,467,495,502],damp_com:248,damp_drud:248,dampen:[307,502],dampflag:[341,410],dan:17,danger:[3,12,239,346,400,499],dangl:175,daniel:9,darden:[366,399],darkblu:200,darkcyan:200,darken:199,darkgoldenrod:200,darkgrai:200,darkgreen:200,darkkhaki:200,darkmagenta:200,darkolivegreen:200,darkorang:200,darkorchid:200,darkr:200,darksalmon:200,darkseagreen:200,darkslateblu:200,darkslategrai:200,darkturquois:200,darkviolet:200,dasgupta:298,dash:[410,498],dat:[6,95,192,209,477],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,308],dataset:308,datatyp:3,date:[0,4,6,12,13,195,443,444,507],datom1:121,datom2:121,datom3:121,datom4:121,datum:[3,6,43,67,70,71,81,97,114,121,196,213],davenport:429,davi:340,david:[9,19,365,366,464,466],daw:[404,441],dbg:14,dcd:[3,6,7,196,198,199,200,201,290,482,486],ddim:195,deactiv:426,dealt:246,debug:[6,7,11,12,13,14,17,124,128,171,172,290,295,363,365,380,414,435,470,479,480,488,491,498,507],deby:[],decai:[96,396,473],decid:[3,6,12,16,73,260,296,307,336,496],decipher:368,declar:198,declin:323,decod:199,decompos:[91,452],decomposit:[3,5,7,18,64,209,290,311],decoupl:[6,502],decreas:[3,196,197,206,207,214,223,226,232,237,239,247,334,365],decrement:312,deepli:362,deeppink:200,deepskyblu:200,def:[12,13,479],defaul:63,defect:[6,72,170,433],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,186,187,189,190,191,192,193,194,195,196,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,230,231,232,234,237,238,239,242,245,246,247,248,249,250,258,260,262,263,264,265,266,267,268,269,270,271,273,274,275,278,280,281,282,283,284,285,286,288,289,290,292,293,294,296,298,300,305,307,308,309,310,313,317,321,323,325,326,327,328,329,331,332,333,335,337,338,340,341,342,343,344,345,346,348,349,350,351,352,353,354,355,358,359,360,361,363,365,366,368,370,372,373,374,375,376,377,378,379,380,382,383,384,385,387,388,389,390,391,392,393,394,396,397,399,400,401,402,403,405,406,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,433,434,435,436,437,438,440,441,443,444,445,446,447,448,449,450,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,481,482,484,485,486,487,490,491,492,493,495,496,498,499,502,503,504,505,506,507,508],definit:[2,3,6,8,12,13,80,82,122,146,200,212,213,214,215,216,217,218,226,234,245,268,308,325,337,340,343,345,347,359,363,374,383,386,394,401,402,406,416,441,448,450,452,468,479,481,483,490,492,506,507],defint:499,deform:[],deg2theta:171,deg:502,degener:[3,292],degrad:[8,18,289,366,490],degre:[3,6,8,20,21,24,28,29,32,35,36,38,67,81,96,97,99,101,102,104,106,107,112,118,149,150,151,152,153,154,155,156,157,158,159,160,161,162,164,165,171,172,178,179,182,183,190,192,195,199,212,223,230,239,241,242,247,248,253,263,264,268,269,270,271,282,283,284,286,290,292,306,307,310,326,327,328,333,349,351,355,358,360,373,399,404,412,491,499,502,508],degress:[152,212],del:495,delai:[3,6,12,376,403,499],deleg:413,delet:[2,3,7,8,12,55,59,62,65,170,175,176,203,212,213,215,216,217,218,221,223,236,239,263,308,326,327,346,348,364,374,376,379,435,460,481,482,483,484,492,493,498,503,505,507,508],delete_atom:[],delete_bond:[],delete_el:209,deli:195,delimit:[479,507],deloc:[264,406,451],delr:430,delt_lo:495,delta:[],delta_1:386,delta_3:386,delta_7:386,delta_conf:3,delta_ij:[430,441],delta_mu:[],delta_pi:386,delta_r:441,delta_sigma:386,delta_ua:[],delx:195,delz:195,dem:[],demand:302,demo:11,demon:287,demonstr:[297,430],den:293,dendrim:412,denniston:[9,250,252,253,254,289],denomin:[7,177],denot:[124,230,248,289,300,302,396,411,413,444,448,450],dens:[73,223,406],densiti:[3,6,7,9,18,41,42,61,105,122,132,146,158,170,172,204,205,209,212,216,217,220,226,237,250,253,256,257,289,293,294,298,335,340,368,370,374,381,386,404,430,431,432,441,445,451,455,457,458,459,481,490,491,499,506],density_continu:450,density_summ:450,depart:[0,7],departur:[261,297],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,63,65,67,70,71,72,73,81,96,97,108,114,115,118,119,120,121,125,146,149,155,159,160,166,172,173,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,199,200,203,204,205,206,207,210,212,214,215,216,218,219,220,222,224,226,232,233,238,241,242,243,245,247,248,250,252,253,260,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,288,299,302,304,307,309,310,311,317,323,326,327,328,330,332,334,335,337,339,340,343,344,345,346,348,349,350,351,352,354,355,358,360,366,368,373,374,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,430,431,433,434,436,437,438,440,441,443,444,445,446,451,452,453,461,462,463,464,465,466,467,469,471,472,473,476,478,481,483,484,487,491,493,495,498,499,501,507,508],dependend:6,depflag:12,dephas:[476,495],depos:227,deposit:[],deprec:[3,298,443],depth:[52,150,199,335,409,445],dequidt:9,der:[91,113,394,395,426,443,444,472,502],deriv:[6,7,8,9,38,57,65,91,146,166,192,213,224,226,239,247,260,263,265,266,267,268,269,270,271,288,294,298,302,332,333,335,340,341,344,372,374,382,386,394,399,406,407,411,420,424,425,430,433,443,444,461,463,472,502],derjagin:472,derlet:288,descend:200,descent:[7,372],descib:[41,199,298],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,64,65,70,72,73,75,92,116,119,122,124,136,146,147,150,151,152,156,157,160,163,165,166,170,171,172,174,175,184,189,192,196,197,198,203,204,205,212,213,214,215,216,217,218,220,223,224,225,226,227,229,230,235,240,241,244,245,246,247,248,249,250,252,253,254,258,262,263,264,268,276,285,288,290,295,296,297,298,299,300,307,312,320,323,324,325,326,327,328,329,330,331,332,333,338,340,341,343,348,365,366,368,371,372,373,374,375,379,382,383,385,387,388,389,391,392,393,394,395,396,399,404,406,407,409,410,411,413,416,418,419,420,421,422,423,424,425,426,427,428,429,430,433,434,440,441,442,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,469,471,472,473,474,476,478,479,481,482,483,484,485,491,494,495,498,507,508,509],descript:[],descriptor:[146,196,414],deserno:366,design:[0,3,6,7,8,11,13,14,15,17,124,154,157,171,209,223,229,230,263,264,288,289,308,330,335,383,384,385,388,391,396,398,406,426,427,428,431,432,441,444,463],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,61,73,92,95,118,123,147,154,172,185,195,212,218,224,226,237,239,240,247,248,249,253,263,284,292,293,294,295,298,302,307,310,323,326,327,328,329,334,341,356,362,365,366,368,371,373,374,375,400,404,412,427,428,462,464,466,477,478,479,481,485,490,495,496,498,499,507,508,509],desk:7,desktop:[4,6,7,10,12,199],despit:502,destabil:386,destre:358,destroi:[9,11,40,221,222],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,65,68,69,70,73,77,80,94,95,98,107,109,111,113,115,117,118,120,123,125,146,147,149,150,151,152,155,165,166,167,169,172,173,176,177,180,191,195,196,197,199,200,203,204,205,209,212,213,214,215,216,218,220,222,223,224,225,226,227,237,239,240,241,242,244,245,247,249,250,254,260,261,262,263,264,265,266,267,268,269,270,271,275,277,282,283,284,285,286,289,292,293,294,296,297,299,300,301,307,310,311,323,326,327,328,329,330,331,333,334,335,336,337,338,339,346,348,350,359,365,366,369,373,374,376,377,380,381,382,383,385,386,388,390,391,392,393,394,395,396,399,400,406,407,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,429,430,434,435,440,443,444,445,451,452,453,461,468,471,472,474,479,481,482,483,484,486,487,490,491,493,496,499,500,507,508,511],detect:[2,3,12,43,63,65,90,96,238,293,334,375,395,412,417,476,478,481,492,495,507],determ:380,determin:[1,3,6,8,9,12,15,40,41,43,52,59,60,61,63,64,70,73,91,107,113,115,118,124,125,133,147,160,161,170,171,172,195,196,197,199,200,201,202,206,207,208,211,212,213,214,215,216,217,218,219,220,224,226,227,230,232,239,242,243,245,247,248,253,258,260,261,263,269,270,271,282,283,284,286,288,290,293,294,297,304,305,306,307,308,309,313,315,317,323,326,327,328,330,336,337,340,341,342,343,344,345,346,359,365,366,368,374,376,377,380,382,383,390,395,399,403,404,408,410,413,414,422,430,433,435,444,445,451,460,463,467,472,478,481,482,484,486,488,491,495,497,498,500,506,507,508],determinist:311,detil:114,devan:[9,446],devanathan:466,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,244,268,292,297,298,301,382,386,406,432,433,451,469,483],devemi:9,deviat:[261,268,288,408],deviator:9,devic:[1,3,12,15,17,244,380],device_typ:380,devin:[299,395],devis:432,dfactor:199,dff:502,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,366],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,301,433],dhi:[61,195,226,293],dhug:[261,297],dhugoniot:[261,297],dia:430,diagnost:[],diagon:[3,6,87,146,147,148,224,263,294,307,338,448,450],diagonalstyl:452,diagram:[42,124,171,191,220,290],diallo:412,diam:[199,200,293,374],diamet:[3,6,41,43,119,172,196,197,199,200,204,205,247,293,307,323,325,339,341,374,394,409,410,420,445,468,472,481,482,491],diamond:[368,406,430],diamter:[41,293],dick:6,dicsuss:260,dictat:[210,261],did:[3,12,373,400,403,404,410,435,464,466,489],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,168,337,365],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,63,66,70,72,73,91,96,99,101,102,126,146,149,150,151,152,153,155,158,159,160,161,162,164,165,166,172,173,175,180,191,192,195,196,199,200,203,205,208,210,212,215,220,221,222,223,224,225,226,230,235,238,239,240,241,242,243,244,247,248,250,260,263,264,265,266,267,269,270,271,273,275,278,280,281,282,283,286,288,290,292,294,297,298,299,302,305,307,310,312,320,321,323,326,327,328,331,332,333,335,338,339,340,341,344,348,349,359,362,364,365,366,368,369,371,372,374,375,377,378,379,380,381,382,386,390,391,393,394,395,400,401,402,404,406,409,410,411,413,416,418,419,421,422,429,430,431,432,434,435,437,441,443,444,445,446,447,448,450,451,452,453,461,462,463,464,466,468,469,472,475,476,478,479,481,483,484,485,486,489,490,491,493,495,496,498,499,500,502,506,507,508,509],differenti:[1,3,6,29,192,365,396,441,465],difficult:[224,290,380,412,490],difficulti:[96,112,310,443],diffract:[],diffus:[],digit:[2,3,200,348,433,507],dih_table1:192,dih_table2:192,dihder:[],dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:222,dihydrid:406,dij:310,dilat:[],dim1:3,dim2:3,dim:[3,61,73,149,153,154,155,158,159,160,161,162,164,172,195,216,226,245,341,368,430,484,506,507,508],dimdim:507,dimems:289,dimens:[],dimensinon:73,dimension:[3,40,96,118,124,146,149,152,153,154,155,158,159,160,161,162,164,171,194,212,216,262,289,335,368,371,375,441,481,491],dimensionless:[110,127,128,130,133,135,137,142,146,335,366,452,472],diment:3,dimentionless:141,dimer:[6,307,430],dimgrai:200,dimstr:[42,220],dinola:[294,326],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,196,197,325,502],dir1:492,dir2:492,dir:[1,3,4,8,10,11,12,261,288,297,322,441,443,444,479,492,507],dirac:146,direc:441,direct:[],directli:[3,6,8,9,11,12,91,119,146,148,196,197,198,199,206,232,241,245,250,289,308,327,339,341,342,343,344,368,372,380,381,382,387,389,390,396,399,404,406,418,422,435,438,446,460,479,491,492,493,499,507],directoi:14,directori:[1,2,3,6,7,8,11,12,13,14,15,16,62,197,201,225,246,292,298,301,311,319,323,332,333,375,379,381,382,386,393,395,396,404,405,407,414,415,426,430,431,432,433,437,441,442,443,444,451,452,462,464,465,466,469,479,481,482,483,492,507],disabl:[3,12,16,335,417,479,494,507],disadvantag:[6,220],disallow:[196,226,263],disappear:483,discard:[2,3,42,73,214,216,220,336,344,478,483,484],discontinu:[192,373,424],discourag:430,discov:[13,336],discret:[6,8,41,43,199,200,247,250],discuss:[],disk:[6,88,89,96,165,194,227,239,293,479],disloc:[72,433],disord:[40,72,433],disp:[],dispar:445,disperion:[399,422],dispers:[3,6,7,9,170,289,365,366,390,399,422,427,435,444,463,469],displac:[],displace_atom:[],displace_box:61,displacemet:484,displai:[11,13,22,37,45,56,180,191,196,199,350,359,393,461],dispters:3,disregard:433,dissip:[6,9,41,84,85,234,240,247,289,311,332,333,388,400,401,402,410,427,428,461],dissolut:221,dist:[6,71,95,114,123,196,290,306,403,460,476,508],distanc:[],distinct:[6,230,304,365,445],distinguish:[6,90,146,253,406,480,507],distort:[170,381],distrbut:381,distribut:[],distro:[117,393,440,441],ditto:[8,12,14,15,16,17,18,43,121,222,473,479],div:8,divd:123,diverg:[3,12,40,307,333,483,502,509],divid:[3,6,16,42,95,118,123,132,134,147,169,170,180,191,200,212,213,215,220,226,288,331,338,343,365,373,375,407,444,451,469,490,498,507],divis:[6,250,386,416,426,478,499,507],dl_poli:[6,7],dlambda:166,dlammps_async_imd:244,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,199],dlammps_gzip:[3,12,196,199,334,481,482,486],dlammps_jpeg:[3,12,199],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,199],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,196],dlen:491,dlmp_intel_offload:[9,12,16],dlo:[61,195,226,293],dlopen:6,dlvo:[7,394,472],dm_lb:250,dmax:[323,371],dmpvtk:197,dmpvtp:197,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,59,61,65,68,70,77,91,94,98,107,109,110,111,113,115,117,118,120,123,125,147,150,151,152,165,167,169,172,173,174,180,191,195,196,197,198,199,200,201,203,204,205,210,211,212,213,214,215,216,217,218,227,239,247,248,258,263,264,269,270,271,275,282,283,284,285,286,293,296,307,320,323,326,327,328,337,341,344,346,348,350,359,364,373,374,375,380,381,382,385,393,395,396,404,405,407,412,413,415,416,430,431,432,435,437,440,441,442,452,461,462,464,466,468,469,479,481,482,483,484,486,489,490,491,498,499,507,508,509,510],docuement:445,dodd:43,dodgerblu:200,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,61,64,65,69,72,73,74,91,92,95,109,113,116,122,123,124,148,150,152,154,155,160,162,166,171,172,173,174,176,178,180,185,191,192,195,196,197,198,199,200,203,209,210,212,216,219,220,222,223,224,226,230,232,235,236,239,2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445],epsilon_i_b:[409,445],epsilon_i_c:[409,445],epsilon_ij:435,epsilon_j:[409,435,445],epsilon_j_:445,epsilon_j_a:[409,445],epsilon_j_b:[409,445],epsilon_j_c:[409,445],epsilon_lj:445,epton:440,eqch:167,eqeq:[443,444],eqp:399,eqq:399,equal:[2,3,6,8,11,12,17,40,42,55,65,67,70,71,73,78,81,90,91,95,97,114,116,121,123,125,147,150,166,168,170,172,195,199,200,203,204,205,206,207,210,213,214,215,218,219,220,224,226,227,232,239,240,242,243,245,247,248,250,253,254,260,261,268,279,288,290,293,295,297,298,299,302,304,306,307,309,312,317,319,326,327,328,331,332,333,335,337,338,340,343,345,346,348,364,368,373,375,376,377,379,380,395,400,402,408,409,412,416,427,433,434,441,443,444,445,447,448,449,451,452,453,463,468,469,473,477,478,479,481,483,484,488,489,492,495,497,499,507,508],equat:[3,6,7,8,9,95,112,118,124,171,180,191,203,224,230,231,234,235,241,247,248,250,253,261,262,263,264,268,284,288,290,297,298,302,310,311,323,331,335,338,340,341,343,345,358,365,366,394,399,400,402,406,407,410,415,427,428,430,435,445,448,450,455,456,458,459,473,502],equi:264,equidist:262,equil:[3,298,369,488,511],equilater:491,equilibr:[3,4,5,6,7,9,61,95,172,203,210,213,223,224,239,261,263,264,284,285,297,298,299,300,331,332,333,338,395,396,443,444,477,491],equilibria:338,equilibribum:[221,222],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,44,48,49,50,52,54,57,61,155,156,179,181,224,226,239,240,241,248,250,263,268,284,297,298,302,306,310,312,320,323,330,331,333,338,349,351,355,358,395,430,437,451,502],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:209,equival:[6,12,13,29,61,63,130,131,139,144,170,174,200,215,218,224,226,239,247,263,284,294,306,307,343,400,406,451,464,466,481,484,489,490,499,502],equlibrium:6,equliibr:[298,300],er3:171,eradiu:[41,119,197,406,481],eras:[309,332],erat:[226,428],erc:396,erfc:[396,418,435],erforc:[119,197],erg:506,erhart:[210,404,464,466],ermscal:383,ernst:9,eror:3,eros:430,erose_form:430,erot:[],errata:[464,466],erratum:340,erron:3,error:[],erta:410,ervel:[119,197,481],escap:[227,502],especi:[8,16,160,172,203,210,220,239,297,302,305,306,380,478],espresso:[9,301],essenti:[8,11,12,27,92,134,153,154,155,158,159,160,161,162,164,181,213,268,289,339,366,382,396,418,466,486,499],essex:29,establish:[91,243],estim:[1,3,6,10,12,38,42,57,95,147,209,220,231,261,323,330,365,366,371,435,444,463,495,499],esu:506,esub:430,eta:[6,250,263,297,298,300,339,405,407,409,441,465,469,506],eta_dot:263,eta_ij:441,eta_ji:407,etag:[41,481],etail:499,etap:263,etap_dot:263,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,63,70,93,94,95,99,115,116,119,121,147,149,152,153,154,155,156,158,159,160,161,162,164,166,172,174,175,176,185,196,197,199,200,203,204,209,210,211,212,215,216,217,218,221,222,226,227,237,239,240,247,263,293,304,308,335,336,344,348,364,365,373,374,375,376,378,404,405,413,426,428,433,439,443,444,462,464,466,469,476,479,481,482,483,488,490,491,495,496,497,498,499,500,502,506,507,509,511],ethernet:18,etol:[373,375,476,495],etot0:297,etot:[6,99,101,102,116,147,158,200,230,248,261,297,498,499],eu2:171,eu3:171,euler:[373,375],eulerian:209,euqat:454,europhi:250,ev_tal:8,evalu:[2,3,9,11,12,38,57,73,91,92,95,113,123,125,146,148,152,162,170,172,195,196,197,199,200,204,205,206,207,209,211,212,213,214,215,216,217,218,219,226,232,240,242,243,245,246,247,248,289,295,298,309,313,317,326,327,328,337,340,343,345,346,348,365,366,371,373,380,433,435,441,447,449,451,463,476,477,479,483,484,486,488,489,490,491,495,497,499,507,508],evalut:[348,479],evan:[160,284],evanseck:[6,20,178,391,493],evapor:[],evaul:[8,373],evdwl:[113,443,444,499],even:[3,6,8,12,15,17,18,34,40,42,53,59,61,63,65,72,73,92,113,125,170,173,174,188,192,196,197,200,203,204,205,210,211,212,215,216,217,218,220,221,222,224,226,227,230,245,248,261,263,264,289,293,302,304,307,308,319,323,331,335,338,340,344,346,357,365,371,373,375,380,385,406,407,410,413,416,435,445,469,470,474,481,482,484,486,487,488,490,491,493,496,498,499,500,502,511],evenli:[3,42,147,192,220,250,416,470],event:[],eventu:[3,6,12,15,174,298,495],ever:[9,55,57,246,323],evera:[394,409,445,461],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,73,74,95,119,125,134,160,175,196,197,198,199,200,201,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,231,236,237,239,241,243,244,245,250,251,259,263,264,268,287,288,289,293,294,295,296,297,298,299,300,302,304,305,307,308,310,312,323,325,326,327,328,329,330,331,334,335,336,337,338,346,348,364,366,375,376,377,380,400,403,413,426,443,444,451,457,475,476,477,481,483,485,486,488,489,490,495,496,497,499,507,511],everyth:[8,113],everywher:[122,420],eviri:406,evolut:[241,250,290,476],evolv:[250,290,336],ewald:[2,3,5,6,7,8,9,12,92,116,124,147,336,365,366,373,387,389,390,396,399,406,418,422,438,446,461,463],ewald_disp:399,ewalddisp:3,exact:[22,42,45,73,128,166,175,180,220,223,240,241,247,248,249,293,302,303,323,335,350,365,393,483,488,495,507,509,511],exactli:[3,6,12,14,17,38,42,43,57,61,73,74,95,122,150,156,163,172,192,204,205,215,220,226,231,235,240,247,248,249,264,276,277,285,289,297,323,328,329,342,380,393,400,404,410,413,427,435,463,483,484,491,495,507],exager:502,examin:[6,8,17,223,289],examp:[479,507],exampl:[],exce:[3,6,16,17,18,42,60,73,174,211,212,215,216,217,218,220,224,226,231,236,263,289,304,308,314,315,323,373,380,481,507],exceed:[3,42,61,220,226,263,323,489],excel:406,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,61,62,65,73,93,94,114,115,118,123,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,172,176,178,179,180,181,182,183,184,186,187,189,190,191,192,195,196,197,200,203,206,212,213,215,219,220,224,226,233,238,239,242,245,247,249,263,264,265,266,267,268,269,270,271,272,273,276,277,280,282,283,284,285,286,290,299,300,307,309,310,320,323,326,328,329,335,339,343,346,347,348,349,350,351,352,354,355,358,359,360,365,366,368,370,374,375,376,378,379,380,381,382,384,387,388,389,390,391,392,393,394,395,396,398,399,400,404,405,406,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,428,431,436,437,438,440,443,444,445,446,453,461,462,463,464,465,466,469,471,472,473,476,478,479,481,483,484,486,489,490,491,492,493,495,499,502,506,507,508,510],excess:[214,406],exchang:[2,3,6,8,63,64,203,209,210,239,247,299,307,331,335,338,365,380,406,496],exchange:365,excit:406,exclud:[3,6,9,12,16,17,65,73,118,146,152,159,160,176,196,212,216,221,222,251,259,292,305,307,330,341,346,373,374,376,388,410,413,416,427,428,435,460,493],exclus:[1,3,12,16,91,380,395,433,435,490,500],excurs:[263,476],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,62,173,199,244,301,348,364,367,379,477,479,489,492,495,507],exempl:451,exemplari:240,exemplifi:406,exert:[6,245,248,302,342,343,344,366],exhaust:[209,379,507],exhibit:[96,263,372,406,490],exist:[3,6,7,8,11,12,13,16,37,56,61,70,72,128,172,173,191,198,199,200,203,208,219,222,224,227,239,292,293,295,346,347,349,351,352,353,355,359,369,374,380,401,402,413,443,460,470,477,479,481,482,483,492,493,494,507,508,509],exit:[2,3,11,12,42,59,196,220,235,364,379,479,480,489,498,507],exlanatori:3,exp:[],expand:[],expans:[12,146,196,492,507],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,73,107,153,164,170,192,220,232,239,241,260,288,294,296,297,302,307,346,366,376,393,430,433,435,476,479,481,483,486,490,495,507],expens:[6,73,200,288,292,307,335,346,365,366,376,380,479],experi:[6,13,15,17,219,227,244,253,262,294,306,307,371,375,400,435,490,495],experienc:[6,12,252,253],experiment:[239,365,380,495],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,61,65,67,70,71,73,74,75,78,79,81,90,97,152,160,192,196,197,199,200,203,212,213,218,220,222,224,226,263,288,296,307,320,346,348,364,365,368,374,375,379,385,404,416,451,453,468,479,482,483,486,488,491,502,507,511],explan:[3,6,61,119,146,196,197,212,262,288,413,475,478,479,481,490],explanatori:[3,8,123,196,197,211,212,215,216,217,307,374,478,507],explantori:[3,303],explic:434,explicit:[6,9,11,22,45,79,91,119,122,166,180,204,205,226,314,315,350,370,382,383,386,391,393,404,406,417,427,467,475,478,482,485],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,73,115,118,149,159,162,170,172,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,216,219,226,233,238,240,242,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,296,297,299,307,309,310,326,328,329,335,339,343,349,351,352,354,355,358,360,374,380,381,382,384,387,388,389,390,391,392,393,394,395,396,397,399,400,403,404,405,407,408,409,410,411,412,413,417,418,419,420,421,422,423,424,425,426,427,431,433,435,436,437,438,440,445,446,453,454,455,456,457,458,459,461,462,463,464,465,466,467,469,471,472,473,481,483,484,490,491,493,494,500,502],explictli:[16,494],exploit:[15,17,290],explor:[124,171],expon:[3,298,300,404,409,412,426,434,446],exponenti:[91,441,462,469,473,495,507],expos:11,exposit:[209,400,403],express:[6,146,158,172,204,205,224,260,288,298,335,341,348,386,404,406,420,430,451,452,461,507],expressiont:386,extend:[],extens:[3,6,9,17,45,46,47,54,56,65,86,87,88,91,92,95,99,102,103,113,115,123,125,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,197,203,206,207,210,218,219,225,228,232,237,238,239,241,242,243,245,247,249,261,263,268,277,288,289,305,306,307,309,312,317,320,322,326,327,328,329,330,332,333,335,337,340,344,345,409,430,433,444,445,452,498,499],extent:[1,3,42,43,46,59,73,170,174,196,208,216,220,245,342,345,365,368,382,447,449,463,478,481,484],exterior:[3,6,170,344],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,63,73,107,115,116,118,124,147,149,150,151,153,155,158,159,160,161,162,164,165,171,172,173,174,178,200,215,220,222,263,295,296,297,307,323,373,374,377,378,399,410,413,416,430,435,478,479,481,484,493,502,507],extract:[3,6,11,13,36,65,91,113,121,123,125,204,205,300,375,396,407,430,452,479,486,498],extract_atom:11,extract_comput:[11,479],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,60,199,214,224,226,263,333,406,465,502],extrema:426,extrins:209,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[168,337],f_a:[464,465,466],f_ave:123,f_c:465,f_f:466,f_fix_id:297,f_foo:507,f_harm:333,f_i:[29,441],f_id:[6,73,123,125,196,197,203,211,212,213,214,215,216,217,218,258,325,337,499,507],f_ij:441,f_indent:218,f_int:332,f_j:29,f_jj:95,f_k:441,f_langevin:335,f_max:[297,302],f_msst:261,f_r:[248,464,465,466],f_sigma:386,f_solid:333,f_ss:6,f_temp:[],face:[3,6,59,61,73,160,170,174,208,216,217,340,342,343,344,345,368,409,430,445,481,484],face_threshold:170,facet:170,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,241,293,323,333,410,451,493],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,59,60,61,74,91,95,107,114,121,122,124,146,166,171,174,178,189,195,196,199,200,204,205,213,220,224,226,227,239,244,247,249,250,261,263,264,268,290,294,298,306,310,313,315,323,327,331,338,339,340,344,355,366,368,374,380,382,383,386,387,389,391,396,397,398,400,401,402,406,410,413,417,418,430,433,435,437,438,444,446,453,462,467,478,481,484,485,490,493,495,496,499,502,506,507],factori:[3,479],factoriz:365,fail:[3,9,11,12,61,176,224,227,365,373,375,398,444,479],failur:[127,448,480,507],fairli:[11,435,490,495],faken:75,falcon:244,fall:[3,6,200,215,293,479,507],fals:[90,346,348,451,507],fame:8,famili:[469,478],familiar:[0,11],fan:441,far:[3,6,12,17,59,61,63,90,196,197,200,201,220,221,222,224,227,263,288,306,307,323,340,351,355,371,375,376,468,479,481,486,499],farago:247,farrel:[464,466],farther:196,fashion:[6,8,42,73,172,200,203,204,205,210,216,220,222,227,239,241,245,260,261,263,265,266,267,268,269,270,271,279,282,283,284,285,286,296,297,299,307,312,316,322,325,333,335,339,340,341,343,345,375,413,427,484,493,507,510],fasolino:415,fast:[6,7,9,12,13,17,40,196,197,274,297,336,365,366,388,427,428,433,461,463,483,488,490,499,508,511],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,63,65,110,115,118,149,159,178,179,181,182,183,184,186,187,189,190,192,196,197,200,206,219,220,226,233,238,242,246,247,263,265,266,267,268,269,270,271,272,273,280,282,283,284,286,294,298,299,307,309,310,323,326,328,330,332,335,339,343,349,351,352,354,355,358,360,365,366,377,378,380,381,382,384,386,387,388,389,390,391,392,393,394,395,396,399,400,404,405,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,436,437,438,440,445,446,453,461,462,463,464,465,466,469,471,472,473,476,484,490,494,502],fastest:[1,6,14,17,160,216,335,336,380,478],fatal:[3,498],fault:[72,444],faulti:12,fava:409,favor:223,favorit:7,fbmc:330,fcc:[],fcm:[279,507],fdirect:230,fdotr:414,fdt:[],fdti:91,fe2:171,fe3:171,fe_md_boundari:209,featu:8,featur:[],fecr:404,feedback:[7,244],feel:[7,244,245,253,288,344,346,375,435],felling:432,felt:344,femtosecond:506,fene:[],fennel:[396,418],fep:[],ferguson:[6,178,493],fermi:[1,9,10,12,15,158,380,466],fermion:406,fernando:429,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,65,201,211,212,213,215,216,217,218,248,263,293,296,298,310,337,365,373,374,375,382,451,478,481,486,490,492,500,509],fewer:[1,3,11,15,16,63,253,490],fewest:3,fextern:237,feynman:290,fff:479,ffield:[395,407,443,444,451],ffmpeg:[3,12,199],ffplai:199,fft:[1,3,7,9,11,12,14,15,92,115,116,147,289,365,366,490],fft_inc:[12,366],fft_lib:12,fft_path:12,fftbench:[365,500],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:460,fictiti:[6,206,207,232,237,241,290,306,396,418,422,460],field1:[482,486],field2:482,field:[],fifth:[320,437],figur:[1,3,8,12,297,478,479],fij:399,file0:288,file1:[11,13,288,334,348,374,486,488,492],file2:[11,13,334,348,374,486,488,492],file:[],file_from:198,filen:374,filenam:[3,12,13,38,42,57,192,196,197,199,200,201,209,212,213,214,215,216,217,218,220,225,235,288,292,295,298,299,300,303,304,307,308,334,335,362,363,364,374,375,381,382,386,396,404,405,407,415,430,431,432,437,441,442,443,444,451,452,462,463,464,465,466,469,477,478,479,482,483,488,492,499,507,509,510,511],filennam:488,filep:[3,196,197,200,483,488,511],filepo:304,fill:[7,9,172,199,293,335,368,376,386,433,444,484],filter:[200,209],final_integr:8,final_integrate_respa:8,finchham:[6,154,398],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,63,73,75,91,123,175,192,201,210,223,224,235,236,239,262,288,293,294,302,306,371,373,375,376,396,413,418,422,430,451,461,463,502,507],find_custom:8,fine:[16,17,176,206,232,333,376,380,507],finer:[146,172,507],finest:365,finger:[172,195,260,484],finish:[6,11,42,220,348,362,364,365,377,379,380,468,486,507,508],finit:[],finni:[7,404,461],finvers:230,fiorin:[9,225],fire:[],firebrick:200,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,59,61,63,64,73,83,92,95,108,109,110,112,118,122,123,133,136,139,140,144,147,157,160,166,168,170,171,173,174,175,179,192,196,197,198,199,200,201,203,204,212,213,215,216,217,218,220,223,226,235,239,240,245,250,260,261,262,263,288,290,295,296,297,299,304,307,310,312,320,321,323,324,325,332,333,334,335,337,341,346,348,349,356,368,373,374,375,376,379,380,381,382,385,386,387,389,391,393,395,396,404,406,407,410,411,413,414,415,416,417,418,422,427,428,430,432,433,435,437,441,443,444,451,452,460,462,463,464,465,466,469,473,476,477,478,479,481,482,483,486,488,490,493,494,495,498,499,502,507,508,509,511],fischer:[6,9,19,20,178,391,493],fit:[3,6,9,12,38,57,192,235,306,323,382,386,415,430,435,456,463,465,489,507],five:[75,158,297,374,386,431,481,495],fix:[],fix_adapt:[166,205,426],fix_atom_swap:[],fix_bal:64,fix_deposit:[3,210,293],fix_eo:9,fix_evapor:210,fix_flux:209,fix_gcmc:[210,374],fix_gl:241,fix_gld:241,fix_grav:293,fix_id:[3,224,261,263,265,266,267,268,269,270,271,294,297],fix_modifi:[],fix_mov:[195,341],fix_nh:8,fix_npt:241,fix_nvt:[210,239],fix_poem:[3,6,9],fix_pour:[3,227],fix_qbmsst:9,fix_qeq:[3,395],fix_rattl:310,fix_reax_bond:443,fix_rigid:[253,385],fix_saed_vtk:308,fix_setforc:8,fix_shak:310,fix_shardlow:9,fix_srd:3,fix_styl:268,fix_temp_rescal:329,fixedpoint:[224,263],fixextern:237,fixid:209,fji:399,flag1:[229,378],flag2:[229,378],flag:[3,8,9,11,12,14,15,16,17,41,68,76,77,83,90,93,94,98,108,109,111,124,167,171,175,196,197,199,200,201,218,223,225,229,244,247,251,253,259,260,289,296,307,320,322,323,330,334,343,346,363,366,374,378,379,380,382,412,417,430,433,460,476,478,479,481,482,483,485,486,487,491,507],flag_buck:390,flag_coul:[390,399,422],flag_lj:[399,422],flagfld:[388,427,428],flaghi:[3,388,427,428],flaglog:[388,427,428],flagn:229,flagvf:[388,427,428],flat:[6,335,340,341,345],flavor:[2,7,12],fld:[],flen:383,flex_press:383,flexibl:[3,6,8,173,199,212,216,225,241,264,331,338,406,465,499],flip:[3,6,226,263,342,343],floor:507,flop:12,floralwhit:200,flow:[],fluctuat:[6,66,91,224,239,240,247,250,263,268,288,289,311,333,335,358,402],fluid:[],fluid_veloc:254,flush:[3,200,498],flux:[],flv:199,fly:[7,9,12,42,199,203,209,214,227,230,307,310,336,386,433,499,502],fmackai:9,fmag:228,fmass:290,fmax:[373,499],fmomentum:230,fmsec:[2,200,247,248,260,263,294,307,326,327,490,501,506,508],fname:364,fno:[9,12,16],fnorm:[373,499],fnpt:230,fnvt:230,foce:413,fock:383,focu:310,fogarti:[9,300,444],foil:[146,288,452],fold:[321,490],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,61,65,66,72,73,75,84,95,96,101,102,112,119,122,123,125,146,147,150,151,152,158,160,165,168,170,172,173,178,181,182,183,184,186,187,189,190,192,196,198,199,200,203,209,210,211,212,213,214,215,216,217,218,220,225,226,227,230,231,234,235,237,239,240,241,244,246,247,248,250,253,261,263,268,269,270,271,282,283,284,286,289,290,292,295,296,297,298,300,302,304,306,307,308,310,325,326,327,328,331,332,333,334,335,337,338,346,347,351,352,353,354,355,358,360,363,368,370,373,374,375,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,435,436,437,438,440,441,442,443,444,445,446,448,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,468,469,471,472,473,474,476,478,479,481,482,484,486,488,489,490,493,495,496,497,502,507,508,510],foo:[4,8,11,12,196,199,237,479,492,507],foot:6,footprint:[12,380],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:253,forcefield:[306,412],forcegroup:250,forcezero:371,ford:399,forestgreen:200,forev:73,forget:[248,502],forgiv:263,fork:[12,196],form:[2,3,6,8,12,19,22,45,55,65,68,76,77,79,83,91,93,94,96,98,108,109,111,122,146,147,166,167,176,180,200,203,204,205,222,240,241,247,249,253,260,284,289,300,302,306,307,335,340,344,349,350,353,358,370,372,374,375,382,383,386,393,401,402,404,406,408,412,413,417,429,430,432,433,437,438,441,443,444,445,451,452,453,461,463,464,465,466,472,475,478,479,481,486,491,498,502,507],formal:[6,80,82,95,240,241,247,263,290,323,331,451],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,70,79,180,192,196,197,198,199,200,201,212,215,216,217,218,220,222,235,289,292,296,298,300,303,307,308,319,334,335,346,347,350,370,374,375,381,382,386,393,404,407,417,430,432,442,443,444,446,452,463,469,470,478,479,481,482,483,486,497,498,499,507,509],former:[6,12,16,40,42,200,220,335,339,386,388,487,493,507],formerli:[7,13],formul:[1,9,41,66,147,206,232,247,263,284,298,300,306,310,334,365,382,386,404,406,409,430,440],formula:[2,3,6,7,13,21,22,37,45,55,56,72,75,91,93,94,95,99,101,102,111,118,124,125,147,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,171,172,177,179,180,191,195,196,204,205,206,207,212,213,214,215,218,219,226,232,242,243,245,247,248,260,288,289,295,304,309,317,321,323,326,327,328,337,340,343,345,346,348,349,350,352,359,368,374,382,383,385,386,391,392,393,394,399,400,404,405,409,410,411,412,414,417,418,420,421,422,424,425,427,428,430,434,435,436,445,446,453,461,462,463,464,465,466,469,471,472,477,481,484,491,498,499,506,507,508],forth:[1,6,11,12,13,14,15,379,479,484,488],fortran:[3,6,9,11,12,13,237,404,413,430,443,444],fortun:8,forward:[3,8,91,364,375,380],foster:[386,440,441],foul:175,found:[3,6,9,12,75,166,196,223,225,239,244,250,2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:335,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,40,41,42,57,59,61,64,73,82,83,90,91,108,109,136,168,173,174,192,195,196,197,199,200,201,204,205,208,209,213,220,222,223,224,226,233,235,239,240,244,245,246,247,248,250,255,259,260,261,262,263,268,277,289,290,291,296,297,302,305,306,307,309,311,322,323,325,330,332,333,334,335,336,337,340,341,342,343,345,346,348,365,369,372,373,375,382,383,399,400,403,433,442,443,444,451,463,476,478,479,481,483,484,486,488,489,491,495,496,499,502,507,508,509,511],initial_integr:8,initial_integrate_respa:8,initialis:442,initialt:335,inlclud:11,inlcud:[],inlin:479,inner2:[391,411],inner:[3,8,16,196,245,348,364,371,372,373,375,379,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,397,399,400,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,440,442,443,444,445,446,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,468,469,470,471,472,473,474,490,495,507],inner_distance_cutoff:412,innergroup:253,innermost:[38,57,73,378,463,490],innernod:253,innner:424,inordin:336,inorgan:[6,469],inp:[225,348,452,469],input1:[67,70,71,81,97,114,119,120,121,123,125,325],input2:[67,70,71,81,97,114,119,120,121,123,125,325],input:[],input_doubl:3,inquir:313,insensit:12,insert:[3,5,7,8,9,12,61,172,203,227,239,245,293,365,452,460,479,485,502],insid:[2,3,6,8,11,73,135,141,172,196,197,200,211,216,217,227,228,236,239,245,250,253,293,307,323,340,342,343,344,345,346,363,368,420,479,480,481,483,484,491,495,507],insight:[6,13],instabl:[250,399,450],instal:[],instanc:[6,9,11,204,225,241,342,408,413,435,441,479,502],instantan:[6,65,223,224,240,241,263,268,289,294,297,302,304,307,330,487,499],instanti:[6,11,12,209,413,478],instead:[1,3,6,8,11,12,13,17,18,41,42,61,63,65,72,73,94,108,123,150,154,176,192,196,197,205,212,215,216,217,218,220,224,225,239,247,250,253,254,289,295,305,307,325,343,363,365,366,369,376,380,389,390,404,417,419,426,430,433,476,484,488,495,497,502,507],institut:[9,244,292],instruct:[],insuffici:[3,6,12],insult:263,insur:[3,6,11,12,17,40,41,63,75,107,109,172,173,192,196,197,199,200,206,221,222,227,232,233,236,237,239,242,247,259,295,296,305,307,323,335,340,344,345,346,348,364,374,376,380,394,409,413,439,445,463,474,478,479,481,482,486,489,490,498,499,507,508],int_max:3,inteatom:10,integ:[3,6,8,11,12,40,41,43,66,70,72,73,112,119,121,123,125,146,170,172,175,176,178,182,183,187,192,195,196,199,200,210,212,216,217,221,222,223,227,229,237,239,240,241,244,247,248,249,250,289,292,293,296,297,302,307,323,325,327,330,334,335,354,365,368,388,400,402,403,416,430,443,444,448,450,452,476,478,479,480,481,489,490,491,495,498,507,508],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,214,240,442,481],intens:[1,3,6,9,65,68,76,77,90,93,94,95,98,108,109,110,111,118,120,122,123,124,125,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,167,168,169,171,203,212,213,215,216,217,218,220,221,222,223,231,236,243,253,261,263,268,304,307,308,323,331,335,337,338,498,499],intepol:507,inter:[14,18,43,63,64,152,175,176,196,223,247,249,262,299,307,365,375,386,491,502,507,509,511],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,34,37,40,41,43,45,51,53,55,56,59,63,65,67,71,74,79,81,91,92,96,97,112,113,114,116,118,121,122,128,129,130,131,133,134,135,136,137,138,139,141,142,143,144,146,147,148,150,151,165,166,170,173,174,175,176,177,178,180,184,185,188,191,196,197,203,204,205,221,222,223,238,239,244,245,247,249,253,277,288,290,292,293,298,300,306,307,314,315,323,324,330,335,339,340,341,344,345,350,351,352,353,355,357,359,365,366,373,374,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,444,445,446,448,450,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,476,479,481,483,485,486,490,491,493,498,499,502,509],interatom:[3,4,7,9,10,172,196,262,332,333,381,386,404,406,414,430,433,451,465,507],intercept:124,interchang:6,interconnect:18,interconvert:406,intereract:40,interesect:344,interest:[1,5,7,8,9,11,13,73,171,290,330,333,366,405,428,443,444,479,507],interf:380,interfac:[],interfer:[12,263,382],interg:[6,502],intergr:[490,494],interi:428,interior:[3,6,42,344,484],interlac:430,interleav:[6,172,489],intermedi:[6,12,61,199,262,288,358,375,479,480,489,493],intermix:476,intermolecular:382,intern:[],internal_element_set:209,internal_quadratur:209,internet:246,interpenetr:430,interpentr:[455,456,458],interpol:[6,15,38,57,105,192,199,200,209,235,250,288,365,366,375,386,435,444,457,463,464],interpret:[2,6,11,199,215,410,453,476,479,495,507],interrupt:297,intersect:[3,6,124,200,344,346,484],intersert:344,interspers:373,interstiti:[170,433],intertia:[3,98],interv:[3,6,95,198,213,247,263,297,302,303,315,451,457,476,495,507],intestieti:124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5,16,17,18,55,200,244,290,336,380,479,500],taskset:16,tatb:[4,303],tatom:502,tau:[3,161,214,247,248,250,263,294,307,326,327,332,333,335,501,506],tau_1:240,tau_k:240,tau_n_k:240,tb3:171,tbead:164,tbp:386,tchain:[263,264,268,284,285,307],tcl:302,tcom:248,tcsh:[11,12,393],tdamp:[247,263,264,268,307,326,327],tdephas:476,tdrude:[157,230,248,502],teal:200,tech:[7,9,13],technic:[6,7,9,250,300,323,444],techniqu:[6,7,9,91,203,224,261,297,307,339,342,366,435,463,502],technolgi:9,technolog:[9,14,19,244],tell:[2,6,11,12,37,56,191,203,289,359,376,443,444,461,479,483,502],telsa:17,temeperatur:11,temp:[],temp_drud:502,temp_eff:102,tempcom:[150,151,165],temper:[],temperar:290,temperatur:[],temperature_definit:209,tempfix:496,templ:[7,9,18],templat:[3,8,13,17,19,41,172,173,175,227,239,293,307,310,374,481],templeton2010:209,templeton2011:209,templeton:[9,209],tempor:240,temporari:[2,3,488],temporarili:[192,306,494,495],ten:14,tend:[29,263,288],tensil:[7,226],tensor:[3,6,8,65,86,87,93,94,95,98,111,118,133,136,137,138,139,142,143,144,146,147,148,149,150,151,152,153,154,155,156,158,159,160,161,162,163,164,165,224,250,253,263,264,268,292,294,307,338,365,366,374,406,427,428,433,448,450,499,507],tenth:[133,204,364],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,41,46,47,63,91,92,93,95,116,118,147,148,150,151,160,165,166,179,180,181,192,200,204,205,211,213,215,218,226,232,240,241,242,247,248,249,250,262,263,264,265,266,267,268,269,270,271,282,283,284,286,290,294,297,306,307,321,326,327,328,335,337,339,341,349,350,360,365,373,376,381,382,386,387,388,389,390,391,392,394,395,396,397,398,399,400,401,402,404,405,406,407,409,410,411,418,422,425,426,427,428,430,431,432,433,435,436,438,445,451,460,462,464,465,466,469,472,490,491,493,499,502],termin:[124,263,373,375,448,450,480,489],termostat:327,terrel:372,terri:7,tersoff:[],tersoff_1:[464,465,466],tersoff_2:[464,465,466],tersoff_mod:465,tertiari:184,tessel:[9,170],test:[],test_descriptor_str:3,testf:192,testu:192,tether:[6,305,312,320,322,333,408],tetot:[9,451],tex:8,texa:440,texas_holdem:306,text:[2,3,4,6,7,8,12,13,38,42,57,192,196,197,199,200,203,209,212,213,214,215,216,217,218,220,225,235,244,295,334,335,347,366,368,375,404,407,417,430,452,463,477,481,482,498,507,509],textur:17,tfac_insert:239,tfactor:[3,200],tfinal:507,tfix:306,tflag:199,tfmc:[],th4:171,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,40,41,42,43,57,59,60,61,63,65,70,73,78,90,92,96,110,112,114,118,121,122,125,147,170,173,174,175,181,192,195,196,198,200,203,208,210,212,215,216,217,218,220,221,222,223,224,226,227,228,231,235,236,239,240,241,242,245,246,247,250,261,288,289,293,294,295,296,297,298,300,302,305,306,307,308,311,312,313,319,320,321,323,327,328,330,331,335,338,339,340,341,342,343,344,345,346,348,365,366,371,372,373,374,375,376,377,380,385,386,387,389,390,391,404,406,409,410,416,427,428,430,435,443,444,445,451,453,460,461,462,463,466,468,470,472,473,476,477,478,479,481,482,483,484,485,486,489,490,493,495,496,498,507,508,509],thank:[244,464,466],thb:444,thb_cutoff:444,thb_cutoff_sq:444,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,42,43,44,46,47,48,49,50,52,54,55,56,57,59,61,63,65,66,68,70,72,73,76,77,83,86,88,91,92,93,94,95,98,108,109,111,113,114,115,118,120,121,122,123,125,146,149,150,152,154,155,158,159,165,167,169,170,172,174,175,176,178,179,181,182,183,184,186,187,189,190,191,192,196,197,199,200,203,204,205,206,208,211,212,213,215,216,217,218,219,220,221,222,223,224,226,227,232,233,238,239,240,242,243,244,247,248,250,253,260,263,265,266,267,268,269,270,271,272,273,274,275,280,282,283,284,286,292,293,294,295,296,298,299,306,307,308,309,310,323,324,326,327,328,330,334,335,337,338,339,341,343,344,346,347,348,349,351,352,353,354,355,358,359,360,363,365,366,368,370,372,373,374,375,376,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,398,399,400,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,436,437,438,440,441,443,444,445,446,451,452,453,460,461,462,463,464,465,466,467,468,469,470,471,472,473,477,479,481,482,483,484,485,486,490,491,493,494,499,502,507,509,510],them:[1,2,3,6,7,8,9,11,12,13,14,17,40,41,42,55,61,73,95,108,113,120,123,125,148,174,179,196,199,200,201,211,212,213,215,216,217,218,220,223,224,226,236,244,247,248,259,263,265,266,267,268,269,270,271,282,283,286,288,294,296,304,305,306,307,310,323,326,327,328,330,334,335,337,341,342,343,345,346,349,366,368,374,375,376,380,381,386,393,404,407,409,413,416,435,445,453,468,476,479,481,488,493,496,502,507,508],themselv:[6,9,11,175,204,205,220,248,365,366,375,377,381,386,396,404,426,430,431,432,452,507],theor:330,theorem:[240,247,311,386,402],theoret:[110,244,297,462],theori:[3,6,9,12,41,146,209,225,241,263,289,365,366,386,433,472,495],thereaft:[73,255,291,307,331,338,479],therebi:[336,427,428],therefor:[3,6,12,66,91,157,230,239,248,250,310,330,366,398,442,444,462,467,490,502],therein:[6,430],thereof:91,thermal:[],thermo:[],thermo_modifi:[],th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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","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/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 dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/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 eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<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 distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<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":221,"default":[37,40,41,56,59,60,61,63,64,73,91,92,96,107,108,110,112,113,124,128,129,146,152,160,161,165,171,172,175,177,191,194,195,196,197,199,200,201,202,204,205,206,208,209,210,212,216,217,218,221,222,224,225,226,227,231,236,239,240,245,247,248,249,250,251,253,258,261,263,264,268,284,285,289,290,293,294,295,296,297,299,302,304,305,307,308,323,325,330,331,332,333,336,338,340,342,346,359,363,365,366,368,369,371,372,374,376,377,378,380,383,386,388,406,427,428,433,435,443,444,460,461,476,477,478,481,482,484,486,488,489,490,493,495,497,498,499,500,501,506,508,509,510],"function":507,"long":[214,387,389,390,391,392,396,398,399,418,422,426,438,446],"new":8,"static":12,acceler:1,ackland:66,acknowledg:7,adapt:[204,205],addforc:206,addit:[12,13],addtorqu:207,adiabat:6,adjust_dt:313,adp:381,airebo:382,alloi:404,amber2lmp:13,amber:6,angl:[8,67],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:68,append:208,arrai:6,aspher:[6,9,86,150,265,269,273,274,282],atc:[9,209],atom:[6,7,8,66,69,72,73,74,75,78,79,80,82,83,85,89,96,100,101,104,105,106,112,116,117,119,146,147,170,208,210,211,296,507],atom_modifi:40,atom_styl:41,attract:5,aug:[],aveforc:219,awpmd:[9,383],balanc:[42,220],barostat:6,basal:69,beck:384,berendsen:[294,326],between:6,binary2txt:13,bodi:[6,8,9,43,70,151,266,270,275,283,385],bond:[8,13,71,221,222,223,303],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,58],bop:386,born:[387,398],boundari:[7,59],box:[6,60,224],brownian:388,buck:[389,390,398,429],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:72,ch2lmp:13,chain:13,change_box:61,charmm:[6,20,178,391,426],chunk:[6,68,73,77,94,98,109,111,120,152,167,169,212],citat:7,class2:[9,21,44,179,349,392],clear:62,cluster:74,cmm:9,cna:75,code:6,coeffici:6,colloid:[9,340,394,472],colvar:[9,13,225],com:[76,77,153],comb3:395,comb:[299,395],come:5,comm_modifi:63,comm_styl:64,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,507],compute_modifi:107,condit:7,conduct:[6,331],conserv:401,constant:[6,507],constraint:7,contact:[78,126],contact_radiu:[],coord:79,core:6,coreshel:9,correl:[213,214],cosin:[23,24,25,26,27,28,181],cossq:351,coul:[387,389,390,391,392,396,397,398,411,418,422,426,438,446],coupl:6,creat:222,create_atom:172,create_bond:173,create_box:174,createatom:13,creation:7,csld:327,csvr:327,cubic:420,cuda:[9,14,115,118,149,159,206,219,233,238,242,263,272,309,310,326,328,339,387,389,391,392,404,410,411,418,419,421,424,436,462,464],custom:[8,196,197],cut:[50,383,389,392,396,399,406,408,418,419,426,434,438],cvff:352,damag:[80,127],data2xmovi:13,data:6,databas:13,deby:[396,418],dec:[],defgrad:133,deform:[155,156,226],delete_atom:175,delete_bond:176,delta:24,deposit:227,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],diagnost:7,diel:397,dielectr:177,diffract:9,diffus:6,dihedr:[8,81],dihedral_coeff:180,dihedral_styl:[2,178,179,181,182,183,184,185,186,187,188,189,190,191,192,193],dilat:82,dimens:194,dipol:[6,9,29,399],direct:230,directori:4,discuss:6,disp:6,displac:[83,90],displace_atom:195,distanc:353,distribut:[7,12],document:0,dpd:[9,84,85,400,401,402],drag:228,dreid:[6,412],drude:[6,9,157,229,230,248],dsf:[396,418],dsmc:403,dump:[6,8,196,197,198,199,201],dump_modifi:200,dynam:298,eam:[13,404],echo:202,edip:405,eff:[9,13,101,102,156,158,163,249,264,276,285,329,406],efield:232,eim:407,elast:6,emac:13,energi:[129,402],enforce2d:233,ensembl:7,erot:[86,87,88,89],error:[3,128],evapor:236,event:90,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,503,504,505,506,507,508,509,510,511],exp:[27,181],expand:[47,421],extend:[8,11],extern:237,fcc:288,fdt:402,featur:[7,8,507],feb:[],fene:[46,47],fep:[9,13,91,205],field:[6,7],file:6,finit:6,fire:298,fix:[2,6,8,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,507],fix_modifi:[204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345],fld:[],flow:6,fluid:250,flux:[95,148],forc:[6,7,148,324],fourier:[30,31,182,354],freez:238,from:[6,11],futur:5,gauss:408,gaybern:409,gcmc:239,gener:[1,6,7,13],get:12,gld:240,gle:241,global:6,gpu:[9,15,384,387,389,391,392,394,396,399,400,404,408,409,411,418,419,420,421,434,436,445,446,453,462,463,464,471,472,473],gran:[341,410],granular:[6,9],graviti:242,gromac:411,group2ndx:347,group:[92,346,507],gyrat:[93,94],h5md:[9,196,198],harmon:[32,48,49,50,183,186,340,355,437],hbond:412,heat:[95,148,243],heatconduct:454,helix:184,hertz:[410,447],hexord:96,histo:215,histori:[5,410],hook:410,hourglass:128,hourglass_error:[],how:6,hybrid:[33,51,185,356,413],idealga:455,imag:[196,199],imd:244,implicit:391,improp:[8,97],improper_coeff:350,improper_styl:[2,349,351,352,353,354,355,356,357,358,359,360,361],includ:362,inclus:8,indent:245,indic:0,individu:2,induc:6,inertia:98,info:[0,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,363],input:[2,6,8],instal:11,instruct:[],integr:[6,7],integrate_tlsph:314,integrate_ulsph:315,intel:[9,16,20,32,48,178,183,189,263,272,273,284,352,355,389,391,409,418,462,464],interfac:[6,11],intern:129,internal_energi:[],introduct:7,invers:230,ipi:246,ipp:13,jan:[],jul:[],jump:364,kate:13,keyword:[435,507],kim:[9,414],kokko:[9,17],kspace:[2,8,9,336],kspace_modifi:365,kspace_styl:[6,366],label:367,lammp:[0,1,2,6,7,8,11,12],langevin:[247,248,249],lattic:368,lcbop:415,lennard:429,librari:[6,11,12],limit:[277,328],line:[12,278,416],linear:[425,436],lineforc:255,list:[2,417],lj1043:340,lj126:340,lj93:340,lj96:419,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,67,70,71,81,97,114,121],log:369,lowercas:4,lubric:427,lubricateu:428,make:12,manybodi:9,mar:0,mass:370,math:507,matlab:13,mdf:429,meam:[9,430,431,432],measur:1,mesh:140,meso:[104,105,106,256,257],meso_:[],meso_rho:[],meso_t:[],messag:3,mgpt:[9,433],micelle2d:13,mie:434,min_modifi:371,min_styl:372,minim:[8,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,230,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,373],misc:9,mod:[335,465],model:[6,7],modifi:8,molecul:[9,374],molfil:[9,196,201],moltempl:13,momentum:[251,259],morri:459,mors:[52,412,436],move:260,move_tri_surf:316,movi:[196,199],mpi:11,mpiio:9,msd:[108,109,110],msi2lmp:13,msm:[387,389,391,396,418],msst:261,multi:[6,7,186],multipl:6,nb3b:437,ndx2group:347,neb:[262,375],neigh:[135,141],neigh_modifi:376,neighbor:377,nemd:6,newton:378,next:379,nharmon:187,noforc:[274,279],non:[6,7],none:[34,53,188,357,439],nongauss:110,nonlinear:54,nph:[263,264,265,266,267,307],nphug:268,npt:[263,264,269,270,271,307],num:[135,141],numer:507,nve:[272,273,274,275,276,277,278,279,280,281,307],nvt:[263,264,282,283,284,285,286,307],omega:111,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,44,46,47,48,49,50,52,54,55,57,178,179,181,182,183,184,186,187,189,190,192,242,263,265,267,268,269,271,272,280,282,284,286,299,349,351,352,354,355,358,360,381,382,384,387,388,389,390,391,392,394,395,396,397,399,400,404,407,408,409,410,411,412,413,418,419,420,421,422,423,424,425,426,427,431,432,436,437,438,440,445,446,453,462,463,464,465,466,469,471,472,473],onewai:287,open:7,oper:507,opl:189,opt:[9,19,391,404,418,422,436],optim:1,option:[6,8,12],orient:288,orientord:112,orthogon:6,other:6,output:[6,7,8,12,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224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