From cd078405e003285ef2bfab002add4723089a07d8 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 21 Oct 2015 18:52:59 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14131 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 900 ++++++++++++++++++------------------ doc/Manual.html.html | 4 +- doc/Manual.txt | 4 +- doc/Section_accelerate.html | 53 ++- doc/Section_accelerate.txt | 40 +- doc/Section_commands.html | 6 +- doc/Section_commands.txt | 2 +- doc/Section_packages.html | 215 ++++++--- doc/Section_packages.txt | 126 ++++- doc/Section_start.html | 78 ++-- doc/Section_start.txt | 76 ++- doc/accelerate_intel.html | 350 +++++++------- doc/accelerate_intel.txt | 344 +++++++------- doc/accelerate_kokkos.html | 164 +++---- doc/accelerate_kokkos.txt | 164 ++++--- doc/accelerate_omp.html | 141 +++--- doc/accelerate_omp.txt | 139 +++--- doc/accelerate_opt.html | 53 +-- doc/accelerate_opt.txt | 49 +- doc/genindex.html | 4 + doc/pair_hybrid.html | 14 +- doc/pair_hybrid.txt | 15 +- doc/pair_style.html | 1 + doc/pair_vashishta.html | 461 ++++++++++++------ doc/searchindex.js | 2 +- 25 files changed, 1858 insertions(+), 1547 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index e1682ec3aa..dd72c5f5fa 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,478 +1,454 @@ - - - -LAMMPS Users Manual - - - - - - - - - -
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
+ + + + + + + + + LAMMPS Documentation — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ + + - - -
- -

- -

LAMMPS Documentation -

-

5 Oct 2015 version -

-

Version info: -

-

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

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

+

LAMMPS Documentation

+
+

10 Aug 2015 version

+
+
+

Version info:

+

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

-
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. - -
  • If you browse the HTML doc pages included in your tarball, they -describe the version you have. - -
  • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. - -
  • There is also a Developer.pdf file in the doc +the first page of the manual (this page).

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

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

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS.

    • +
+

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

+

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

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL).

+

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

- - - - -
- -

The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses.

+
+

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

-

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

-

PDF file of the entire manual, generated by -htmldoc -

-

-

-
  1. -Introduction - - -
  2. Getting started - - -
  3. Commands - - -
  4. Packages - - -
  5. Accelerating LAMMPS performance - - -
  6. How-to discussions - - -
  7. Example problems - -
  8. Performance & scalability - -
  9. Additional tools - -
  10. Modifying & extending LAMMPS - - -
  11. Python interface - - -
  12. Errors - - -
  13. Future and history - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +we can improve the LAMMPS documentation.

+

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

+

PDF file of the entire manual, generated by +htmldoc

+
+ +
+
+
+
+

Indices and tables

+ +
+ + +
+
+ + +
+
+ +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/Manual.html.html b/doc/Manual.html.html index 25313b5990..86ebc9f291 100644 --- a/doc/Manual.html.html +++ b/doc/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

25 Sep 2015 version +

5 Oct 2015 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index 06b7a0bf0b..f47482fdf2 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -5 Oct 2015 version :c,h4 +10 Aug 2015 version :c,h4 Version info: :h4 diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index 0737f4bea1..ca0cc25882 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -275,7 +275,8 @@ standard non-accelerated versions. Some require appropriate hardware to be present on your system, e.g. GPUs or Intel Xeon Phi coprocessors.

All of these commands are in packages provided with LAMMPS. An -overview of packages is give in Section packages. These are the accelerator packages +overview of packages is give in Section packages.

+

These are the accelerator packages currently in LAMMPS, either as standard or user packages:

@@ -303,6 +304,30 @@ currently in LAMMPS, either as standard or user packages:

+

Inverting this list, LAMMPS currently has acceleration support for +three kinds of hardware, via the listed packages:

+ ++++ + + + + + + + + + + + +
Many-core CPUsUSER-INTEL, KOKKOS, USER-OMP, OPT packages
NVIDIA GPUsUSER-CUDA, GPU, KOKKOS packages
Intel PhiUSER-INTEL, KOKKOS packages
+

Which package is fastest for your hardware may depend on the size +problem you are running and what commands (accelerated and +non-accelerated) are invoked by your input script. While these doc +pages include performance guidelines, there is no substitute for +trying out the different packages appropriate to your hardware.

Any accelerated style has the same name as the corresponding standard style, except that a suffix is appended. Otherwise, the syntax for the command that uses the style is identical, their functionality is @@ -345,7 +370,7 @@ listed above:

install the accelerator package | make yes-opt, make yes-user-intel, etc |
-
only for USER-INTEL, KOKKOS, USER-OMP packages |
+
only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
@@ -355,15 +380,14 @@ listed above:

- - -
re-build LAMMPS make machine
run a LAMMPS simulationlmp_machine < in.script
-
run a LAMMPS simulation | lmp_machine < in.script |
+
re-build LAMMPS | make machine |
+
mpirun -np 32 lmp_machine -in in.script |
+
only for USER-CUDA and KOKKOS packages |
package command, <br> @@ -376,8 +400,8 @@ only if defaults need to be changed |
-

The first 4 steps can be done as a single command, using the -src/Make.py tool. The Make.py tool is discussed in Section 2.4 of the manual, and its use is +

Note that the first 4 steps can be done as a single command, using the +src/Make.py tool. This tool is discussed in Section 2.4 of the manual, and its use is illustrated in the individual accelerator sections. Typically these steps only need to be done once, to create an executable that uses one or more accelerator packages.

@@ -389,12 +413,13 @@ script.

Warning

With a few exceptions, you can build a single LAMMPS -executable with all its accelerator packages installed. Note that the -USER-INTEL and KOKKOS packages require you to choose one of their -options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda, -or Phi for KOKKOS. Here are the exceptions; you cannot build a single -executable with:

+executable with all its accelerator packages installed. Note however +that the USER-INTEL and KOKKOS packages require you to choose one of +their hardware options when building for a specific platform. +I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP, +Cuda, or Phi option for the KOKKOS package.

+

These are the exceptions. You cannot build a single executable with:

-
-

2.4. Building LAMMPS via the Make.py script

+
+

2.4. Building LAMMPS via the Make.py tool

The src directory includes a Make.py script, written in Python, which can be used to automate various steps of the build process. It is particularly useful for working with the accelerator packages, as well diff --git a/doc/Section_start.txt b/doc/Section_start.txt index dfd6caaddc..744229991a 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -628,10 +628,6 @@ One way to do this is install and use cygwin to build LAMMPS with a standard unix style make program, just as you would on a Linux box; see src/MAKE/MACHINES/Makefile.cygwin. -The other way to do this is using Visual Studio and project files. -See the src/WINDOWS directory and its README.txt file for instructions -on both a basic build and a customized build with pacakges you select. - :line 2.3 Making LAMMPS with optional packages :h4,link(start_3) @@ -670,41 +666,43 @@ package. You can also type lmp_machine -h :pre to run your executable with the optional "-h command-line -switch"_#start_7 for "help", which will list the styles and commands -known to your executable. +switch"_#start_7 for "help", which will simply list the styles and +commands known to your executable, and immediately exit. There are two kinds of packages in LAMMPS, standard and user packages. More information about the contents of standard and user packages is given in "Section_packages"_Section_packages.html of the manual. The difference between standard and user packages is as follows: -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means we will answer questions about them, debug and fix them if -necessary, and keep them compatible with future changes to LAMMPS. +Standard packages, such as molecule or kspace, are supported by the +LAMMPS developers and are written in a syntax and style consistent +with the rest of LAMMPS. This means we will answer questions about +them, debug and fix them if necessary, and keep them compatible with +future changes to LAMMPS. -User packages have been contributed by users, and always begin with -the user prefix. If they are a single command (single file), they are -typically in the user-misc package. Otherwise, they are a a set of -files grouped together which add a specific functionality to the code. +User packages, such as user-atc or user-omp, have been contributed by +users, and always begin with the user prefix. If they are a single +command (single file), they are typically in the user-misc package. +Otherwise, they are a a set of files grouped together which add a +specific functionality to the code. User packages don't necessarily meet the requirements of the standard packages. If you have problems using a feature provided in a user -package, you will likely need to contact the contributor directly to -get help. Information on how to submit additions you make to LAMMPS -as a user-contributed package is given in "this -section"_Section_modify.html#mod_15 of the documentation. +package, you may need to contact the contributor directly to get help. +Information on how to submit additions you make to LAMMPS as single +files or either a standard or user-contributed package are given in +"this section"_Section_modify.html#mod_15 of the documentation. -Some packages (both standard and user) require additional libraries. -See more details below. +Some packages (both standard and user) require additional auxiliary +libraries when building LAMMPS. See more details below. :line [{Including/excluding packages:}] :link(start_3_2) -To use or not use a package you must include or exclude it before -building LAMMPS. From the src directory, this is typically as simple -as: +To use (or not use) a package you must include it (or exclude it) +before building LAMMPS. From the src directory, this is typically as +simple as: make yes-colloid make g++ :pre @@ -715,10 +713,10 @@ make no-manybody make g++ :pre IMPORTANT NOTE: You should NOT include/exclude packages and build -LAMMPS in a single make command by using multiple targets, e.g. make +LAMMPS in a single make command using multiple targets, e.g. make yes-colloid g++. This is because the make procedure creates a list of source files that will be out-of-date for the build if the package -configuration changes during the same command. +configuration changes within the same command. Some packages have individual files that depend on other packages being included. LAMMPS checks for this and does the right thing. @@ -777,34 +775,34 @@ options. [{Packages that require extra libraries:}] :link(start_3_3) A few of the standard and user packages require additional auxiliary -libraries. Most of them are provided with LAMMPS, in which case they -must be compiled first, before LAMMPS is built if you wish to include +libraries. Many of them are provided with LAMMPS, in which case they +must be compiled first, before LAMMPS is built, if you wish to include that package. If you get a LAMMPS build error about a missing library, this is likely the reason. See the "Section_packages"_Section_packages.html doc page for a list of packages that have these kinds of auxiliary libraries. The lib directory in the distribution has sub-directories with package -names that correspond to the needed auxiliary libs, e.g. lib/reax. +names that correspond to the needed auxiliary libs, e.g. lib/gpu. Each sub-directory has a README file that gives more details. Code for most of the auxiliary libraries is included in that directory. Examples are the USER-ATC and MEAM packages. A few of the lib sub-directories do not include code, but do include -instructions and sometimes scripts that automate the process of +instructions (and sometimes scripts) that automate the process of downloading the auxiliary library and installing it so LAMMPS can link -to it. Examples are the KIM and VORONOI and USER-MOLFILE and USER-SMD +to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD packages. The lib/python directory (for the PYTHON package) contains only a choice of Makefile.lammps.* files. This is because no auxiliary code or libraries are needed, only the Python library and other system libs -that already available on your system. However, the Makefile.lammps -file is needed to tell the LAMMPS build which libs to use and where to -find them. +that should already available on your system. However, the +Makefile.lammps file is needed to tell LAMMPS which libs to use and +where to find them. For libraries with provided code, the sub-directory README file -(e.g. lib/reax/README) has instructions on how to build that library. +(e.g. lib/atc/README) has instructions on how to build that library. Typically this is done by typing something like: make -f Makefile.g++ :pre @@ -830,10 +828,10 @@ fail. As explained in the lib/package/README files, the settings in Makefile.lammps are used to specify additional system libraries and their locations so that LAMMPS can build with the auxiliary library. -For example, if the MEAM or REAX packages are used, the auxiliary -libraries consist of F90 code, built with a Fortran complier. To link -that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS -is built with, typically requires additional Fortran-to-C libraries be +For example, if the MEAM package is used, the auxiliary library +consists of F90 code, built with a Fortran complier. To link that +library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is +built with, typically requires additional Fortran-to-C libraries be included in the link. Another example are the BLAS and LAPACK libraries needed to use the USER-ATC or USER-AWPMD packages. @@ -936,7 +934,7 @@ CCFLAGS: add -restrict :ul :line -2.4 Building LAMMPS via the Make.py script :h4,link(start_4) +2.4 Building LAMMPS via the Make.py tool :h4,link(start_4) The src directory includes a Make.py script, written in Python, which can be used to automate various steps of the build process. It is diff --git a/doc/accelerate_intel.html b/doc/accelerate_intel.html index 16722b968b..1977931d96 100644 --- a/doc/accelerate_intel.html +++ b/doc/accelerate_intel.html @@ -128,216 +128,182 @@

5.USER-INTEL package

The USER-INTEL package was developed by Mike Brown at Intel -Corporation. It provides a capability to accelerate simulations by -offloading neighbor list and non-bonded force calculations to Intel(R) -Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package). -Additionally, it supports running simulations in single, mixed, or -double precision with vectorization, even if a coprocessor is not -present, i.e. on an Intel(R) CPU. The same C++ code is used for both -cases. When offloading to a coprocessor, the routine is run twice, -once with an offload flag.

-

The USER-INTEL package can be used in tandem with the USER-OMP -package. This is useful when offloading pair style computations to -coprocessors, so that other styles not supported by the USER-INTEL -package, e.g. bond, angle, dihedral, improper, and long-range -electrostatics, can run simultaneously in threaded mode on the CPU -cores. Since less MPI tasks than CPU cores will typically be invoked -when running with coprocessors, this enables the extra CPU cores to be -used for useful computation.

-

If LAMMPS is built with both the USER-INTEL and USER-OMP packages -installed, this mode of operation is made easier to use, with the -“-suffix hybrid intel omp” command-line switch -or the suffix hybrid intel omp command will both set a -second-choice suffix to “omp” so that styles from the USER-OMP package will be -used if available, after first testing if a style from the USER-INTEL -package is available.

-

When using the USER-INTEL package, you must choose at build time whether the -binary will support offload to Xeon Phi coprocessors. Binaries supporting -offload can still be run in CPU-only (host-only) mode.

-

Here is a quick overview of how to use the USER-INTEL package -for CPU-only acceleration:

-
    -
  • specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost
    • -
  • specify -openmp with LINKFLAGS in your Makefile.machine
    • -
  • include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS
    • -
  • specify how many OpenMP threads per MPI task to use
    • -
  • use USER-INTEL and (optionally) USER-OMP styles in your input script
    • -
-

Note that many of these settings can only be used with the Intel -compiler, as discussed below.

-

Using the USER-INTEL package to offload work to the Intel(R) -Xeon Phi(TM) coprocessor is the same except for these additional -steps:

-
    -
  • add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine
    • -
  • add the flag -offload to LINKFLAGS in your Makefile.machine
    • -
-

The latter two steps in the first case and the last step in the -coprocessor case can be done using the “-pk intel” and “-sf intel” -command-line switches respectively. Or -the effect of the “-pk” or “-sf” switches can be duplicated by adding -the package intel or suffix intel -commands respectively to your input script.

+Corporation. It provides two methods for accelerating simulations, +depending on the hardware you have. The first is acceleration on +Intel(R) CPUs by running in single, mixed, or double precision with +vectorization. The second is acceleration on Intel(R) Xeon Phi(TM) +coprocessors via offloading neighbor list and non-bonded force +calculations to the Phi. The same C++ code is used in both cases. +When offloading to a coprocessor from a CPU, the same routine is run +twice, once on the CPU and once with an offload flag.

+

Note that the USER-INTEL package supports use of the Phi in “offload” +mode, not “native” mode like the KOKKOS package.

+

Also note that the USER-INTEL package can be used in tandem with the +USER-OMP package. This is useful when +offloading pair style computations to the Phi, so that other styles +not supported by the USER-INTEL package, e.g. bond, angle, dihedral, +improper, and long-range electrostatics, can run simultaneously in +threaded mode on the CPU cores. Since less MPI tasks than CPU cores +will typically be invoked when running with coprocessors, this enables +the extra CPU cores to be used for useful computation.

+

As illustrated below, if LAMMPS is built with both the USER-INTEL and +USER-OMP packages, this dual mode of operation is made easier to use, +via the “-suffix hybrid intel omp” command-line switch or the suffix hybrid intel omp command. Both set a second-choice suffix to “omp” so +that styles from the USER-INTEL package will be used if available, +with styles from the USER-OMP package as a second choice.

+

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

+
use an Intel compiler
+use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost
+make yes-user-intel yes-user-omp     # including user-omp is optional
+make mpi                             # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi
+make intel_cpu                       # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper
+Make.py -v -p intel omp -intel cpu -a file mpich_icc   # or one-line build via Make.py for MPICH
+Make.py -v -p intel omp -intel cpu -a file ompi_icc    # or for OpenMPI
+Make.py -v -p intel omp -intel cpu -a file intel_cpu   # or for Intel MPI wrapper
+
+
+
lmp_machine -sf intel -pk intel 0 omp 16 -in in.script    # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP
+mpirun -np 32 lmp_machine -sf intel -in in.script         # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP
+lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script         # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP
+mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script      # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP
+
+
+

Here is a quick overview of how to use the USER-INTEL package for the +same CPUs as above (16 cores/node), with an additional Xeon Phi(TM) +coprocessor per node. More details follow.

+
Same as above for building, with these additions/changes:
+add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine
+add the flag -offload to LINKFLAGS in Makefile.machine
+for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi"
+
+
+
mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script                 # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script            # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP
+mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP
+
+

Required hardware/software:

+

Your compiler must support the OpenMP interface. Use of an Intel(R) +C++ compiler is recommended, but not required. However, g++ will not +recognize some of the settings listed above, so they cannot be used. +Optimizations for vectorization have only been tested with the +Intel(R) compiler. Use of other compilers may not result in +vectorization, or give poor performance.

+

The recommended version of the Intel(R) compiler is 14.0.1.106. +Versions 15.0.1.133 and later are also supported. If using Intel(R) +MPI, versions 15.0.2.044 and later are recommended.

To use the offload option, you must have one or more Intel(R) Xeon Phi(TM) coprocessors and use an Intel(R) C++ compiler.

-

Optimizations for vectorization have only been tested with the -Intel(R) compiler. Use of other compilers may not result in -vectorization or give poor performance.

-

Use of an Intel C++ compiler is recommended, but not required (though -g++ will not recognize some of the settings, so they cannot be used). -The compiler must support the OpenMP interface.

-

The recommended version of the Intel(R) compiler is 14.0.1.106. -Versions 15.0.1.133 and later are also supported. If using Intel(R) -MPI, versions 15.0.2.044 and later are recommended.

Building LAMMPS with the USER-INTEL package:

-

You can choose to build with or without support for offload to a -Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a -coprocessor, the same binary can be used on nodes with and without -coprocessors installed. However, if you do not have coprocessors -on your system, building without offload support will produce a -smaller binary.

-

You can do either in one line, using the src/Make.py script, described -in Section 2.4 of the manual. Type -“Make.py -h” for help. If run from the src directory, these commands -will create src/lmp_intel_cpu and lmp_intel_phi using -src/MAKE/Makefile.mpi as the starting Makefile.machine:

-
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi
-Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi
-
-
-

Note that this assumes that your MPI and its mpicxx wrapper -is using the Intel compiler. If it is not, you should -leave off the “-cc icc” switch.

-

Or you can follow these steps:

-
cd lammps/src
-make yes-user-intel
-make yes-user-omp (if desired)
-make machine
-
-
-

Note that if the USER-OMP package is also installed, you can use -styles from both packages, as described below.

-

The Makefile.machine needs a “-fopenmp” flag for OpenMP support in -both the CCFLAGS and LINKFLAGS variables. You also need to add --DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.

+

The lines above illustrate how to include/build with the USER-INTEL +package, for either CPU or Phi support, in two steps, using the “make” +command. Or how to do it with one command via the src/Make.py script, +described in Section 2.4 of the manual. +Type “Make.py -h” for help. Because the mechanism for specifing what +compiler to use (Intel in this case) is different for different MPI +wrappers, 3 versions of the Make.py command are shown.

+

Note that if you build with support for a Phi coprocessor, the same +binary can be used on nodes with or without coprocessors installed. +However, if you do not have coprocessors on your system, building +without offload support will produce a smaller binary.

+

If you also build with the USER-OMP package, you can use styles from +both packages, as described below.

+

Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must +include “-fopenmp”. Likewise, if you use an Intel compiler, the +CCFLAGS setting must include “-restrict”. For Phi support, the +“-DLMP_INTEL_OFFLOAD” (CCFLAGS) and “-offload” (LINKFLAGS) settings +are required. The other settings listed above are optional, but will +typically improve performance. The Make.py command will add all of +these automatically.

If you are compiling on the same architecture that will be used for -the runs, adding the flag -xHost to CCFLAGS will enable -vectorization with the Intel(R) compiler. Otherwise, you must -provide the correct compute node architecture to the -x option -(e.g. -xAVX).

-

In order to build with support for an Intel(R) Xeon Phi(TM) -coprocessor, the flag -offload should be added to the LINKFLAGS line -and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.

-

Example makefiles Makefile.intel_cpu and Makefile.intel_phi are -included in the src/MAKE/OPTIONS directory with settings that perform -well with the Intel(R) compiler. The latter file has support for -offload to coprocessors; the former does not.

-

Notes on CPU and core affinity:

-

Setting core affinity is often used to pin MPI tasks and OpenMP -threads to a core or group of cores so that memory access can be -uniform. Unless disabled at build time, affinity for MPI tasks and -OpenMP threads on the host will be set by default on the host -when using offload to a coprocessor. In this case, it is unnecessary -to use other methods to control affinity (e.g. taskset, numactl, -I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script -with the no_affinity option to the package intel -command or by disabling the option at build time (by adding --DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile). -Disabling this option is not recommended, especially when running -on a machine with hyperthreading disabled.

-

Running with the USER-INTEL package from the command line:

+the runs, adding the flag -xHost to CCFLAGS enables vectorization +with the Intel(R) compiler. Otherwise, you must provide the correct +compute node architecture to the -x option (e.g. -xAVX).

+

Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi +are included in the src/MAKE/OPTIONS directory with settings that +perform well with the Intel(R) compiler. The latter has support for +offload to Phi coprocessors; the former does not.

+

Run with the USER-INTEL package from the command line:

The mpirun or mpiexec command sets the total number of MPI tasks used by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.

-

If you plan to compute (any portion of) pairwise interactions using -USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU, -you need to choose how many OpenMP threads per MPI task to use. Note -that the product of MPI tasks * OpenMP threads/task should not exceed -the physical number of cores (on a node), otherwise performance will -suffer.

-

If LAMMPS was built with coprocessor support for the USER-INTEL -package, you also need to specify the number of coprocessor/node and -optionally the number of coprocessor threads per MPI task to use. Note that -coprocessor threads (which run on the coprocessor) are totally -independent from OpenMP threads (which run on the CPU). The default -values for the settings that affect coprocessor threads are typically -fine, as discussed below.

-

Use the “-sf intel” command-line switch, -which will automatically append “intel” to styles that support it. -OpenMP threads per MPI task can be set via the “-pk intel Nphi omp Nt” or -“-pk omp Nt” command-line switches, which -set Nt = # of OpenMP threads per MPI task to use. The “-pk omp” form -is only allowed if LAMMPS was also built with the USER-OMP package.

-

Use the “-pk intel Nphi” command-line switch to set Nphi = # of Xeon Phi(TM) -coprocessors/node, if LAMMPS was built with coprocessor support. All -the available coprocessor threads on each Phi will be divided among -MPI tasks, unless the tptask option of the “-pk intel” command-line switch is used to limit the coprocessor -threads per MPI task. See the package intel command -for details.

-
CPU-only without USER-OMP (but using Intel vectorization on CPU):
-mpirun -np 32 lmp_machine -sf intel -in in.script         # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes)
-lmp_machine -sf intel -pk intel 0 omp 16 -in in.script    # 1 MPI task and 16 threads
-
-
-
CPU-only with USER-OMP (and Intel vectorization on CPU):
-lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -in in.script         # 1 MPI task on a 16-core node with 16 threads
-mpirun -np 4 lmp_machine -sf hybrid intel omp -pk omp 4 -in in.script     # 4 MPI tasks each with 4 threads on a single 16-core node
-
-
-
CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP:
-mpirun -np 32 -ppn 16 lmp_machine -sf intel -pk intel 1 -in in.script                 # 2 nodes with 16 MPI tasks on each, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script            # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor
-mpirun -np 16 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor, USER-OMP package for some styles
-
-
-

Note that if the “-sf intel” switch is used, it also invokes a -default command: package intel 1. If the “-sf hybrid intel omp” -switch is used, the default USER-OMP command package omp 0 is -also invoked. Both set the number of OpenMP threads per MPI task via the -OMP_NUM_THREADS environment variable. The first command sets the number of -Xeon Phi(TM) coprocessors/node to 1 (and the precision mode to “mixed”, as one -of its option defaults). The latter command is not invoked if LAMMPS was not -built with the USER-OMP package. The Nphi = 1 value for the first command is -ignored if LAMMPS was not built with coprocessor support.

-

Using the “-pk intel” or “-pk omp” switches explicitly allows for -direct setting of the number of OpenMP threads per MPI task, and -additional options for either of the USER-INTEL or USER-OMP packages. -In particular, the “-pk intel” switch sets the number of -coprocessors/node and can limit the number of coprocessor threads per -MPI task. The syntax for these two switches is the same as the -package omp and package intel commands. -See the package command doc page for details, including -the default values used for all its options if these switches are not +

If you compute (any portion of) pairwise interactions using USER-INTEL +pair styles on the CPU, or use USER-OMP styles on the CPU, you need to +choose how many OpenMP threads per MPI task to use. If both packages +are used, it must be done for both packages, and the same thread count +value should be used for both. Note that the product of MPI tasks * +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer.

+

When using the USER-INTEL package for the Phi, you also need to +specify the number of coprocessor/node and optionally the number of +coprocessor threads per MPI task to use. Note that coprocessor +threads (which run on the coprocessor) are totally independent from +OpenMP threads (which run on the CPU). The default values for the +settings that affect coprocessor threads are typically fine, as +discussed below.

+

As in the lines above, use the “-sf intel” or “-sf hybrid intel omp” +command-line switch, which will +automatically append “intel” to styles that support it. In the second +case, “omp” will be appended if an “intel” style does not exist.

+

Note that if either switch is used, it also invokes a default command: +package intel 1. If the “-sf hybrid intel omp” switch +is used, the default USER-OMP command package omp 0 is +also invoked (if LAMMPS was built with USER-OMP). Both set the number +of OpenMP threads per MPI task via the OMP_NUM_THREADS environment +variable. The first command sets the number of Xeon Phi(TM) +coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only), +and the precision mode to “mixed” (default value).

+

You can also use the “-pk intel Nphi” command-line switch to explicitly set Nphi = # of Xeon +Phi(TM) coprocessors/node, as well as additional options. Nphi should +be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi += 0 for a CPU-only build. All the available coprocessor threads on +each Phi will be divided among MPI tasks, unless the tptask option +of the “-pk intel” command-line switch is +used to limit the coprocessor threads per MPI task. See the package intel command for details, including the default values +used for all its options if not specified, and how to set the number +of OpenMP threads via the OMP_NUM_THREADS environment variable if +desired.

+

If LAMMPS was built with the USER-OMP package, you can also use the +“-pk omp Nt” command-line switch to +explicitly set Nt = # of OpenMP threads per MPI task to use, as well +as additional options. Nt should be the same threads per MPI task as +set for the USER-INTEL package, e.g. via the “-pk intel Nphi omp Nt” +command. Again, see the package omp command for +details, including the default values used for all its options if not specified, and how to set the number of OpenMP threads via the OMP_NUM_THREADS environment variable if desired.

Or run with the USER-INTEL package by editing an input script:

The discussion above for the mpirun/mpiexec command, MPI tasks/node, OpenMP threads per MPI task, and coprocessor threads per MPI task is the same.

-

Use the suffix intel command, or you can explicitly add an -“intel” suffix to individual styles in your input script, e.g.

+

Use the suffix intel or suffix hybrid intel omp commands, or you can explicitly add an “intel” or +“omp” suffix to individual styles in your input script, e.g.

pair_style lj/cut/intel 2.5

You must also use the package intel command, unless the “-sf intel” or “-pk intel” command-line switches were used. It specifies how many coprocessors/node to use, as well as other OpenMP threading and -coprocessor options. Its doc page explains how to set the number of -OpenMP threads via an environment variable if desired.

+coprocessor options. The package doc page explains how +to set the number of OpenMP threads via an environment variable if +desired.

If LAMMPS was also built with the USER-OMP package, you must also use the package omp command to enable that package, unless the “-sf hybrid intel omp” or “-pk omp” command-line switches were used. It specifies how many -OpenMP threads per MPI task to use, as well as other options. Its doc -page explains how to set the number of OpenMP threads via an -environment variable if desired.

+OpenMP threads per MPI task to use (should be same as the setting for +the USER-INTEL package), as well as other options. Its doc page +explains how to set the number of OpenMP threads via an environment +variable if desired.

Speed-ups to expect:

-

If LAMMPS was not built with coprocessor support when including the -USER-INTEL package, then acclerated styles will run on the CPU using -vectorization optimizations and the specified precision. This may -give a substantial speed-up for a pair style, particularly if mixed or -single precision is used.

+

If LAMMPS was not built with coprocessor support (CPU only) when +including the USER-INTEL package, then acclerated styles will run on +the CPU using vectorization optimizations and the specified precision. +This may give a substantial speed-up for a pair style, particularly if +mixed or single precision is used.

If LAMMPS was built with coproccesor support, the pair styles will run on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The performance of a Xeon Phi versus a multi-core CPU is a function of @@ -347,6 +313,20 @@ single, mixed).

See the Benchmark page of the LAMMPS web site for performance of the USER-INTEL package on different hardware.

+
+

Warning

+

Setting core affinity is often used to pin MPI tasks +and OpenMP threads to a core or group of cores so that memory access +can be uniform. Unless disabled at build time, affinity for MPI tasks +and OpenMP threads on the host (CPU) will be set by default on the +host when using offload to a coprocessor. In this case, it is +unnecessary to use other methods to control affinity (e.g. taskset, +numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input +script with the no_affinity option to the package intel command or by disabling the option at build time +(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your +Makefile). Disabling this option is not recommended, especially when +running on a machine with hyperthreading disabled.

+

Guidelines for best performance on an Intel(R) Xeon Phi(TM) coprocessor:

    diff --git a/doc/accelerate_intel.txt b/doc/accelerate_intel.txt index b78dbd6297..bebcbcfb52 100644 --- a/doc/accelerate_intel.txt +++ b/doc/accelerate_intel.txt @@ -12,215 +12,177 @@ 5.3.3 USER-INTEL package :h4 The USER-INTEL package was developed by Mike Brown at Intel -Corporation. It provides a capability to accelerate simulations by -offloading neighbor list and non-bonded force calculations to Intel(R) -Xeon Phi(TM) coprocessors (not native mode like the KOKKOS package). -Additionally, it supports running simulations in single, mixed, or -double precision with vectorization, even if a coprocessor is not -present, i.e. on an Intel(R) CPU. The same C++ code is used for both -cases. When offloading to a coprocessor, the routine is run twice, -once with an offload flag. +Corporation. It provides two methods for accelerating simulations, +depending on the hardware you have. The first is acceleration on +Intel(R) CPUs by running in single, mixed, or double precision with +vectorization. The second is acceleration on Intel(R) Xeon Phi(TM) +coprocessors via offloading neighbor list and non-bonded force +calculations to the Phi. The same C++ code is used in both cases. +When offloading to a coprocessor from a CPU, the same routine is run +twice, once on the CPU and once with an offload flag. -The USER-INTEL package can be used in tandem with the USER-OMP -package. This is useful when offloading pair style computations to -coprocessors, so that other styles not supported by the USER-INTEL -package, e.g. bond, angle, dihedral, improper, and long-range -electrostatics, can run simultaneously in threaded mode on the CPU -cores. Since less MPI tasks than CPU cores will typically be invoked -when running with coprocessors, this enables the extra CPU cores to be -used for useful computation. +Note that the USER-INTEL package supports use of the Phi in "offload" +mode, not "native" mode like the "KOKKOS +package"_accelerate_kokkos.html. -If LAMMPS is built with both the USER-INTEL and USER-OMP packages -installed, this mode of operation is made easier to use, with the -"-suffix hybrid intel omp" "command-line switch"_Section_start.html#start_7 -or the "suffix hybrid intel omp"_suffix.html command will both set a -second-choice suffix to "omp" so that styles from the USER-OMP package will be -used if available, after first testing if a style from the USER-INTEL -package is available. +Also note that the USER-INTEL package can be used in tandem with the +"USER-OMP package"_accelerate_omp.html. This is useful when +offloading pair style computations to the Phi, so that other styles +not supported by the USER-INTEL package, e.g. bond, angle, dihedral, +improper, and long-range electrostatics, can run simultaneously in +threaded mode on the CPU cores. Since less MPI tasks than CPU cores +will typically be invoked when running with coprocessors, this enables +the extra CPU cores to be used for useful computation. -When using the USER-INTEL package, you must choose at build time whether the -binary will support offload to Xeon Phi coprocessors. Binaries supporting -offload can still be run in CPU-only (host-only) mode. +As illustrated below, if LAMMPS is built with both the USER-INTEL and +USER-OMP packages, this dual mode of operation is made easier to use, +via the "-suffix hybrid intel omp" "command-line +switch"_Section_start.html#start_7 or the "suffix hybrid intel +omp"_suffix.html command. Both set a second-choice suffix to "omp" so +that styles from the USER-INTEL package will be used if available, +with styles from the USER-OMP package as a second choice. -Here is a quick overview of how to use the USER-INTEL package -for CPU-only acceleration: +Here is a quick overview of how to use the USER-INTEL package for CPU +acceleration, assuming one or more 16-core nodes. More details +follow. -specify these CCFLAGS in your src/MAKE/Makefile.machine: -openmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost -specify -openmp with LINKFLAGS in your Makefile.machine -include the USER-INTEL package and (optionally) USER-OMP package and build LAMMPS -specify how many OpenMP threads per MPI task to use -use USER-INTEL and (optionally) USER-OMP styles in your input script :ul +use an Intel compiler +use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits +use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost +make yes-user-intel yes-user-omp # including user-omp is optional +make mpi # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi +make intel_cpu # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper +Make.py -v -p intel omp -intel cpu -a file mpich_icc # or one-line build via Make.py for MPICH +Make.py -v -p intel omp -intel cpu -a file ompi_icc # or for OpenMPI +Make.py -v -p intel omp -intel cpu -a file intel_cpu # or for Intel MPI wrapper :pre -Note that many of these settings can only be used with the Intel -compiler, as discussed below. +lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP +mpirun -np 32 lmp_machine -sf intel -in in.script # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP +lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP +mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP :pre -Using the USER-INTEL package to offload work to the Intel(R) -Xeon Phi(TM) coprocessor is the same except for these additional -steps: +Here is a quick overview of how to use the USER-INTEL package for the +same CPUs as above (16 cores/node), with an additional Xeon Phi(TM) +coprocessor per node. More details follow. -add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in your Makefile.machine -add the flag -offload to LINKFLAGS in your Makefile.machine :ul +Same as above for building, with these additions/changes: +add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine +add the flag -offload to LINKFLAGS in Makefile.machine +for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi" :pre -The latter two steps in the first case and the last step in the -coprocessor case can be done using the "-pk intel" and "-sf intel" -"command-line switches"_Section_start.html#start_7 respectively. Or -the effect of the "-pk" or "-sf" switches can be duplicated by adding -the "package intel"_package.html or "suffix intel"_suffix.html -commands respectively to your input script. +mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP +mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP +mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP :pre [Required hardware/software:] -To use the offload option, you must have one or more Intel(R) Xeon -Phi(TM) coprocessors and use an Intel(R) C++ compiler. - +Your compiler must support the OpenMP interface. Use of an Intel(R) +C++ compiler is recommended, but not required. However, g++ will not +recognize some of the settings listed above, so they cannot be used. Optimizations for vectorization have only been tested with the Intel(R) compiler. Use of other compilers may not result in -vectorization or give poor performance. - -Use of an Intel C++ compiler is recommended, but not required (though -g++ will not recognize some of the settings, so they cannot be used). -The compiler must support the OpenMP interface. +vectorization, or give poor performance. The recommended version of the Intel(R) compiler is 14.0.1.106. -Versions 15.0.1.133 and later are also supported. If using Intel(R) +Versions 15.0.1.133 and later are also supported. If using Intel(R) MPI, versions 15.0.2.044 and later are recommended. +To use the offload option, you must have one or more Intel(R) Xeon +Phi(TM) coprocessors and use an Intel(R) C++ compiler. + [Building LAMMPS with the USER-INTEL package:] -You can choose to build with or without support for offload to a -Intel(R) Xeon Phi(TM) coprocessor. If you build with support for a -coprocessor, the same binary can be used on nodes with and without -coprocessors installed. However, if you do not have coprocessors -on your system, building without offload support will produce a -smaller binary. +The lines above illustrate how to include/build with the USER-INTEL +package, for either CPU or Phi support, in two steps, using the "make" +command. Or how to do it with one command via the src/Make.py script, +described in "Section 2.4"_Section_start.html#start_4 of the manual. +Type "Make.py -h" for help. Because the mechanism for specifing what +compiler to use (Intel in this case) is different for different MPI +wrappers, 3 versions of the Make.py command are shown. -You can do either in one line, using the src/Make.py script, described -in "Section 2.4"_Section_start.html#start_4 of the manual. Type -"Make.py -h" for help. If run from the src directory, these commands -will create src/lmp_intel_cpu and lmp_intel_phi using -src/MAKE/Makefile.mpi as the starting Makefile.machine: +Note that if you build with support for a Phi coprocessor, the same +binary can be used on nodes with or without coprocessors installed. +However, if you do not have coprocessors on your system, building +without offload support will produce a smaller binary. -Make.py -p intel omp -intel cpu -o intel_cpu -cc icc -a file mpi -Make.py -p intel omp -intel phi -o intel_phi -cc icc -a file mpi :pre +If you also build with the USER-OMP package, you can use styles from +both packages, as described below. -Note that this assumes that your MPI and its mpicxx wrapper -is using the Intel compiler. If it is not, you should -leave off the "-cc icc" switch. - -Or you can follow these steps: - -cd lammps/src -make yes-user-intel -make yes-user-omp (if desired) -make machine :pre - -Note that if the USER-OMP package is also installed, you can use -styles from both packages, as described below. - -The Makefile.machine needs a "-fopenmp" flag for OpenMP support in -both the CCFLAGS and LINKFLAGS variables. You also need to add --DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS. +Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must +include "-fopenmp". Likewise, if you use an Intel compiler, the +CCFLAGS setting must include "-restrict". For Phi support, the +"-DLMP_INTEL_OFFLOAD" (CCFLAGS) and "-offload" (LINKFLAGS) settings +are required. The other settings listed above are optional, but will +typically improve performance. The Make.py command will add all of +these automatically. If you are compiling on the same architecture that will be used for -the runs, adding the flag {-xHost} to CCFLAGS will enable -vectorization with the Intel(R) compiler. Otherwise, you must -provide the correct compute node architecture to the -x option -(e.g. -xAVX). +the runs, adding the flag {-xHost} to CCFLAGS enables vectorization +with the Intel(R) compiler. Otherwise, you must provide the correct +compute node architecture to the -x option (e.g. -xAVX). -In order to build with support for an Intel(R) Xeon Phi(TM) -coprocessor, the flag {-offload} should be added to the LINKFLAGS line -and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line. +Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi +are included in the src/MAKE/OPTIONS directory with settings that +perform well with the Intel(R) compiler. The latter has support for +offload to Phi coprocessors; the former does not. -Example makefiles Makefile.intel_cpu and Makefile.intel_phi are -included in the src/MAKE/OPTIONS directory with settings that perform -well with the Intel(R) compiler. The latter file has support for -offload to coprocessors; the former does not. - -[Notes on CPU and core affinity:] - -Setting core affinity is often used to pin MPI tasks and OpenMP -threads to a core or group of cores so that memory access can be -uniform. Unless disabled at build time, affinity for MPI tasks and -OpenMP threads on the host will be set by default on the host -when using offload to a coprocessor. In this case, it is unnecessary -to use other methods to control affinity (e.g. taskset, numactl, -I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script -with the {no_affinity} option to the "package intel"_package.html -command or by disabling the option at build time (by adding --DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile). -Disabling this option is not recommended, especially when running -on a machine with hyperthreading disabled. - -[Running with the USER-INTEL package from the command line:] +[Run with the USER-INTEL package from the command line:] The mpirun or mpiexec command sets the total number of MPI tasks used by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -If you plan to compute (any portion of) pairwise interactions using -USER-INTEL pair styles on the CPU, or use USER-OMP styles on the CPU, -you need to choose how many OpenMP threads per MPI task to use. Note -that the product of MPI tasks * OpenMP threads/task should not exceed -the physical number of cores (on a node), otherwise performance will -suffer. +If you compute (any portion of) pairwise interactions using USER-INTEL +pair styles on the CPU, or use USER-OMP styles on the CPU, you need to +choose how many OpenMP threads per MPI task to use. If both packages +are used, it must be done for both packages, and the same thread count +value should be used for both. Note that the product of MPI tasks * +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer. -If LAMMPS was built with coprocessor support for the USER-INTEL -package, you also need to specify the number of coprocessor/node and -optionally the number of coprocessor threads per MPI task to use. Note that -coprocessor threads (which run on the coprocessor) are totally -independent from OpenMP threads (which run on the CPU). The default -values for the settings that affect coprocessor threads are typically -fine, as discussed below. +When using the USER-INTEL package for the Phi, you also need to +specify the number of coprocessor/node and optionally the number of +coprocessor threads per MPI task to use. Note that coprocessor +threads (which run on the coprocessor) are totally independent from +OpenMP threads (which run on the CPU). The default values for the +settings that affect coprocessor threads are typically fine, as +discussed below. -Use the "-sf intel" "command-line switch"_Section_start.html#start_7, -which will automatically append "intel" to styles that support it. -OpenMP threads per MPI task can be set via the "-pk intel Nphi omp Nt" or -"-pk omp Nt" "command-line switches"_Section_start.html#start_7, which -set Nt = # of OpenMP threads per MPI task to use. The "-pk omp" form -is only allowed if LAMMPS was also built with the USER-OMP package. +As in the lines above, use the "-sf intel" or "-sf hybrid intel omp" +"command-line switch"_Section_start.html#start_7, which will +automatically append "intel" to styles that support it. In the second +case, "omp" will be appended if an "intel" style does not exist. -Use the "-pk intel Nphi" "command-line -switch"_Section_start.html#start_7 to set Nphi = # of Xeon Phi(TM) -coprocessors/node, if LAMMPS was built with coprocessor support. All -the available coprocessor threads on each Phi will be divided among -MPI tasks, unless the {tptask} option of the "-pk intel" "command-line -switch"_Section_start.html#start_7 is used to limit the coprocessor -threads per MPI task. See the "package intel"_package.html command -for details. +Note that if either switch is used, it also invokes a default command: +"package intel 1"_package.html. If the "-sf hybrid intel omp" switch +is used, the default USER-OMP command "package omp 0"_package.html is +also invoked (if LAMMPS was built with USER-OMP). Both set the number +of OpenMP threads per MPI task via the OMP_NUM_THREADS environment +variable. The first command sets the number of Xeon Phi(TM) +coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only), +and the precision mode to "mixed" (default value). -CPU-only without USER-OMP (but using Intel vectorization on CPU): -mpirun -np 32 lmp_machine -sf intel -in in.script # 32 MPI tasks on as many nodes as needed (e.g. 2 16-core nodes) -lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 MPI task and 16 threads :pre +You can also use the "-pk intel Nphi" "command-line +switch"_Section_start.html#start_7 to explicitly set Nphi = # of Xeon +Phi(TM) coprocessors/node, as well as additional options. Nphi should +be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi += 0 for a CPU-only build. All the available coprocessor threads on +each Phi will be divided among MPI tasks, unless the {tptask} option +of the "-pk intel" "command-line switch"_Section_start.html#start_7 is +used to limit the coprocessor threads per MPI task. See the "package +intel"_package.html command for details, including the default values +used for all its options if not specified, and how to set the number +of OpenMP threads via the OMP_NUM_THREADS environment variable if +desired. -CPU-only with USER-OMP (and Intel vectorization on CPU): -lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -in in.script # 1 MPI task on a 16-core node with 16 threads -mpirun -np 4 lmp_machine -sf hybrid intel omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node :pre - -CPUs + Xeon Phi(TM) coprocessors with or without USER-OMP: -mpirun -np 32 -ppn 16 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes with 16 MPI tasks on each, 240 total threads on coprocessor -mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor -mpirun -np 16 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks on each node, 2 threads for each task, 240 total threads on coprocessor, USER-OMP package for some styles :pre - -Note that if the "-sf intel" switch is used, it also invokes a -default command: "package intel 1"_package.html. If the "-sf hybrid intel omp" -switch is used, the default USER-OMP command "package omp 0"_package.html is -also invoked. Both set the number of OpenMP threads per MPI task via the -OMP_NUM_THREADS environment variable. The first command sets the number of -Xeon Phi(TM) coprocessors/node to 1 (and the precision mode to "mixed", as one -of its option defaults). The latter command is not invoked if LAMMPS was not -built with the USER-OMP package. The Nphi = 1 value for the first command is -ignored if LAMMPS was not built with coprocessor support. - -Using the "-pk intel" or "-pk omp" switches explicitly allows for -direct setting of the number of OpenMP threads per MPI task, and -additional options for either of the USER-INTEL or USER-OMP packages. -In particular, the "-pk intel" switch sets the number of -coprocessors/node and can limit the number of coprocessor threads per -MPI task. The syntax for these two switches is the same as the -"package omp"_package.html and "package intel"_package.html commands. -See the "package"_package.html command doc page for details, including -the default values used for all its options if these switches are not +If LAMMPS was built with the USER-OMP package, you can also use the +"-pk omp Nt" "command-line switch"_Section_start.html#start_7 to +explicitly set Nt = # of OpenMP threads per MPI task to use, as well +as additional options. Nt should be the same threads per MPI task as +set for the USER-INTEL package, e.g. via the "-pk intel Nphi omp Nt" +command. Again, see the "package omp"_package.html command for +details, including the default values used for all its options if not specified, and how to set the number of OpenMP threads via the OMP_NUM_THREADS environment variable if desired. @@ -230,8 +192,9 @@ The discussion above for the mpirun/mpiexec command, MPI tasks/node, OpenMP threads per MPI task, and coprocessor threads per MPI task is the same. -Use the "suffix intel"_suffix.html command, or you can explicitly add an -"intel" suffix to individual styles in your input script, e.g. +Use the "suffix intel"_suffix.html or "suffix hybrid intel +omp"_suffix.html commands, or you can explicitly add an "intel" or +"omp" suffix to individual styles in your input script, e.g. pair_style lj/cut/intel 2.5 :pre @@ -239,24 +202,26 @@ You must also use the "package intel"_package.html command, unless the "-sf intel" or "-pk intel" "command-line switches"_Section_start.html#start_7 were used. It specifies how many coprocessors/node to use, as well as other OpenMP threading and -coprocessor options. Its doc page explains how to set the number of -OpenMP threads via an environment variable if desired. +coprocessor options. The "package"_package.html doc page explains how +to set the number of OpenMP threads via an environment variable if +desired. If LAMMPS was also built with the USER-OMP package, you must also use the "package omp"_package.html command to enable that package, unless the "-sf hybrid intel omp" or "-pk omp" "command-line switches"_Section_start.html#start_7 were used. It specifies how many -OpenMP threads per MPI task to use, as well as other options. Its doc -page explains how to set the number of OpenMP threads via an -environment variable if desired. +OpenMP threads per MPI task to use (should be same as the setting for +the USER-INTEL package), as well as other options. Its doc page +explains how to set the number of OpenMP threads via an environment +variable if desired. [Speed-ups to expect:] -If LAMMPS was not built with coprocessor support when including the -USER-INTEL package, then acclerated styles will run on the CPU using -vectorization optimizations and the specified precision. This may -give a substantial speed-up for a pair style, particularly if mixed or -single precision is used. +If LAMMPS was not built with coprocessor support (CPU only) when +including the USER-INTEL package, then acclerated styles will run on +the CPU using vectorization optimizations and the specified precision. +This may give a substantial speed-up for a pair style, particularly if +mixed or single precision is used. If LAMMPS was built with coproccesor support, the pair styles will run on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The @@ -269,6 +234,19 @@ See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site for performance of the USER-INTEL package on different hardware. +IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks +and OpenMP threads to a core or group of cores so that memory access +can be uniform. Unless disabled at build time, affinity for MPI tasks +and OpenMP threads on the host (CPU) will be set by default on the +host when using offload to a coprocessor. In this case, it is +unnecessary to use other methods to control affinity (e.g. taskset, +numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input +script with the {no_affinity} option to the "package +intel"_package.html command or by disabling the option at build time +(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your +Makefile). Disabling this option is not recommended, especially when +running on a machine with hyperthreading disabled. + [Guidelines for best performance on an Intel(R) Xeon Phi(TM) coprocessor:] diff --git a/doc/accelerate_kokkos.html b/doc/accelerate_kokkos.html index 31088c43de..23fccc5cad 100644 --- a/doc/accelerate_kokkos.html +++ b/doc/accelerate_kokkos.html @@ -127,23 +127,22 @@

    Return to Section accelerate overview

    5.KOKKOS package

    -

    The KOKKOS package was developed primaritly by Christian Trott -(Sandia) with contributions of various styles by others, including -Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). -The underlying Kokkos library was written -primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all -Sandia).

    +

    The KOKKOS package was developed primarily by Christian Trott (Sandia) +with contributions of various styles by others, including Sikandar +Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The +underlying Kokkos library was written primarily by Carter Edwards, +Christian Trott, and Dan Sunderland (all Sandia).

    The KOKKOS package contains versions of pair, fix, and atom styles that use data structures and macros provided by the Kokkos library, which is included with LAMMPS in lib/kokkos.

    The Kokkos library is part of -Trilinos and can also -be downloaded from Github. Kokkos is a +Trilinos and can also be +downloaded from Github. Kokkos is a templated C++ library that provides two key abstractions for an application like LAMMPS. First, it allows a single implementation of an application kernel (e.g. a pair style) to run efficiently on different kinds of hardware, such as a GPU, Intel Phi, or many-core -chip.

    +CPU.

    The Kokkos library also provides data abstractions to adjust (at compile time) the memory layout of basic data structures like 2d and 3d arrays and allow the transparent utilization of special hardware @@ -153,53 +152,80 @@ chosen to optimize performance on different platforms. Again this functionality is hidden from the developer, and does not affect how the kernel is coded.

    These abstractions are set at build time, when LAMMPS is compiled with -the KOKKOS package installed. This is done by selecting a “host” and -“device” to build for, compatible with the compute nodes in your -machine (one on a desktop machine or 1000s on a supercomputer).

    -

    All Kokkos operations occur within the context of an individual MPI -task running on a single node of the machine. The total number of MPI -tasks used by LAMMPS (one or multiple per compute node) is set in the -usual manner via the mpirun or mpiexec commands, and is independent of -Kokkos.

    -

    Kokkos provides support for two different modes of execution per MPI -task. This means that computational tasks (pairwise interactions, -neighbor list builds, time integration, etc) can be parallelized for -one or the other of the two modes. The first mode is called the -“host” and is one or more threads running on one or more physical CPUs -(within the node). Currently, both multi-core CPUs and an Intel Phi -processor (running in native mode, not offload mode like the -USER-INTEL package) are supported. The second mode is called the -“device” and is an accelerator chip of some kind. Currently only an -NVIDIA GPU is supported via Cuda. If your compute node does not have -a GPU, then there is only one mode of execution, i.e. the host and -device are the same.

    -

    When using the KOKKOS package, you must choose at build time whether -you are building for OpenMP, GPU, or for using the Xeon Phi in native -mode.

    -

    Here is a quick overview of how to use the KOKKOS package:

    +the KOKKOS package installed. All Kokkos operations occur within the +context of an individual MPI task running on a single node of the +machine. The total number of MPI tasks used by LAMMPS (one or +multiple per compute node) is set in the usual manner via the mpirun +or mpiexec commands, and is independent of Kokkos.

    +

    Kokkos currently provides support for 3 modes of execution (per MPI +task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs), +and OpenMP (for Intel Phi). Note that the KOKKOS package supports +running on the Phi in native mode, not offload mode like the +USER-INTEL package supports. You choose the mode at build time to +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 +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

    +
    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
+
    +
    • 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
    -

    The latter two steps can be done using the “-k on”, “-pk kokkos” and -“-sf kk” command-line switches -respectively. Or the effect of the “-pk” or “-sf” switches can be -duplicated by adding the package kokkos or suffix kk commands respectively to your input script.

    +

    Here is a quick overview of how to use the KOKKOS package for GPUs, +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 +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

    +
    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
+
    +
    +
    mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes
+
    +
    +

    Here is a quick overview of how to use the KOKKOS package +for the Intel Phi:

    +
    use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+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

    Required hardware/software:

    -

    The KOKKOS package can be used to build and run LAMMPS on the -following kinds of hardware:

    -
      -
    • CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles)
      • -
    • CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
      • -
    • Phi: on one or more Intel Phi coprocessors (per node)
      • -
    • GPU: on the GPUs of a node with additional OpenMP threading on the CPUs
      • -

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

    -

    Note that Intel Xeon Phi coprocessors are supported in “native” mode, -not “offload” mode like the USER-INTEL package supports.

    -

    Only NVIDIA GPUs are currently supported.

    +

    To build with Kokkos support for CPUs, your compiler must support the +OpenMP interface. You should have one or more multi-core CPUs so that +multiple threads can be launched by each MPI task running on a CPU.

    +

    To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software +version 6.5 or later must be installed on your system. See the +discussion for the USER-CUDA and +GPU packages for details of how to check and do +this.

    Warning

    For good performance of the KOKKOS package on GPUs, @@ -207,12 +233,12 @@ you must have Kepler generation GPUs (or later). The Kokkos library exploits texture cache options not supported by Telsa generation GPUs (or older).

    -

    To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be -installed on your system. See the discussion above for the USER-CUDA -and GPU packages for details of how to check and do this.

    +

    To build with Kokkos support for Intel Xeon Phi coprocessors, your +sysmte must be configured to use them in “native” mode, not “offload” +mode like the USER-INTEL package supports.

    Building LAMMPS with the KOKKOS package:

    -

    You must choose at build time whether to build for OpenMP, Cuda, or -Phi.

    +

    You must choose at build time whether to build for CPUs (OpenMP), +GPUs, or Phi.

    You can do any of these in one line, using the src/Make.py script, described in Section 2.4 of the manual. Type “Make.py -h” for help. If run from the src directory, these @@ -220,11 +246,10 @@ commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and lmp_kokkos_phi. Note that the OMP and PHI options use src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.

    -
    Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
-
    -
    +

    The latter two steps can be done using the “-k on”, “-pk kokkos” and +“-sf kk” command-line switches +respectively. Or the effect of the “-pk” or “-sf” switches can be +duplicated by adding the package kokkos or suffix kk commands respectively to your input script.

    Or you can follow these steps:

    CPU-only (run all-MPI or with OpenMP threading):

    cd lammps/src
@@ -384,29 +409,6 @@ which will automatically append “kk” to styles that support it.  Use
 the “-pk kokkos” command-line switch if
 you wish to change any of the default package kokkos
 optionns set by the “-k on” command-line switch.
    
-
    host=OMP, dual hex-core nodes (12 threads/node):
-mpirun -np 12 lmp_g++ -in in.lj                           # MPI-only mode with no Kokkos
-mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj              # MPI-only mode with Kokkos
-mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj          # one MPI task, 12 threads
-mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj           # two MPI tasks, 6 threads/task
-mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj   # ditto on 16 nodes
-
    
-
    
-
    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
    
-
    host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
-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
-
    
-
    
-
    host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes
-
    
-
    
 
    Note that the default for the package kokkos command is
 to use “full” neighbor lists and set the Newton flag to “off” for both
 pairwise and bonded interactions.  This typically gives fastest
diff --git a/doc/accelerate_kokkos.txt b/doc/accelerate_kokkos.txt
index dd9143bc67..4ca026f31d 100644
--- a/doc/accelerate_kokkos.txt
+++ b/doc/accelerate_kokkos.txt
@@ -11,25 +11,24 @@
 
 5.3.4 KOKKOS package :h4
 
-The KOKKOS package was developed primaritly by Christian Trott
-(Sandia) with contributions of various styles by others, including
-Sikandar Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).
-The underlying Kokkos library was written
-primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all
-Sandia).
+The KOKKOS package was developed primarily by Christian Trott (Sandia)
+with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).  The
+underlying Kokkos library was written primarily by Carter Edwards,
+Christian Trott, and Dan Sunderland (all Sandia).
 
 The KOKKOS package contains versions of pair, fix, and atom styles
 that use data structures and macros provided by the Kokkos library,
 which is included with LAMMPS in lib/kokkos.
 
 The Kokkos library is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also
-be downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
+"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also be
+downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
 templated C++ library that provides two key abstractions for an
 application like LAMMPS.  First, it allows a single implementation of
 an application kernel (e.g. a pair style) to run efficiently on
 different kinds of hardware, such as a GPU, Intel Phi, or many-core
-chip.
+CPU.
 
 The Kokkos library also provides data abstractions to adjust (at
 compile time) the memory layout of basic data structures like 2d and
@@ -41,76 +40,105 @@ functionality is hidden from the developer, and does not affect how
 the kernel is coded.
 
 These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed.  This is done by selecting a "host" and
-"device" to build for, compatible with the compute nodes in your
-machine (one on a desktop machine or 1000s on a supercomputer).
+the KOKKOS package installed.  All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine.  The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos.
 
-All Kokkos operations occur within the context of an individual MPI
-task running on a single node of the machine.  The total number of MPI
-tasks used by LAMMPS (one or multiple per compute node) is set in the
-usual manner via the mpirun or mpiexec commands, and is independent of
-Kokkos.
+Kokkos currently provides support for 3 modes of execution (per MPI
+task).  These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
+and OpenMP (for Intel Phi).  Note that the KOKKOS package supports
+running on the Phi in native mode, not offload mode like the
+USER-INTEL package supports.  You choose the mode at build time to
+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
+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
+
+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
 
-Kokkos provides support for two different modes of execution per MPI
-task.  This means that computational tasks (pairwise interactions,
-neighbor list builds, time integration, etc) can be parallelized for
-one or the other of the two modes.  The first mode is called the
-"host" and is one or more threads running on one or more physical CPUs
-(within the node).  Currently, both multi-core CPUs and an Intel Phi
-processor (running in native mode, not offload mode like the
-USER-INTEL package) are supported.  The second mode is called the
-"device" and is an accelerator chip of some kind.  Currently only an
-NVIDIA GPU is supported via Cuda.  If your compute node does not have
-a GPU, then there is only one mode of execution, i.e. the host and
-device are the same.
 
-When using the KOKKOS package, you must choose at build time whether
-you are building for OpenMP, GPU, or for using the Xeon Phi in native
-mode.
 
-Here is a quick overview of how to use the KOKKOS package:
 
 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
 
-The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_7
-respectively.  Or the effect of the "-pk" or "-sf" switches can be
-duplicated by adding the "package kokkos"_package.html or "suffix
-kk"_suffix.html commands respectively to your input script.
+Here is a quick overview of how to use the KOKKOS package for GPUs,
+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
+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
+
+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
+
+mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes :pre
+
+Here is a quick overview of how to use the KOKKOS package
+for the Intel Phi:
+
+use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+
+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:]
 
-The KOKKOS package can be used to build and run LAMMPS on the
-following kinds of hardware:
-
-CPU-only: one MPI task per CPU core (MPI-only, but using KOKKOS styles) 
-CPU-only: one or a few MPI tasks per node with additional threading via OpenMP
-Phi: on one or more Intel Phi coprocessors (per node)
-GPU: on the GPUs of a node with additional OpenMP threading on the CPUs :ul
-
 Kokkos support within LAMMPS must be built with a C++11 compatible
 compiler.  If using gcc, version 4.8.1 or later is required.
 
-Note that Intel Xeon Phi coprocessors are supported in "native" mode,
-not "offload" mode like the USER-INTEL package supports.
+To build with Kokkos support for CPUs, your compiler must support the
+OpenMP interface.  You should have one or more multi-core CPUs so that
+multiple threads can be launched by each MPI task running on a CPU.
 
-Only NVIDIA GPUs are currently supported.
+To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+version 6.5 or later must be installed on your system.  See the
+discussion for the "USER-CUDA"_accelerate_cuda.html and
+"GPU"_accelerate_gpu.html packages for details of how to check and do
+this.
 
 IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
 you must have Kepler generation GPUs (or later).  The Kokkos library
 exploits texture cache options not supported by Telsa generation GPUs
 (or older).
 
-To build the KOKKOS package for GPUs, NVIDIA Cuda software version 6.5 or later must be
-installed on your system.  See the discussion above for the USER-CUDA
-and GPU packages for details of how to check and do this.
+To build with Kokkos support for Intel Xeon Phi coprocessors, your
+sysmte must be configured to use them in "native" mode, not "offload"
+mode like the USER-INTEL package supports.
 
 [Building LAMMPS with the KOKKOS package:]
 
-You must choose at build time whether to build for OpenMP, Cuda, or
-Phi.
+You must choose at build time whether to build for CPUs (OpenMP),
+GPUs, or Phi.
 
 You can do any of these in one line, using the src/Make.py script,
 described in "Section 2.4"_Section_start.html#start_4 of the manual.
@@ -120,9 +148,12 @@ lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
 option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
 
-Make.py -p kokkos -kokkos omp -o kokkos_omp -a file mpi 
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+The latter two steps can be done using the "-k on", "-pk kokkos" and
+"-sf kk" "command-line switches"_Section_start.html#start_7
+respectively.  Or the effect of the "-pk" or "-sf" switches can be
+duplicated by adding the "package kokkos"_package.html or "suffix
+kk"_suffix.html commands respectively to your input script.
+
 
 Or you can follow these steps:
 
@@ -301,26 +332,7 @@ you wish to change any of the default "package kokkos"_package.html
 optionns set by the "-k on" "command-line
 switch"_Section_start.html#start_7.
 
-host=OMP, dual hex-core nodes (12 threads/node):
-mpirun -np 12 lmp_g++ -in in.lj                           # MPI-only mode with no Kokkos
-mpirun -np 12 lmp_g++ -k on -sf kk -in in.lj              # MPI-only mode with Kokkos
-mpirun -np 1 lmp_g++ -k on t 12 -sf kk -in in.lj          # one MPI task, 12 threads
-mpirun -np 2 lmp_g++ -k on t 6 -sf kk -in in.lj           # two MPI tasks, 6 threads/task 
-mpirun -np 32 -ppn 2 lmp_g++ -k on t 6 -sf kk -in in.lj   # ditto on 16 nodes :pre
 
-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
-
-host=OMP, device=CUDA, node = dual hex-core CPUs and a single GPU:
-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
-
-host=OMP, device=CUDA, node = dual 8-core CPUs and 2 GPUs:
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes :pre
 
 Note that the default for the "package kokkos"_package.html command is
 to use "full" neighbor lists and set the Newton flag to "off" for both
diff --git a/doc/accelerate_omp.html b/doc/accelerate_omp.html
index 2a78e2f1f1..605d444025 100644
--- a/doc/accelerate_omp.html
+++ b/doc/accelerate_omp.html
@@ -130,72 +130,55 @@
 
    The USER-OMP package was developed by Axel Kohlmeyer at Temple
 University.  It provides multi-threaded versions of most pair styles,
 nearly all bonded styles (bond, angle, dihedral, improper), several
-Kspace styles, and a few fix styles.  The package currently
-uses the OpenMP interface for multi-threading.
    
-
    Here is a quick overview of how to use the USER-OMP package:
    
-
      
-
    • use the -fopenmp flag for compiling and linking in your Makefile.machine
      • 
-
    • include the USER-OMP package and build LAMMPS
      • 
-
    • use the mpirun command to set the number of MPI tasks/node
      • 
-
    • specify how many threads per MPI task to use
      • 
-
    • use USER-OMP styles in your input script
      • 
-
    
-
    The latter two steps can be done using the “-pk omp” and “-sf omp”
-command-line switches respectively.  Or
-the effect of the “-pk” or “-sf” switches can be duplicated by adding
-the package omp or suffix omp commands
-respectively to your input script.
    
+Kspace styles, and a few fix styles.  The package currently uses the
+OpenMP interface for multi-threading.
    
+
    Here is a quick overview of how to use the USER-OMP package, assuming
+one or more 16-core nodes.  More details follow.
    
+
    use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
+make yes-user-omp
+make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
+make omp                                   # or Makefile.omp already has settings
+Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py
+
    
+
    
+
    lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+
    
+
    
 
    Required hardware/software:
    
 
    Your compiler must support the OpenMP interface.  You should have one
-or more multi-core CPUs so that multiple threads can be launched by an
-MPI task running on a CPU.
    
+or more multi-core CPUs so that multiple threads can be launched by
+each MPI task running on a CPU.
    
 
    Building LAMMPS with the USER-OMP package:
    
-
    To do this in one line, use the src/Make.py script, described in
-Section 2.4 of the manual.  Type “Make.py
--h” for help.  If run from the src directory, this command will create
-src/lmp_omp using src/MAKE/Makefile.mpi as the starting
-Makefile.machine:
    
-
    Make.py -p omp -o omp -a file mpi
-
    
-
    
-
    Or you can follow these steps:
    
-
    cd lammps/src
-make yes-user-omp
-make machine
-
    
-
    
-
    The CCFLAGS setting in Makefile.machine needs “-fopenmp” to add OpenMP
-support.  This works for both the GNU and Intel compilers.  Without
-this flag the USER-OMP styles will still be compiled and work, but
-will not support multi-threading.  For the Intel compilers the CCFLAGS
-setting also needs to include “-restrict”.
    
+
    The lines above illustrate how to include/build with the USER-OMP
+package in two steps, using the “make” command.  Or how to do it with
+one command via the src/Make.py script, described in Section 2.4 of the manual.  Type “Make.py -h” for
+help.
    
+
    Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
+include “-fopenmp”.  Likewise, if you use an Intel compiler, the
+CCFLAGS setting must include “-restrict”.  The Make.py command will
+add these automatically.
    
 
    Run with the USER-OMP package from the command line:
    
 
    The mpirun or mpiexec command sets the total number of MPI tasks used
 by LAMMPS (one or multiple per compute node) and the number of MPI
 tasks used per node.  E.g. the mpirun command in MPICH does this via
 its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
    
-
    You need to choose how many threads per MPI task will be used by the
-USER-OMP package.  Note that the product of MPI tasks * threads/task
-should not exceed the physical number of cores (on a node), otherwise
-performance will suffer.
    
-
    Use the “-sf omp” command-line switch,
-which will automatically append “omp” to styles that support it.  Use
-the “-pk omp Nt” command-line switch, to
-set Nt = # of OpenMP threads per MPI task to use.
    
-
    lmp_machine -sf omp -pk omp 16 -in in.script                       # 1 MPI task on a 16-core node
-mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script           # 4 MPI tasks each with 4 threads on a single 16-core node
-mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script   # ditto on 8 16-core nodes
-
    
-
    
-
    Note that if the “-sf omp” switch is used, it also issues a default
-package omp 0 command, which sets the number of threads
-per MPI task via the OMP_NUM_THREADS environment variable.
    
-
    Using the “-pk” switch explicitly allows for direct setting of the
-number of threads and additional options.  Its syntax is the same as
-the “package omp” command.  See the package command doc
-page for details, including the default values used for all its
-options if it is not specified, and how to set the number of threads
-via the OMP_NUM_THREADS environment variable if desired.
    
+
    You need to choose how many OpenMP threads per MPI task will be used
+by the USER-OMP package.  Note that the product of MPI tasks *
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer.
    
+
    As in the lines above, use the “-sf omp” command-line switch, which will automatically append
+“omp” to styles that support it.  The “-sf omp” switch also issues a
+default package omp 0 command, which will set the
+number of threads per MPI task via the OMP_NUM_THREADS environment
+variable.
    
+
    You can also use the “-pk omp Nt” command-line switch, to explicitly set Nt = # of OpenMP
+threads per MPI task to use, as well as additional options.  Its
+syntax is the same as the package omp command whose doc
+page gives details, including the default values used if it is not
+specified.  It also gives more details on how to set the number of
+threads via the OMP_NUM_THREADS environment variable.
    
 
    Or run with the USER-OMP package by editing an input script:
    
 
    The discussion above for the mpirun/mpiexec command, MPI tasks/node,
 and threads/MPI task is the same.
    
@@ -205,25 +188,24 @@ and threads/MPI task is the same.

    You must also use the package omp command to enable the -USER-OMP package, unless the “-sf omp” or “-pk omp” command-line switches were used. It specifies how many -threads per MPI task to use, as well as other options. Its doc page -explains how to set the number of threads via an environment variable -if desired.

    +USER-OMP package. When you do this you also specify how many threads +per MPI task to use. The command doc page explains other options and +how to set the number of threads via the OMP_NUM_THREADS environment +variable.

    Speed-ups to expect:

    Depending on which styles are accelerated, you should look for a reduction in the “Pair time”, “Bond time”, “KSpace time”, and “Loop time” values printed at the end of a run.

    You may see a small performance advantage (5 to 20%) when running a USER-OMP style (in serial or parallel) with a single thread per MPI -task, versus running standard LAMMPS with its standard -(un-accelerated) styles (in serial or all-MPI parallelization with 1 -task/core). This is because many of the USER-OMP styles contain -similar optimizations to those used in the OPT package, as described -above.

    -

    With multiple threads/task, the optimal choice of MPI tasks/node and -OpenMP threads/task can vary a lot and should always be tested via -benchmark runs for a specific simulation running on a specific -machine, paying attention to guidelines discussed in the next +task, versus running standard LAMMPS with its standard un-accelerated +styles (in serial or all-MPI parallelization with 1 task/core). This +is because many of the USER-OMP styles contain similar optimizations +to those used in the OPT package, described in Section accelerate 5.3.6.

    +

    With multiple threads/task, the optimal choice of number of MPI +tasks/node and OpenMP threads/task can vary a lot and should always be +tested via benchmark runs for a specific simulation running on a +specific machine, paying attention to guidelines discussed in the next sub-section.

    A description of the multi-threading strategy used in the USER-OMP package and some performance examples are presented here

    @@ -239,7 +221,7 @@ circumstances:

    • Individual compute nodes have a significant number of CPU cores but the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx -(Clovertown) and 54xx (Harpertown) quad core processors. Running one +(Clovertown) and 54xx (Harpertown) quad-core processors. Running one MPI task per CPU core will result in significant performance degradation, so that running with 4 or even only 2 MPI tasks per node is faster. Running in hybrid MPI+OpenMP mode will reduce the @@ -274,15 +256,16 @@ of MPI tasks assigned to the KSpace calculation.

      • Additional performance tips are as follows:

      • The best parallel efficiency from omp styles is typically achieved -when there is at least one MPI task per physical processor, -i.e. socket or die.
        • +when there is at least one MPI task per physical CPU chip, i.e. socket +or die.
      • It is usually most efficient to restrict threading to a single socket, i.e. use one or more MPI task per socket.
        • -
      • Several current MPI implementation by default use a processor affinity -setting that restricts each MPI task to a single CPU core. Using -multi-threading in this mode will force the threads to share that core -and thus is likely to be counterproductive. Instead, binding MPI -tasks to a (multi-core) socket, should solve this issue.
        • +
      • IMPORTANT NOTE: By default, several current MPI implementations use a +processor affinity setting that restricts each MPI task to a single +CPU core. Using multi-threading in this mode will force all threads +to share the one core and thus is likely to be counterproductive. +Instead, binding MPI tasks to a (multi-core) socket, should solve this +issue.

      Restrictions

      diff --git a/doc/accelerate_omp.txt b/doc/accelerate_omp.txt index 9d461f5199..7a5bef9d97 100644 --- a/doc/accelerate_omp.txt +++ b/doc/accelerate_omp.txt @@ -14,50 +14,40 @@ The USER-OMP package was developed by Axel Kohlmeyer at Temple University. It provides multi-threaded versions of most pair styles, nearly all bonded styles (bond, angle, dihedral, improper), several -Kspace styles, and a few fix styles. The package currently -uses the OpenMP interface for multi-threading. +Kspace styles, and a few fix styles. The package currently uses the +OpenMP interface for multi-threading. -Here is a quick overview of how to use the USER-OMP package: +Here is a quick overview of how to use the USER-OMP package, assuming +one or more 16-core nodes. More details follow. -use the -fopenmp flag for compiling and linking in your Makefile.machine -include the USER-OMP package and build LAMMPS -use the mpirun command to set the number of MPI tasks/node -specify how many threads per MPI task to use -use USER-OMP styles in your input script :ul +use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine +make yes-user-omp +make mpi # build with USER-OMP package, if settings added to Makefile.mpi +make omp # or Makefile.omp already has settings +Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py :pre -The latter two steps can be done using the "-pk omp" and "-sf omp" -"command-line switches"_Section_start.html#start_7 respectively. Or -the effect of the "-pk" or "-sf" switches can be duplicated by adding -the "package omp"_package.html or "suffix omp"_suffix.html commands -respectively to your input script. +lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads +mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task +mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre [Required hardware/software:] Your compiler must support the OpenMP interface. You should have one -or more multi-core CPUs so that multiple threads can be launched by an -MPI task running on a CPU. +or more multi-core CPUs so that multiple threads can be launched by +each MPI task running on a CPU. [Building LAMMPS with the USER-OMP package:] -To do this in one line, use the src/Make.py script, described in -"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py --h" for help. If run from the src directory, this command will create -src/lmp_omp using src/MAKE/Makefile.mpi as the starting -Makefile.machine: +The lines above illustrate how to include/build with the USER-OMP +package in two steps, using the "make" command. Or how to do it with +one command via the src/Make.py script, described in "Section +2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for +help. -Make.py -p omp -o omp -a file mpi :pre - -Or you can follow these steps: - -cd lammps/src -make yes-user-omp -make machine :pre - -The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP -support. This works for both the GNU and Intel compilers. Without -this flag the USER-OMP styles will still be compiled and work, but -will not support multi-threading. For the Intel compilers the CCFLAGS -setting also needs to include "-restrict". +Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must +include "-fopenmp". Likewise, if you use an Intel compiler, the +CCFLAGS setting must include "-restrict". The Make.py command will +add these automatically. [Run with the USER-OMP package from the command line:] @@ -66,30 +56,25 @@ by LAMMPS (one or multiple per compute node) and the number of MPI tasks used per node. E.g. the mpirun command in MPICH does this via its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. -You need to choose how many threads per MPI task will be used by the -USER-OMP package. Note that the product of MPI tasks * threads/task -should not exceed the physical number of cores (on a node), otherwise -performance will suffer. +You need to choose how many OpenMP threads per MPI task will be used +by the USER-OMP package. Note that the product of MPI tasks * +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer. -Use the "-sf omp" "command-line switch"_Section_start.html#start_7, -which will automatically append "omp" to styles that support it. Use -the "-pk omp Nt" "command-line switch"_Section_start.html#start_7, to -set Nt = # of OpenMP threads per MPI task to use. +As in the lines above, use the "-sf omp" "command-line +switch"_Section_start.html#start_7, which will automatically append +"omp" to styles that support it. The "-sf omp" switch also issues a +default "package omp 0"_package.html command, which will set the +number of threads per MPI task via the OMP_NUM_THREADS environment +variable. -lmp_machine -sf omp -pk omp 16 -in in.script # 1 MPI task on a 16-core node -mpirun -np 4 lmp_machine -sf omp -pk omp 4 -in in.script # 4 MPI tasks each with 4 threads on a single 16-core node -mpirun -np 32 -ppn 4 lmp_machine -sf omp -pk omp 4 -in in.script # ditto on 8 16-core nodes :pre - -Note that if the "-sf omp" switch is used, it also issues a default -"package omp 0"_package.html command, which sets the number of threads -per MPI task via the OMP_NUM_THREADS environment variable. - -Using the "-pk" switch explicitly allows for direct setting of the -number of threads and additional options. Its syntax is the same as -the "package omp" command. See the "package"_package.html command doc -page for details, including the default values used for all its -options if it is not specified, and how to set the number of threads -via the OMP_NUM_THREADS environment variable if desired. +You can also use the "-pk omp Nt" "command-line +switch"_Section_start.html#start_7, to explicitly set Nt = # of OpenMP +threads per MPI task to use, as well as additional options. Its +syntax is the same as the "package omp"_package.html command whose doc +page gives details, including the default values used if it is not +specified. It also gives more details on how to set the number of +threads via the OMP_NUM_THREADS environment variable. [Or run with the USER-OMP package by editing an input script:] @@ -102,11 +87,10 @@ Use the "suffix omp"_suffix.html command, or you can explicitly add an pair_style lj/cut/omp 2.5 :pre You must also use the "package omp"_package.html command to enable the -USER-OMP package, unless the "-sf omp" or "-pk omp" "command-line -switches"_Section_start.html#start_7 were used. It specifies how many -threads per MPI task to use, as well as other options. Its doc page -explains how to set the number of threads via an environment variable -if desired. +USER-OMP package. When you do this you also specify how many threads +per MPI task to use. The command doc page explains other options and +how to set the number of threads via the OMP_NUM_THREADS environment +variable. [Speed-ups to expect:] @@ -116,16 +100,16 @@ time" values printed at the end of a run. You may see a small performance advantage (5 to 20%) when running a USER-OMP style (in serial or parallel) with a single thread per MPI -task, versus running standard LAMMPS with its standard -(un-accelerated) styles (in serial or all-MPI parallelization with 1 -task/core). This is because many of the USER-OMP styles contain -similar optimizations to those used in the OPT package, as described -above. +task, versus running standard LAMMPS with its standard un-accelerated +styles (in serial or all-MPI parallelization with 1 task/core). This +is because many of the USER-OMP styles contain similar optimizations +to those used in the OPT package, described in "Section accelerate +5.3.6"_accelerate_opt.html. -With multiple threads/task, the optimal choice of MPI tasks/node and -OpenMP threads/task can vary a lot and should always be tested via -benchmark runs for a specific simulation running on a specific -machine, paying attention to guidelines discussed in the next +With multiple threads/task, the optimal choice of number of MPI +tasks/node and OpenMP threads/task can vary a lot and should always be +tested via benchmark runs for a specific simulation running on a +specific machine, paying attention to guidelines discussed in the next sub-section. A description of the multi-threading strategy used in the USER-OMP @@ -146,7 +130,7 @@ circumstances: Individual compute nodes have a significant number of CPU cores but the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx -(Clovertown) and 54xx (Harpertown) quad core processors. Running one +(Clovertown) and 54xx (Harpertown) quad-core processors. Running one MPI task per CPU core will result in significant performance degradation, so that running with 4 or even only 2 MPI tasks per node is faster. Running in hybrid MPI+OpenMP mode will reduce the @@ -184,17 +168,18 @@ of MPI tasks assigned to the KSpace calculation. :l,ule Additional performance tips are as follows: The best parallel efficiency from {omp} styles is typically achieved -when there is at least one MPI task per physical processor, -i.e. socket or die. :ulb,l +when there is at least one MPI task per physical CPU chip, i.e. socket +or die. :ulb,l It is usually most efficient to restrict threading to a single socket, i.e. use one or more MPI task per socket. :l -Several current MPI implementation by default use a processor affinity -setting that restricts each MPI task to a single CPU core. Using -multi-threading in this mode will force the threads to share that core -and thus is likely to be counterproductive. Instead, binding MPI -tasks to a (multi-core) socket, should solve this issue. :l,ule +IMPORTANT NOTE: By default, several current MPI implementations use a +processor affinity setting that restricts each MPI task to a single +CPU core. Using multi-threading in this mode will force all threads +to share the one core and thus is likely to be counterproductive. +Instead, binding MPI tasks to a (multi-core) socket, should solve this +issue. :l,ule [Restrictions:] diff --git a/doc/accelerate_opt.html b/doc/accelerate_opt.html index fc5c779528..09c0da0ff5 100644 --- a/doc/accelerate_opt.html +++ b/doc/accelerate_opt.html @@ -132,41 +132,30 @@ Technologies), David Richie, and Vincent Natoli (Stone Ridge Technologies). It contains a handful of pair styles whose compute() methods were rewritten in C++ templated form to reduce the overhead due to if tests and other conditional code.

      -

      Here is a quick overview of how to use the OPT package:

      -
        -
      • include the OPT package and build LAMMPS
        • -
      • use OPT pair styles in your input script
        • -
      -

      The last step can be done using the “-sf opt” command-line switch. Or the effect of the “-sf” switch -can be duplicated by adding a suffix opt command to your -input script.

      +

      Here is a quick overview of how to use the OPT package. More details +follow.

      +
      make yes-opt
+make mpi                               # build with the OPT pacakge
+Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py
+
      +
      +
      lmp_mpi -sf opt -in in.script                # run in serial
+mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
+
      +

      Required hardware/software:

      None.

      Building LAMMPS with the OPT package:

      -

      Include the package and build LAMMPS:

      -

      To do this in one line, use the src/Make.py script, described in -Section 2.4 of the manual. Type “Make.py --h” for help. If run from the src directory, this command will create -src/lmp_opt using src/MAKE/Makefile.mpi as the starting -Makefile.machine:

      -
      Make.py -p opt -o opt -a file mpi
-
      -
      -

      Or you can follow these steps:

      -
      cd lammps/src
-make yes-opt
-make machine
-
      -
      -

      If you are using Intel compilers, then the CCFLAGS setting in -Makefile.machine needs to include “-restrict”.

      +

      The lines above illustrate how to build LAMMPS with the OPT package in +two steps, using the “make” command. Or how to do it with one command +via the src/Make.py script, described in Section 2.4 of the manual. Type “Make.py -h” for +help.

      +

      Note that if you use an Intel compiler to build with the OPT package, +the CCFLAGS setting in your Makefile.machine must include “-restrict”. +The Make.py command will add this automatically.

      Run with the OPT package from the command line:

      -

      Use the “-sf opt” command-line switch, -which will automatically append “opt” to styles that support it.

      -
      lmp_machine -sf opt -in in.script
-mpirun -np 4 lmp_machine -sf opt -in in.script
-
      -
      +

      As in the lines above, use the “-sf opt” command-line switch, which will automatically append +“opt” to styles that support it.

      Or run with the OPT package by editing an input script:

      Use the suffix opt command, or you can explicitly add an “opt” suffix to individual styles in your input script, e.g.

      @@ -178,7 +167,7 @@ mpirun -np 4 lmp_machine -sf opt -in in.script of a run. On most machines for reasonable problem sizes, it will be a 5 to 20% savings.

      Guidelines for best performance:

      -

      None. Just try out an OPT pair style to see how it performs.

      +

      Just try out an OPT pair style to see how it performs.

      Restrictions

      None.

      diff --git a/doc/accelerate_opt.txt b/doc/accelerate_opt.txt index 23e853aec2..c2ff978795 100644 --- a/doc/accelerate_opt.txt +++ b/doc/accelerate_opt.txt @@ -17,15 +17,15 @@ Technologies). It contains a handful of pair styles whose compute() methods were rewritten in C++ templated form to reduce the overhead due to if tests and other conditional code. -Here is a quick overview of how to use the OPT package: +Here is a quick overview of how to use the OPT package. More details +follow. -include the OPT package and build LAMMPS -use OPT pair styles in your input script :ul +make yes-opt +make mpi # build with the OPT pacakge +Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py :pre -The last step can be done using the "-sf opt" "command-line -switch"_Section_start.html#start_7. Or the effect of the "-sf" switch -can be duplicated by adding a "suffix opt"_suffix.html command to your -input script. +lmp_mpi -sf opt -in in.script # run in serial +mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre [Required hardware/software:] @@ -33,32 +33,21 @@ None. [Building LAMMPS with the OPT package:] -Include the package and build LAMMPS: +The lines above illustrate how to build LAMMPS with the OPT package in +two steps, using the "make" command. Or how to do it with one command +via the src/Make.py script, described in "Section +2.4"_Section_start.html#start_4 of the manual. Type "Make.py -h" for +help. -To do this in one line, use the src/Make.py script, described in -"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py --h" for help. If run from the src directory, this command will create -src/lmp_opt using src/MAKE/Makefile.mpi as the starting -Makefile.machine: - -Make.py -p opt -o opt -a file mpi :pre - -Or you can follow these steps: - -cd lammps/src -make yes-opt -make machine :pre - -If you are using Intel compilers, then the CCFLAGS setting in -Makefile.machine needs to include "-restrict". +Note that if you use an Intel compiler to build with the OPT package, +the CCFLAGS setting in your Makefile.machine must include "-restrict". +The Make.py command will add this automatically. [Run with the OPT package from the command line:] -Use the "-sf opt" "command-line switch"_Section_start.html#start_7, -which will automatically append "opt" to styles that support it. - -lmp_machine -sf opt -in in.script -mpirun -np 4 lmp_machine -sf opt -in in.script :pre +As in the lines above, use the "-sf opt" "command-line +switch"_Section_start.html#start_7, which will automatically append +"opt" to styles that support it. [Or run with the OPT package by editing an input script:] @@ -75,7 +64,7 @@ of a run. On most machines for reasonable problem sizes, it will be a [Guidelines for best performance:] -None. Just try out an OPT pair style to see how it performs. +Just try out an OPT pair style to see how it performs. [Restrictions:] diff --git a/doc/genindex.html b/doc/genindex.html index 7ef4cf69a7..0dcd605525 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -1938,6 +1938,10 @@ +
      pair_style vashishta +
      + +
      pair_style yukawa
      diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html index 7c116747d2..329c77fec3 100644 --- a/doc/pair_hybrid.html +++ b/doc/pair_hybrid.html @@ -198,11 +198,15 @@ model, then you should just list the sub-style once and use the pair_coeff command to assign parameters for the different type pairs.

      Warning

      -

      An exception to this option to list an individual pair -style multiple times are the pair styles implemented as Fortran -libraries: pair_style meam and pair_style reax (pair_style reax/c is OK). -This is because unlike a C++ class, they can not be instantiated -multiple times, due to the manner in which they were coded in Fortran.

      +

      There are two exceptions to this option to list an +individual pair style multiple times. The first is for pair styles +implemented as Fortran libraries: pair_style meam and +pair_style reax (pair_style reax/c +is OK). This is because unlike a C++ class, they can not be +instantiated multiple times, due to the manner in which they were +coded in Fortran. The second is for GPU-enabled pair styles in the +GPU package. This is b/c the GPU package also currently assumes that +only one instance of a pair style is being used.

      In the pair_coeff commands, the name of a pair style must be added after the I,J type specification, with the remaining coefficients diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt index 202d3f7e04..2955d2ce26 100644 --- a/doc/pair_hybrid.txt +++ b/doc/pair_hybrid.txt @@ -70,12 +70,15 @@ other pairwise potential for several different atom type pairs in your model, then you should just list the sub-style once and use the pair_coeff command to assign parameters for the different type pairs. -IMPORTANT NOTE: An exception to this option to list an individual pair -style multiple times are the pair styles implemented as Fortran -libraries: "pair_style meam"_pair_meam.html and "pair_style -reax"_pair_reax.html ("pair_style reax/c"_pair_reax_c.html is OK). -This is because unlike a C++ class, they can not be instantiated -multiple times, due to the manner in which they were coded in Fortran. +IMPORTANT NOTE: There are two exceptions to this option to list an +individual pair style multiple times. The first is for pair styles +implemented as Fortran libraries: "pair_style meam"_pair_meam.html and +"pair_style reax"_pair_reax.html ("pair_style reax/c"_pair_reax_c.html +is OK). This is because unlike a C++ class, they can not be +instantiated multiple times, due to the manner in which they were +coded in Fortran. The second is for GPU-enabled pair styles in the +GPU package. This is b/c the GPU package also currently assumes that +only one instance of a pair style is being used. In the pair_coeff commands, the name of a pair style must be added after the I,J type specification, with the remaining coefficients diff --git a/doc/pair_style.html b/doc/pair_style.html index 4396eb0b24..761e221414 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -309,6 +309,7 @@ in the pair section of pair_style tip4p/cut - Coulomb for TIP4P water w/out LJ

    • pair_style tip4p/long - long-range Coulombics for TIP4P water w/out LJ
    • pair_style tri/lj - LJ potential between triangles
      • +
    • pair_style vashishta - Vashishta 2-body and 3-body potential
    • pair_style yukawa - Yukawa potential
    • pair_style yukawa/colloid - screened Yukawa potential for finite-size particles
    • pair_style zbl - Ziegler-Biersack-Littmark potential
      • diff --git a/doc/pair_vashishta.html b/doc/pair_vashishta.html index f2b42588e4..37a31cf930 100644 --- a/doc/pair_vashishta.html +++ b/doc/pair_vashishta.html @@ -1,103 +1,219 @@ - -
      LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands -
      + + + + + + + + + pair_style vashishta command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + +
      + + + - - -
      - -

      pair_style vashishta command -

      -

      Syntax: -

      -
      pair_style vashishta 
-
      -

      Examples: -

      -
      pair_style vashishta
-pair_coeff * * SiC.vashishta Si C 
-
      -

      Description: -

      -

      The vashishta style computes the combined 2-body and 3-body + +

      +
      +
      + +
      + +
      +
      +
      + +
      +

      pair_style vashishta command

      +
      +
      +

      pair_style vashishta/omp command

      +
      +

      Syntax

      +
      pair_style vashishta
+
      +
      +
      +
      +

      Examples

      +
      pair_style vashishta
+pair_coeff * * SiC.vashishta Si C
+
      +
      +
      +
      +

      Description

      +

      The vashishta style computes the combined 2-body and 3-body family of potentials developed in the group of Vashishta and -co-workers. By combining repulsive, screened Coulombic, -screened charge-dipole, and dispersion interactions with a -bond-angle energy based on the Stillinger-Weber potential, +co-workers. By combining repulsive, screened Coulombic, +screened charge-dipole, and dispersion interactions with a +bond-angle energy based on the Stillinger-Weber potential, this potential has been used to describe a variety of inorganic -compounds, including SiO2 Vashishta1990, -SiC Vashishta2007, -and InP Branicio2009. -

      -

      The potential for the energy U of a system of atoms is -

      -
      -
      -

      where we follow the notation used in Branicio2009. +compounds, including SiO2 Vashishta1990, +SiC Vashishta2007, +and InP Branicio2009.

      +

      The potential for the energy U of a system of atoms is

      +_images/pair_vashishta.jpg +

      where we follow the notation used in Branicio2009. U2 is a two-body term and U3 is a three-body term. The summation over two-body terms is over all neighbors J within -a cutoff distance = rc. The twobody terms are shifted and -tilted by a linear function so that the energy and force are -both zero at rc. The summation over three-body terms -is over all neighbors J and K within a cut-off distance = r0, -where the exponential screening function becomes zero. -

      -

      Only a single pair_coeff command is used with the vashishta style which +a cutoff distance = rc. The twobody terms are shifted and +tilted by a linear function so that the energy and force are +both zero at rc. The summation over three-body terms +is over all neighbors J and K within a cut-off distance = r0, +where the exponential screening function becomes zero.

      +

      Only a single pair_coeff command is used with the vashishta style which specifies a Vashishta potential file with parameters for all needed elements. These are mapped to LAMMPS atom types by specifying N additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: -

      -
      • filename -
      • N element names = mapping of Vashishta elements to atom types -
      -

      See the pair_coeff doc page for alternate ways -to specify the path for the potential file. -

      -

      As an example, imagine a file SiC.vashishta has parameters for +where N is the number of LAMMPS atom types:

      +
        +
      • filename
        • +
      • N element names = mapping of Vashishta elements to atom types
        • +
      +

      See the pair_coeff doc page for alternate ways +to specify the path for the potential file.

      +

      As an example, imagine a file SiC.vashishta has parameters for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following -pair_coeff command: -

      -
      pair_coeff * * SiC.vashishta Si Si Si C 
-
      -

      The 1st 2 arguments must be * * so as to span all LAMMPS atom types. +pair_coeff command:

      +
      pair_coeff * * SiC.vashishta Si Si Si C
+
      +
      +

      The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the file. The final C argument maps LAMMPS atom type 4 to the C element in the file. If a mapping value is specified as -NULL, the mapping is not performed. This can be used when a vashishta -potential is used as part of the hybrid pair style. The NULL values +NULL, the mapping is not performed. This can be used when a vashishta +potential is used as part of the hybrid pair style. The NULL values are placeholders for atom types that will be used with other -potentials. -

      -

      Vashishta files in the potentials directory of the LAMMPS -distribution have a ".vashishta" suffix. Lines that are not blank or +potentials.

      +

      Vashishta files in the potentials directory of the LAMMPS +distribution have a ”.vashishta” suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of elements. The parameters in a single entry correspond to the two-body -and three-body coefficients in the formulae above: -

      -
      • element 1 (the center atom in a 3-body interaction) -
      • element 2 -
      • element 3 -
      • H (energy units) -
      • eta -
      • Zi (electron charge units) -
      • Zj (electron charge units) -
      • lambda1 (distance units) -
      • D (energy units) -
      • lambda4 (distance units) -
      • W (energy units) -
      • rc (distance units) -
      • B (energy units) -
      • gamma -
      • r0 (distance units) -
      • C -
      • costheta0 -
      -

      The non-annotated parameters are unitless. +and three-body coefficients in the formulae above:

      +
        +
      • element 1 (the center atom in a 3-body interaction)
        • +
      • element 2
        • +
      • element 3
        • +
      • H (energy units)
        • +
      • eta
        • +
      • Zi (electron charge units)
        • +
      • Zj (electron charge units)
        • +
      • lambda1 (distance units)
        • +
      • D (energy units)
        • +
      • lambda4 (distance units)
        • +
      • W (energy units)
        • +
      • rc (distance units)
        • +
      • B (energy units)
        • +
      • gamma
        • +
      • r0 (distance units)
        • +
      • C
        • +
      • costheta0
        • +
      +

      The non-annotated parameters are unitless. The Vashishta potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular @@ -107,9 +223,8 @@ For a single-element simulation, only a single entry is required entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that specify parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 -entries would be required, etc. -

      -

      Depending on the particular version of the Vashishta potential, +entries would be required, etc.

      +

      Depending on the particular version of the Vashishta potential, the values of these parameters may be keyed to the identities of zero, one, two, or three elements. In order to make the input file format unambiguous, general, @@ -125,87 +240,145 @@ even though they only have 1 subscript. The three-body parameters are B, C, costheta0. They appear in the above formulae with three subscripts. Two-body and three-body parameters are handled differently, -as described below. -

      -

      The first element in each entry is the center atom +as described below.

      +

      The first element in each entry is the center atom in a three-body interaction, while the second and third elements are two neighbor atoms. Three-body parameters for a central atom I and two neighbors J and K are taken from the IJK entry. Note that even though three-body parameters do not depend on the order of J and K, LAMMPS stores three-body parameters for both IJK and IKJ. -The user must ensure that these values are equal. +The user must ensure that these values are equal. Two-body parameters for an atom I interacting with atom J are taken from the IJJ entry, where the 2nd and 3rd -elements are the same. Thus the two-body parameters +elements are the same. Thus the two-body parameters for Si interacting with C come from the SiCC entry. Note that even -though two-body parameters (except possibly gamma and r0 in U3) -do not depend on the order of the two elements, +though two-body parameters (except possibly gamma and r0 in U3) +do not depend on the order of the two elements, LAMMPS will get the Si-C value from the SiCC entry and the C-Si value from the CSiSi entry. The user must ensure that these values are equal. Two-body parameters appearing in entries where the 2nd and 3rd elements are different are stored but never used. It is good practice to enter zero for -these values. Note that the three-body function U3 above -contains the two-body parameters gamma and r0. So U3 for a +these values. Note that the three-body function U3 above +contains the two-body parameters gamma and r0. So U3 for a central C atom bonded to an Si atom and a second C atom will take three-body parameters from the CSiC entry, but -two-body parameters from the CCC and CSiSi entries. -

      -
      - -

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

      -

      For atom type pairs I,J and I != J, where types I and J correspond to +two-body parameters from the CCC and CSiSi entries.

      +
      +

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

      +

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

      +

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

      +

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

      +
      +

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

      +

      For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS as -described above from values in the potential file. -

      -

      This pair style does not support the pair_modify -shift, table, and tail options. -

      -

      This pair style does not write its information to binary restart -files, since it is stored in potential files. Thus, you +described above from values in the potential file.

      +

      This pair style does not support the pair_modify +shift, table, and tail options.

      +

      This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. -

      -

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

      -
      - -

      Restrictions: -

      -

      This pair style is part of the MANYBODY package. It is only enabled +script that reads a restart file.

      +

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

      +
      +
      +
      +

      Restrictions

      +

      This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package (which it is by default). See -the Making LAMMPS section for more info. -

      -

      This pair style requires the newton setting to be "on" -for pair interactions. -

      -

      The Vashishta potential files provided with LAMMPS (see the -potentials directory) are parameterized for metal units. +the Making LAMMPS section for more info.

      +

      This pair style requires the newton setting to be “on” +for pair interactions.

      +

      The Vashishta potential files provided with LAMMPS (see the +potentials directory) are parameterized for metal units. You can use the Vashishta potential with any LAMMPS units, but you would need to create your own Vashishta potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. -

      -

      Related commands: -

      -

      pair_coeff -

      -

      Default: none -

      -
      +appropriate units if your simulation doesn’t use “metal” units.

      +
      + +
      - -

      (Vashishta1990) P. Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990). -

      - +
      +
      +
      + -

      (Vashishta2007) P. Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007). -

      - +
      -

      (Branicio2009) Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 -

      - +
      +

      + © Copyright . +

      +
      + Built with Sphinx using a theme provided by Read the Docs. + +
      + +
      +
      + +
      + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/searchindex.js b/doc/searchindex.js index 1a50740453..b1f3ad6921 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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384,385,386,387,393,394,395,406,407,408,409,410,411,415,419,421,422,429,439,441,442,443,451,453,455,456,457,458,459,461,462,464,466,468,470,473,474,477,481,482,483,484,485,486],afterrun:464,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,451,453,454,456,458,463,470,472,482,484],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,451,483],aggress:[231,470],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13,350],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,451,453,470],alia:12,alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,456,459,477],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,453,454,455,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,473,474,475,477,481,482,483,484,485,486],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,456,464],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,398,402,407,408,413,419,422,423,426,428,437,446,448,451,454,456,458,459,460,461,462,463,466,468,469,470,473,474,482,483],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,454],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,456,459,466,467,482],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,474,477],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,456],alphanumer:[3,63,194,281,289,332,356,482],alreadi:[3,7,8,12,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,446,449,452,456,457,461,466,482],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,386,389,390,392,393,394,402,406,407,409,413,415,417,418,419,420,423,424,426,432,433,435,436,437,438,439,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460],co2:[40,164,295,356],coars:[7,9,29,36,40,54,177,277,292,307,391,424,468],coarser:[348,482],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,333,334,339,375,393,397,413,426,428,430,456,458],coeffcient:456,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,451],colberg:189,cold:[6,150,231,358,477],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,456,463,469,475,486],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,449],colllis:307,colloid:[],colombo:39,colon:[192,330,457],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,457,471,473,482],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,458],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,448,459,464,469,477,482],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,453,454,456,477,482],commerci:7,commmand:[3,6,12,59,107,270,450,451,453,470,485],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,456,459,468],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,345,347,358,359,360,362,383,417,453,454,458,465,466,482,484,486],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,451,470,471,477,481],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,453,454,482],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,456,457,461,482],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,451,456,461,464,468,470,473,477,482],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,454,456,459,482],compli:[314,318],complic:[6,7,9,12,13,201,227,454],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,456,457,466,474,482,483],componenet:6,composit:[6,201,238,384],compound:[377,386,387],compres:[71,114,203],compress:[3,6,9,12,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:477,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,485],concav:328,concentr:384,concept:[6,145,155,203,465],conceptu:[3,6,71,153,214,216,357,378,393,409,461],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348,482],conden:[319,441,443],condens:[6,147,319,364,380,384,398],condit:[],conducit:6,conduct:[],cone:459,confid:[3,470],config:[12,188,453],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,451,456,458,459,470],confin:[456,470],conflict:[3,12,40,413,454],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,468],confus:3,conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,456,459,463,477,486],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,453,454,460,477],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,451,457,459],consequ:[1,6,201,319,397,470],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,465,470],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,451,452,454,457,458,459,461,464,466,474,477,482],consider:[6,8,235,236,310,311,312,362,465],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,446,454,456,457,459,460,461,468,477,482],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,461,468,477],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,459,460,475,482],constructor:8,consult:422,consum:[1,287,417,482],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,451,452,453,454,456,457,458,459,461,463,465,468,470,473,474,477,482,484,486],content:[12,18,422,472,474],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,448,456,463,472,481,482,483],contibut:70,contigu:453,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,451,454,456,458,459,464,470,473,474,482,484],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,448,485],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,468,474,477],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,451,453,465,471,472],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,482],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,482],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,451,463,470],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,454,470,481],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,449,454,456,457,458,463,473,477,481,482,484,486],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,451,456,457,459,461,464,466,470,477,482,483],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,454],copper:449,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,469],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,468],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,328,329,350,445,456],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,447,448,449,456,471,474,477],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,453,454,456,466,481,483],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,447,448,449,451,453,454,456,457,459,469,470,471,473,474,477,482],correspondingli:[407,408,465],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,453,465],costheta0:[439,441,443],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,452,453,454,456,458,460,463,464,472,477,482,483],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,448,461,468,474,477,481],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,474,482],counter:[325,451,462,464,470],counterbal:231,counterpart:[188,292,451],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,453,456,469,477,482,484],courtesi:350,coval:[6,29,386,409,477],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,451,469,470,473,474,475,482],cpuremain:474,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,477],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,458,461,482],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,461,470,471],criterioni:470,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,449,456,460,466,484],crossov:1,crossterm:456,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,350,358,460,474,477],crystallin:[6,274,350,442,477],crystallis:314,crystallogr:[118,164],crystallograph:[350,474],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,456],cs_re:[40,456],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443],csinfo:6,csisi:[385,439,441,443],csld:[],cst:384,cstherm:6,cstyle:453,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,477],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,474],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256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220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,466,474,477,483],degress:[145,203],del:470,delai:[3,6,12,358,383,474],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,456,457,459,467,468,473,478,480,482,483],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[454,482],deloc:[252,386],delr:409,delt_lo:470,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:3,delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,456,465,466,474,481],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,216,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,447,448,449,451,453,456,458,459,462,466,468,470,473,474,476,482,483],dependend:6,depflag:12,dephas:[451,470],depos:217,deposit:[],deprec:283,depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,448,477],deriv:[6,7,8,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,448,477],derjagin:448,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,447,448,449,451,453,454,456,457,459,460,466,469,470,473,482,483,484],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,465],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,452,453,454,456,460,465,470,471,473,474,482,483,484],desk:7,desktop:[4,6,7,10,12,17,190],despit:477,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,447,448,454,456,457,458,459,461,462,465,466,468,471,474,475,482,483,486],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,451,453,456,467,470,482],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,448,453,456,457,459,461,463,466,470,472,473,475,481,482,483],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,458],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:477,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,448,456,457,466],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,464],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,448,450,451,453,454,456,458,459,460,461,464,465,466,468,470,471,473,474,475,477,481,482,483,484],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,465],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,459,481,482,483],dimdim:482,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,456,466],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,448],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,477],dir1:467,dir2:467,dir:[1,3,4,8,11,12,249,273,282,306,419,421,422,454,467,482],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,454,466,467,468,474,482],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,454,456,457,458,467,482],disabl:[3,12,16,319,397,454,469,482],disadvantag:[6,210],disallow:[188,216,251],disappear:458,discard:[2,3,41,71,206,210,320,328,453,458,459],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,454],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440],displac:[],displace_atom:[],displace_box:59,displacemet:459,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,451,483],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,454,456,459,465,466,470,474,477,481,483],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386,455],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,449,454],div:8,divd:117,diverg:[3,12,39,292,317,458,477,484],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,465,473,482],divis:[6,238,368,396,406,453,456,474,482],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,456,457,461],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:466,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlopen:6,dlvo:[7,376,448],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,454,456,457,458,459,461,464,465,466,473,474,482,483,484,485],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,452,453,454,456,457,458,459,460,463,464,466,467,468,469,470,473,474,477,482,486],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,456,458],dof:[3,8,112,144,145,158,203,292,483],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,456],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,451,453,456,460,473],domin:[1,386,470],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,454,456],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,451,452,453,454,457,460,461,464,474,475,477,482,483],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,452,456,460,464,469,482,483],dover:200,down:[3,6,7,8,11,39,71,214,235,307,323,362,386,413,455,475],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,453],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,451],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,465,473,477],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:470,dtqm:282,dtype:[115,212],dual:[17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,446,448,449,451,453,456,457,458,465,470,473,474,475,477,482,483],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:461,dump2:461,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:461,dunbrack:[6,20,171,373,468],dunweg:[235,237],duplic:[2,3,14,15,16,17,18,19,41,42,166,210,229,273,456,481],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,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415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,451,454,456,461,465,466,468,470,472,473,474,477,481,482,485],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,453,482,483],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,451],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,456,460,461],enpub:384,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439],enter:[57,155,387,470],enthalpi:[123,253,254,384,473,474,482],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,456,464,465],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443,482],entropi:470,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,453,467,482],epair:[107,191,388,392,421,422,474],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:448,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,447,448,465,477,481],epsilon_0:449,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,350,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,449,452,453,454,456,458,459,463,464,467,470,472,474,482,483],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,449,477],equi:252,equidist:250,equil:[3,283,351,463,486],equilater:466,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,452,466],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,477],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,456,459,464,465,474,477],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,456],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:481,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,456],escap:[217,477],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,453],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,461,474],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,470,474],esu:481,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,481],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,456],etail:474,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,451,454,456,457,458,463,465,466,470,472,473,474,475,477,481,482,484,486],ethernet:18,etol:[355,357,451,470],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,473,474],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,451,452,454,458,459,461,463,464,465,466,470,472,474,482,483],evalut:[332,454],evan:[153,269],evanseck:[6,20,171,373,468],evapor:[],evaul:[8,355],evdwl:[107,421,422,474],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,456,457,459,461,462,463,465,466,468,471,473,474,475,477,486],evenli:[3,41,141,185,210,238,396,446,456],event:[],eventu:[3,6,12,15,167,283,470],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,450,451,452,456,458,460,461,463,464,465,470,471,472,474,482,486],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,451],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,458],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,458,463,470,482,484,486],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,458,459,466,470,482],exager:477,examin:[6,8,9,213,274],examp:[454,482],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,456,482],exceed:[3,41,59,210,216,251,307,464],excel:386,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,327,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,447,448,449,451,453,454,456,458,459,461,464,465,466,467,468,470,474,477,481,482,483,485],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,471],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,468],exclus:[1,3,9,12,16,87,362,377,413,465,475],excurs:451,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,452,454,464,467,470,482],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,482],exhibit:[251,354,386,465],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,446,452,454,456,457,458,467,468,469,482,483,484],exit:[2,3,11,12,41,57,188,210,346,361,454,455,464,473,482],exlanatori:3,exp:[],expand:[],expans:[12,140,188,467,482],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,451,454,456,458,461,465,470,482],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,454],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,465,470],experienc:[6,12,240,241],experiment:[347,362,470],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,454,457,458,461,463,466,477,482,486],explan:[3,6,59,113,140,188,203,250,273,393,450,453,454,456,465],explanatori:[3,8,117,188,202,203,205,206,207,292,356,453,482],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,450,453,457,460],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,327,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,447,448,449,456,458,465,466,468,469,475,477],explictli:[16,469],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,449,470,482],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,482],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,473,474],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,453,456,459],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,453,454,456,459,468,477,482],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,454,461,473],extract_atom:11,extract_comput:[11,454],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,477],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,474,482],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,456,459],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,468],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,453,456,459,460,465,468,470,471,474,477,481,482],factori:[3,454],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,454],failur:[121,426,455,482],fairli:[11,413,465,470],faken:73,falcon:232,fall:[3,6,191,205,278,454,482],fals:[86,330,332,482],fame:8,famili:453,familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,454,456,461,474],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,459,468,482,485],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,458,463,465,474,483,486],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,216,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,327,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,447,448,449,451,465,469,477],fastest:[6,14,17,153,206,319,320,362,453],fatal:[3,473],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,482],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:481,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,468],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,453,456,461,465,467,475,482,484],fewer:[1,3,11,15,16,61,241,465],fewest:3,fextern:225,feynman:275,fff:454,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,465],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,475],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[457,461],field2:457,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,453,454],fij:381,file0:273,file1:[11,13,273,318,332,356,461,463,467],file2:[11,13,318,332,356,461,463,467],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,452,453,454,457,458,463,467,474,482,484,485,486],filennam:463,filep:[3,188,191,458,463,486],filepo:289,fill:[7,165,190,278,319,350,358,368,422,459],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,477,482],find_custom:8,fine:[16,17,169,197,222,317,358,362,482],finer:[140,165,482],finest:347,finger:[165,187,248,459],finish:[6,11,41,210,332,344,346,347,359,361,362,445,461,482,483],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,470],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,449,451,452,453,454,456,457,458,461,463,465,468,469,470,473,474,477,482,483,484,486],fischer:[6,9,19,20,171,373,468],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,464,482],five:[73,151,282,356,368,410,456,470],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,451,453,454,456,457,458,460,461,462,466,482],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,474],flip:[3,6,216,251,326,327],floor:482,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,473],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,474,477],fmackai:9,fmag:218,fmass:275,fmax:[355,474],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,465,476,481,483],fname:346,fno:12,fnorm:[355,474],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,465],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,447,448,449,451,453,454,456,457,458,459,461,463,464,465,468,470,471,472,477,482,483,485],foo:[4,8,11,12,188,190,225,454,467,482],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,477],forgiv:251,fork:[12,188],form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,159,160,169,173,191,194,195,196,212,228,229,235,237,241,248,269,274,285,287,291,292,319,324,328,333,334,341,352,354,356,357,364,365,368,375,384,386,388,392,393,397,409,411,415,416,419,421,422,423,429,430,438,440,441,442,443,448,450,453,454,456,461,466,473,477,482],formal:[6,78,80,91,228,229,235,251,275,307,315],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,173,185,188,189,190,191,192,203,205,206,207,208,210,212,274,277,281,283,285,288,292,293,303,318,319,330,331,334,352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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,451,452,453,456,457,459,461,463,464,465,468,470,472,473,474,475,476,481,483,484,485],"function":482,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,482],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,448],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,482],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92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,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],run_styl:465,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,424],self:306,serial:11,set:[6,466],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,467],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,482],special_bond:468,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:469,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,483,484,485,486],system:6,tabl:[0,6,38,56,185,440,441],tad:470,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:471,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,472],thermo_modifi:473,thermo_styl:474,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:475,timestep:476,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:13,torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:343,uncomput:478,u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\ No newline at end of file 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_serial":12,"abstract":17,"boolean":[3,330,332],"break":[],"byte":[3,12,474],"case":[1,2,3,6,8,9,11,12,13,15,16,17,18,39,40,41,45,46,59,61,63,71,73,104,108,114,116,117,143,144,145,146,148,151,152,153,154,155,157,158,159,163,165,167,168,169,171,188,189,190,191,197,198,202,203,204,205,206,207,208,209,210,212,214,216,220,222,224,227,230,231,233,234,235,236,238,249,251,252,253,254,255,256,257,268,269,271,273,274,279,281,282,283,284,291,292,294,296,298,299,301,304,307,310,311,312,314,315,319,321,322,324,325,327,328,329,330,332,346,347,348,350,352,354,355,356,357,359,361,362,364,373,376,378,380,384,386,389,390,392,393,394,396,406,407,408,409,413,415,419,422,425,427,430,440,441,443,450,452,455,457,459,460,464,465,467,469,471,473,474,475,476,478,482,483,484,486,487],"catch":[1,3,455],"char":[6,8],"class":[1,3,5,6,7,8,9,11,12,13,22,37,44,55,173,184,225,281,334,342,374,393,421,422,438,446,455,457],"default":[],"export":[190,375],"final":[3,5,6,7,8,11,12,17,41,59,87,141,191,202,203,204,205,206,207,208,210,214,216,227,250,251,255,282,286,292,293,296,316,318,319,326,332,355,357,363,364,368,384,387,394,406,409,415,419,420,439,440,441,443,446,452,465,471,478,483,485],"float":[3,6,8,12,40,42,71,113,188,191,203,208,232,281,293,309,386,426,428,455,457,467,474,483],"function":[],"import":[1,2,3,6,11,17,18,71,87,105,165,176,194,203,206,214,227,230,235,236,251,287,292,310,311,312,314,319,329,331,357,393,406,455,457,466,474,478],"int":[3,6,8,11,101,225,227,235,237,287,319,474],"long":[],"new":[],"null":[3,6,91,112,141,165,194,209,215,218,221,248,281,290,294,296,300,301,304,305,325,363,364,377,384,387,390,393,394,395,409,410,411,415,419,421,422,429,439,441,442,443,446,457,460,465,467,484],"public":[0,7,8,12,225,234,387,420],"return":[2,3,6,8,11,14,15,16,17,18,19,41,71,108,117,134,135,139,163,165,191,203,206,207,216,225,332,344,346,390,454,455,456,464,467,473,483],"short":[1,3,6,7,13,16,163,251,292,307,320,348,358,359,362,364,368,369,371,372,373,377,378,380,386,393,398,402,406,409,413,416,424,440,444,452,455,465,467,471,478],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,91,109,112,140,143,152,164,171,172,174,175,176,177,179,180,182,183,185,190,193,197,201,209,216,223,226,230,234,235,238,251,253,254,255,256,257,258,266,268,269,271,284,292,294,295,310,312,316,317,323,327,333,335,336,337,338,341,343,344,346,348,351,357,361,362,363,364,366,369,370,371,372,373,374,376,377,378,381,382,384,385,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,421,423,424,430,439,440,441,442,443,445,446,448,449,450,451,452,454,457,459,464,466,470,472,483,485,487],"throw":474,"true":[6,12,13,17,108,115,188,210,212,216,251,252,273,274,275,279,292,314,318,330,332,362,386,390,439,455,459,467,483],"try":[1,3,8,12,17,19,203,232,238,315,316,317,322,455,483],"var":[3,11,12,165,330,346,468,483],"void":[4,6,7,8,41,168,210,225,460],"while":[1,3,9,10,11,12,13,14,18,71,105,140,148,163,176,188,192,201,207,214,216,220,228,229,234,235,236,238,251,269,282,287,289,320,348,355,362,368,379,384,422,441,443,446,452,455,466,471,478],a10:332,a123:332,a12:423,a2m:[6,91],a_0:[238,319,368],a_0_real:238,a_1:319,a_2:319,a_3:319,a_4:319,a_c:376,a_cc:376,a_f:443,a_i:444,a_ij:368,a_j:444,a_pi:368,a_sigma:368,a_ss:376,aacut:274,aat:172,aatom1:115,aatom2:115,aatom3:115,ab_23_cd:332,abbrevi:12,abc:[3,12,332,455,483],abf:215,abf_integr:13,abi:192,abil:[3,9,214,251,279,292,386],abl:[3,8,11,12,39,86,188,192,213,222,226,315,322,362,455,483,486],ablat:319,about:[0,1,3,4,6,8,9,10,11,12,13,17,39,41,42,61,63,78,108,115,116,118,159,165,188,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,220,221,222,223,224,225,226,227,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,250,255,258,259,260,261,262,263,264,265,266,267,272,273,274,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,294,295,304,305,307,308,310,311,312,313,314,315,316,317,318,319,321,322,323,324,326,327,328,329,330,345,348,354,355,357,362,367,373,378,393,418,422,449,455,458,459,464,465,467,472,476,483,485,487],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,63,64,68,70,71,72,73,76,77,86,87,89,90,91,93,94,96,97,112,114,116,118,140,141,143,144,145,146,147,148,151,152,153,154,155,157,158,159,163,164,165,167,168,171,172,173,174,175,176,177,178,179,180,182,183,185,188,189,190,191,194,195,196,197,198,203,204,205,206,207,208,210,213,214,216,217,222,225,227,231,233,235,236,237,241,250,251,255,275,278,280,285,291,292,296,304,307,310,311,312,313,330,332,333,334,335,336,337,338,339,341,343,348,350,352,356,357,361,362,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,416,418,419,421,422,423,424,429,430,431,432,433,434,435,436,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326,330,333,334,339,346,352,353,355,356,358,360,361,362,363,364,368,375,377,384,385,386,387,393,394,395,406,407,408,409,410,411,415,419,421,422,429,439,441,442,443,446,452,454,456,457,458,459,460,462,463,465,467,469,471,474,475,478,482,483,484,485,486,487],afterrun:465,afterward:3,afterword:41,ag1:164,ag2:164,again:[6,11,12,16,17,62,140,145,147,151,159,188,191,216,231,278,333,346,357,407,408,452,454,455,457,459,464,471,473,483,485],against:[11,12,13,64,217,357,421,422],aggreg:[6,12,65,68,69,79,92,108,115,231,247,290,292,305,452,484],aggress:[231,471],agilio:[9,13],agre:[3,8,185,355,364,395,422],agreement:[5,7],ahd:392,ahead:326,aidan:[0,5,7,9,13,350],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:190,akohlmei:[7,9,13,192,232],aktulga:[7,9,285,422],al2o3_001:[118,293],al3:164,ala:238,alain:9,alat:[273,409],alb:[419,441,443],albeit:291,albert:9,alchem:[87,159],alcohol:322,alcu:[363,368],alcu_eam:419,alderton:381,alejandr:[251,252],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,191,200,210,213,216,238,240,241,263,275,292,295,314,315,319,322,327,353,354,355,359,362,386,408,426,428,452,454,471],alia:[12,16],alias:[1,348],aliceblu:191,align:[6,12,29,41,71,167,185,206,210,233,350,457,460,478],alkali:386,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,158,159,160,161,162,163,164,165,166,167,168,169,171,173,178,184,185,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,244,246,247,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,293,294,295,296,297,298,299,303,304,306,307,308,309,310,311,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,337,342,345,346,347,348,349,350,352,355,356,357,358,359,361,362,363,364,365,367,368,369,371,372,373,374,375,377,378,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,402,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,454,455,456,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,474,475,476,478,482,483,484,485,486,487],allen:[29,87,381,389],allentildeslei:87,allign:3,allindex:331,alloc:[3,5,6,8,9,11,12,60,225,321,356,358,362,417,422,457,465],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,142,144,145,158,163,164,165,167,173,184,185,188,190,191,192,194,195,197,199,200,201,203,204,205,206,207,208,210,212,213,214,215,216,217,221,222,225,227,228,229,230,232,235,238,241,242,246,248,251,252,273,277,279,280,281,282,286,292,293,295,296,298,299,303,307,314,315,316,317,319,320,321,322,323,324,330,332,334,342,347,348,350,355,356,357,358,361,362,365,368,369,370,371,372,373,378,384,386,390,391,392,393,398,402,407,408,413,419,422,423,426,428,437,447,449,452,455,457,459,460,461,462,463,464,467,469,470,471,474,475,483,484],almost:[2,3,12,60,233,282,319,348,359,362,437],alo:378,alon:[6,7,213,288,421,422,455],alond:13,along:[6,8,9,12,29,40,87,118,164,165,187,188,190,213,233,238,239,243,248,250,282,292,295,296,300,304,305,314,318,319,325,328,330,350,353,354,355,357,378,381,390,393,396,398,402,409,421,422,440,457,460,467,468,483],alonso:[410,411],alpha:[6,12,51,195,238,274,282,287,355,363,366,369,378,382,384,385,387,392,397,398,409,414,418,442,444,475,478],alpha_:444,alpha_c:406,alpha_i:[429,444],alpha_ialpha_j:444,alpha_lj:406,alphabet:[2,3,22,37,44,55,63,173,184,194,334,342,356,375,438,457],alphanumer:[3,63,194,281,289,332,356,483],alreadi:[3,7,8,9,12,16,17,18,42,165,166,168,189,199,203,206,207,210,212,216,242,280,282,307,330,356,357,382,391,393,400,408,437,447,450,453,457,458,462,467,483],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,157,158,159,160,161,162,163,165,166,167,168,169,171,173,184,185,186,188,189,190,191,192,194,195,196,197,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,222,225,226,227,228,229,231,232,235,236,237,238,248,249,251,252,253,254,255,256,257,262,265,266,268,269,270,271,273,274,275,277,278,279,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,300,301,304,305,307,310,311,312,313,314,318,319,320,321,323,325,328,330,332,334,339,342,345,347,348,350,351,352,355,356,357,358,359,361,362,368,372,373,375,379,380,381,382,384,385,3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22,389,423,437,447],cloud:478,clovertown:18,clsuter:72,clump1:[277,292],clump2:[277,292],clump3:[277,292],clump:292,cluster:[],clutter:[3,9],cmap:457,cmatrix:229,cmax:409,cmd:[11,12,275,468],cmin:409,cmm:[],cn1:204,cn2:204,cna:[],cnn:204,cnr:[9,13],cnt:[393,461],co2:[40,164,295,356],coars:[7,9,29,36,40,54,177,277,292,307,391,424,469],coarser:[348,483],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,171,172,173,178,333,334,339,375,393,397,413,426,428,430,457,459],coeffcient:457,coeffici:[],coefficienct:382,coefficient0:384,coefficient1:384,coeffieci:[6,366],coeffincientn:384,coexist:[9,227,386],cohes:[6,387,409],coincid:[122,328,373,407,408,452],colberg:189,cold:[6,150,227,231,358,478],coldest:315,coleman8:9,coleman:[9,118,164,293],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,145,153,160,162,165,188,191,203,215,241,247,277,287,290,292,330,347,356,358,376,396,457,464,470,476,487],collid:[221,307,329],colliex:164,collinear:[3,277],collis:[3,238,307,325,329,383,390,450],colllis:307,colloid:[],colombo:39,colon:[192,330,458],color1:191,color2:191,color:[3,9,41,188,190,191,210,228,282,287],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,145,153,160,162,163,164,185,188,191,194,202,203,204,205,206,207,208,241,248,249,282,292,308,309,319,329,388,392,421,422,458,472,474,483],colvar:[],colvarmodul:12,com:[],comamnd:216,comand:[213,459],comannd:362,comb3:[],comb:[],comb_1:284,comb_2:284,combiant:379,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,144,158,188,190,200,205,232,241,251,275,281,311,320,328,331,333,347,348,350,354,362,376,378,379,386,387,393,405,406,429,439,441,443,446,449,460,465,470,478,483],come:[],comfort:[12,13],comm:[0,3,12,61,73,189,232,234,235,348,357,362,382,413,418,440],comm_modifi:[],comm_modift:61,comm_styl:[],command:[],comment:[2,7,11,12,38,56,171,185,188,236,292,319,356,357,363,384,385,387,397,409,415,422,429,439,440,441,442,443,446,454,455,457,478,483],commerci:7,commmand:[3,6,12,59,107,270,451,452,454,471,486],common:[],commonli:[3,6,12,17,25,57,59,105,167,188,190,192,343,391,400,429,441,443,457,460,469],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,169,190,191,210,211,212,214,215,216,232,234,238,240,241,242,251,274,281,283,284,285,292,307,319,330,345,347,358,359,360,362,383,417,454,455,459,466,467,483,485,487],communc:347,comp:[7,189,234,235,295,348,357,386,413,418,423,436,440,442],compact:[63,194,375,438],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,148,163,164,173,184,191,220,283,330,332,347,348,355,357,409,452,471,472,478,482],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,172,173,184,333,334,342,374,438],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,176,188,192,196,202,203,204,205,206,207,208,210,274,286,311,314,321,324,327,347,362,394,413,440,454,455,483],compens:[6,211,212,290,358,386],compet:318,competit:348,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,163,188,189,190,192,232,318,348,362,457,458,462,483],compl:17,complain:[12,17],complement:409,complementari:[7,378,398],complet:[3,6,9,12,15,41,59,71,191,206,210,215,241,275,278,281,307,318,320,332,346,357,362,387,426,428,445,452,457,462,465,469,471,474,478,483],complex:[6,8,11,12,13,25,40,42,62,140,142,153,165,166,238,303,328,345,357,386,440,455,457,460,483],compli:[314,318],complic:[6,7,9,12,13,201,227,455],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,160,161,162,188,190,191,197,198,202,203,204,205,206,207,208,209,213,214,216,217,222,225,230,234,235,238,241,243,247,248,250,251,252,255,256,257,268,269,271,272,274,275,276,279,290,292,294,295,296,300,301,304,307,310,311,312,314,321,322,327,328,329,347,350,354,355,356,357,362,382,386,390,407,408,426,428,429,457,458,467,475,483,484],componenet:6,composit:[6,201,238,384],compound:[377,386,387,446],compres:[71,114,203],compress:[0,3,6,59,71,114,168,188,190,191,203,216,249,255,279,282],compris:[40,328,396,423,445],compton:[118,164],comptu:[3,6],compuat:348,comput:[],computation:[3,6,211,212,319,368],computational:478,compute_arrai:8,compute_fep:[196,406],compute_group_group:227,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,293],compute_scalar:8,compute_temp:8,compute_ti:196,compute_vector:8,compute_xrd:164,concaten:[2,3,486],concav:328,concentr:384,concept:[6,145,155,203,466],conceptu:[3,6,71,153,214,216,357,378,393,409,462],concern:[6,73,87,189,228],concis:[11,318],conclud:12,concret:8,concurr:[9,16,348,483],conden:[319,441,443],condens:[6,147,319,364,380,384,398,446],condit:[],conducit:6,conduct:[],cone:460,confid:[3,471],config:[12,188,454],configfil:215,configur:[1,2,6,12,15,17,38,59,122,167,185,187,188,190,194,214,215,216,217,221,227,234,235,263,275,283,318,345,355,357,364,368,385,409,439,441,443,446,452,457,459,460,471],confin:[457,471],conflict:[3,12,40,413,455],conform:[3,6,13,59,213,214,250,291,296,318,341,357,386,469],confus:[3,446],conjuct:382,conjug:[7,8,235,354,386,421,422],conjunct:[6,7,71,86,87,114,148,153,159,165,169,191,195,196,235,238,242,263,278,279,283,284,285,287,292,307,315,322,327,347,348,357,369,371,375,378,382,386,392,398,413,416,424,444,457,460,464,478,487],connect:[3,6,87,150,168,213,232,277,292,295,304,357,379,390,437,443,454,455,461,478],conput:3,consecut:[3,11,12,39,71,165,191,195,196,217,232,233,378,398,402,452,458,460],consequ:[1,6,201,319,397,471],conserv:[3,194,201,213,220,221,228,231,235,237,238,242,247,249,251,263,292,295,310,311,315,322,323,327,357,381,382,390,404,466,471],consid:[6,9,70,71,78,87,115,147,150,151,168,188,191,195,196,202,204,206,210,212,213,217,239,252,274,292,314,315,318,319,322,348,375,386,393,422,423,437,452,453,455,458,459,460,462,465,467,475,478,483],consider:[6,8,235,236,310,311,312,362,466],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,145,148,150,165,177,187,192,197,198,203,216,217,220,222,225,228,235,236,237,248,251,253,254,255,256,257,258,259,261,262,263,264,266,267,268,269,270,271,279,282,287,289,291,292,310,311,312,313,323,347,348,350,356,357,362,364,368,370,376,378,386,389,393,407,408,409,413,423,426,428,440,447,455,457,458,460,461,462,469,478,483],consistent_fe_initi:200,consit:292,constant:[],constitu:[3,6,241,292,324,328,376,423],constitut:[426,428],constrain:[3,6,8,143,144,145,146,148,151,152,153,154,155,157,158,194,203,217,227,228,233,241,245,277,278,290,292,295,305,315,322,355,356,386,462,469,478],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,118,140,164,214,251,274,291,328,358,362,381,413,437,439,440,460,461,476,483],constructor:8,consult:422,consum:[1,287,417,483],consumpt:345,contact:[],contact_stiff:[425,427],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,145,153,163,164,165,167,171,173,184,185,188,190,191,192,194,195,196,200,202,203,204,205,206,207,208,210,215,217,222,229,233,234,235,236,238,249,263,273,274,277,278,280,282,285,289,292,293,297,307,314,318,319,328,329,332,346,348,356,357,360,361,363,364,365,368,377,378,381,384,385,386,393,394,409,415,419,420,421,422,429,439,440,441,442,443,444,446,452,453,454,455,457,458,459,460,462,464,466,469,471,474,475,478,483,485,487],content:[12,18,422,473,475],context:[3,6,8,12,17,117,191,211,212,217,277,289,323,354,449,457,464,473,482,483,484],contibut:70,contigu:454,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,161,191,194,195,196,201,203,204,205,206,207,208,210,213,214,215,216,217,227,228,229,231,232,233,235,236,237,243,248,249,251,253,254,255,256,257,268,269,270,271,276,278,281,282,292,293,296,306,307,309,316,317,319,325,328,332,346,361,362,368,382,383,400,403,421,422,423,426,428,442,452,455,457,459,460,465,471,474,475,483,485],continuum:[6,7,9,200,319,426,428],contour_integr:200,contract:[59,214,216,251,279,292],contradictori:3,contrain:295,contraint:263,contrari:[229,236],contrast:[1,6,42,55,64,150,216,330,426,428,449,486],contrib:319,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,196,201,202,203,204,205,206,207,208,214,227,235,238,241,242,246,252,269,270,277,278,286,289,292,293,295,321,347,355,357,365,382,383,384,386,393,407,408,413,421,422,469,475,478],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,122,140,174,188,190,194,200,201,210,214,215,216,231,232,235,236,251,253,254,255,256,257,279,284,292,298,299,310,311,312,319,323,345,347,359,386,389,421,422,425,427,439,443,452,454,466,472,473],control_typ:200,controlfil:422,convect:91,conveni:[6,12,29,188,192,208,293,350,429,483],convent:[3,8,9,29,176,183,184,191,291,304,331,384,386,483],converg:[3,6,41,88,188,190,192,197,210,213,214,222,225,255,282,284,287,291,295,353,354,355,357,377,378,398,452,464,471],convers:[3,8,140,190,191,201,204,279,347,378,379,380,386,398,402,406,416,455,471,482],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,165,172,188,190,191,208,249,330,333,335,338,341,350,357,363,384,441,443,450,455,457,458,459,464,474,478,482,483,485,487],convex:328,convinc:[7,12],cook:9,cooki:7,cool:[7,155,231,290],cooordin:188,cooper:[5,7],coord123:114,coord1:[3,114,203,206,207],coord2:[3,114,203,206,207],coord3:[3,114,203,206,207],coord:[],coordiat:355,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,148,154,160,162,163,165,169,187,188,189,190,191,192,194,197,202,203,205,206,207,210,211,212,213,214,215,216,217,220,222,223,225,227,230,231,232,233,234,235,236,248,250,251,253,254,256,257,269,272,273,274,277,278,279,289,290,292,294,295,296,301,304,305,306,307,309,317,318,319,326,327,329,330,350,355,356,357,362,363,364,367,385,452,457,458,460,462,465,467,471,478,483,484],coordn:[114,203],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,190,319,357,375,421,455],copper:450,coproccesor:16,coprocessor:[1,4,7,9,16,17,362,470],coproprocessor:17,copy_arrai:8,copyright:[7,8,277],coral:191,core:[],core_shel:147,coreshel:[6,9,371,378,380],cornel:[6,171,469],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,190,328,329,350,445,457],cornflowerblu:191,cornsilk:191,corpor:16,corr:377,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,147,152,159,190,216,227,229,235,251,252,269,277,279,282,318,324,328,347,357,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,448,449,450,457,472,475,478],correction_max_iter:200,correctli:[3,8,9,11,17,71,81,102,103,143,144,146,148,150,151,152,153,154,157,158,161,188,191,197,217,222,225,236,245,251,252,285,292,295,304,306,325,328,357,358,362,380,408,454,455,457,467,482,484],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,143,144,152,159,164,171,172,173,174,175,176,177,179,180,182,183,185,188,190,191,195,196,197,203,205,206,207,209,212,214,216,223,225,226,230,235,238,239,247,248,249,251,253,254,255,256,257,258,263,266,268,269,271,274,275,279,284,292,294,295,310,312,314,323,324,325,327,328,329,331,333,334,335,336,337,338,341,343,348,352,354,356,357,363,364,366,369,370,371,372,373,374,375,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,413,414,415,416,418,419,421,422,423,424,429,430,439,440,441,442,443,445,446,448,449,450,452,454,455,457,458,460,470,471,472,474,475,478,483],correspondingli:[407,408,466],cosin:[],cosineshift:27,cosmo:[229,234],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,164,190,191,203,206,207,210,211,212,224,251,284,319,347,348,360,378,398,402,413,439,454,466],costheta0:[439,441,443,446],costheta:419,costli:[11,88,229,358],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,145,155,160,162,178,188,190,191,195,196,203,204,206,210,216,225,234,281,282,283,287,290,292,294,307,308,314,318,319,320,324,328,330,332,339,344,346,353,355,358,362,365,388,392,393,421,422,453,454,455,457,459,461,464,465,473,478,483,484],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,116,141,166,170,283,285,320,347,348,355,362,369,371,372,373,374,377,378,379,380,381,386,390,391,393,398,402,406,413,416,421,422,424,438,443,444,446,449,462,469,475,478,482],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,114,116,117,153,163,169,197,198,201,203,205,206,207,209,210,217,222,224,227,233,251,263,278,295,310,311,328,348,355,356,357,359,362,388,392,413,475,483],counter:[325,452,463,465,471],counteract:227,counterbal:231,counterpart:[188,292,452],counterproduct:18,coupl:[],courant:297,cours:[3,8,126,128,159,188,195,196,228,291,304,318,324,326,327,329,330,348,407,430,454,457,470,478,483,485],courtesi:350,coval:[6,29,386,409,478],covari:229,cover:[6,71,185,191,200,238,386,396,445],coverag:[71,206],cpc:234,cpp:[1,3,6,8,9,11,12,13,87,188,195,196,225,295],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,191,194,220,236,320,345,348,362,375,438,452,470,471,474,475,476,483],cpuremain:475,cr2:164,cr3:164,crack:[4,358],crada:[5,7],crai:[5,7,13,18,188],crash:[3,12,358,478],craympi:362,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:200,create_faceset:200,create_group:189,create_nodeset:200,createatom:[],creation:[],crimson:191,critchlei:277,criteria:[3,116,166,190,191,211,212,213,246,355,418,445,459,462,483],criterion:[12,41,121,163,165,168,201,210,213,227,263,284,297,325,330,355,357,377,386,390,462,471,472],criterioni:471,critic:[48,49,249,314,319,355],cross:[3,12,22,71,89,144,173,188,190,202,206,212,216,248,250,269,292,300,304,306,315,322,334,350,357,373,382,383,384,391,392,393,398,400,402,419,424,426,428,441,443,450,457,461,467,485],crossov:1,crossterm:457,crozier:[0,7,13],crucial:282,crystal:[4,6,13,73,273,274,317,350,358,461,475,478],crystallin:[6,274,350,442,478],crystallis:314,crystallogr:[118,164],crystallograph:[350,475],crystallographi:[118,164,350],cs1:164,cs_chunk:6,cs_im:[40,457],cs_re:[40,457],csanyi:[140,420,429],cscl:409,csequ:6,csh:[11,12,375],cshrc:[11,12],csic:[385,439,441,443,446],csinfo:6,csisi:[385,439,441,443,446],csld:[],cst:384,cstherm:6,cstyle:454,csvr:[],ctcm:[363,384],ctemp_cor:220,cterm:296,ctr:9,ctype:11,cu1:164,cu2:164,cu3au:409,cube:[6,41,163,168,210,220,328,350,478],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:368,cummul:[3,6,208,211,212,213,215,224,229,235,237,307,310,311,312,313,315,322,392,475],cumul:[6,201,203,205,206,207,221,227,235,249,251,255,263,292,293,357],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,145,153,155,161,163,166,169,188,189,190,191,192,195,196,200,203,206,207,208,210,211,212,213,214,215,216,217,221,222,225,227,229,232,233,235,241,248,251,252,256,257,263,268,269,271,277,283,284,286,289,290,291,292,295,296,297,298,299,300,301,303,305,306,307,310,311,312,318,319,322,323,324,325,326,327,329,330,332,345,346,347,348,351,352,354,355,356,357,362,368,375,377,381,384,386,387,390,393,394,397,407,408,409,410,411,413,419,421,422,425,426,427,428,430,441,443,444,447,452,453,454,455,457,458,459,460,461,463,464,465,467,469,471,472,474,475,483,484,485,486,487],curv:[6,165,227,274],curvatur:[389,423,450],custom:[],cut0:455,cut1:466,cut2:466,cut:[],cuthi:[273,285],cutinn:[370,407,408],cutlo:[273,285],cutmax:419,cutoff1:[374,381,398,402,406,416,424],cutoff2:[369,371,372,374,380,381,398,402,406,416,424],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,163,166,168,212,213,218,273,282,283,285,287,289,292,307,320,324,328,330,345,347,348,355,358,359,360,362,363,364,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,387,388,389,391,392,393,394,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,455,459,462,466,478,483],cutoffa:385,cutoffc:385,cuu3:384,cval:164,cvd:314,cvel:296,cvff:[],cwiggl:[3,248,324,327,329,483],cyan:[2,190,191],cycl:[3,227,249,251,252,255],cyclic:[3,185],cygwin:12,cylind:[3,4,190,233,278,325,328,460],cylindr:[6,233,304,325],cypress:362,cyrot:368,cyrstal:274,d3q15:238,d3q19:238,d_double_doubl:15,d_e:319,d_flag2:281,d_flag:281,d_name:[113,188,281,309,467],d_single_doubl:15,d_single_singl:15,d_sx:281,d_sy:281,d_sz:281,daan:317,dai:12,daili:12,daivi:269,damag:[],dammak:287,damp:[3,6,194,199,235,236,237,242,251,252,255,279,282,287,292,310,311,323,325,326,354,355,357,369,371,373,378,381,386,390,398,406,416,424,438,444,471,478],damp_com:236,damp_drud:236,dampen:[292,478],dampflag:[325,390],dan:17,danger:[3,12,227,330,382,475],dangl:168,daniel:9,darden:[348,381],darkblu:191,darkcyan:191,darken:190,darkgoldenrod:191,darkgrai:191,darkgreen:191,darkkhaki:191,darkmagenta:191,darkolivegreen:191,darkorang:191,darkorchid:191,darkr:191,darksalmon:191,darkseagreen:191,darkslateblu:191,darkslategrai:191,darkturquois:191,darkviolet:191,dasgupta:283,dash:[390,474],dat:[6,91,185,200,453],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,293],dataset:293,datatyp:3,date:[0,6,12,13,421,422,483],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,188,204],davi:324,david:[9,19,347,348,441,443],daw:[384,419],dbg:14,dcd:[3,6,7,188,189,190,191,192,275,458,462],ddim:187,deactiv:406,dealt:234,debug:[6,7,11,12,13,14,17,118,122,164,165,275,280,345,347,362,394,413,447,455,456,459,464,467,474,483],deby:[],decai:[378,450],decid:[3,6,12,16,71,248,281,292,320,472],decipher:350,declar:189,declin:307,decod:190,decompos:[87,429],decomposit:[3,5,7,18,62,200,275],decoupl:[6,478],decreas:[3,188,197,198,213,216,222,225,227,235,318,347],decrement:296,deepli:344,deeppink:191,deepskyblu:191,def:[12,13,455],defaul:61,defect:[6,70,163],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,171,172,173,174,175,176,177,179,180,182,183,184,185,186,187,188,189,190,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,220,221,222,225,226,227,230,233,234,235,236,237,238,246,248,250,251,252,253,254,255,256,257,259,260,261,264,266,267,268,269,270,271,273,274,275,277,278,279,281,283,285,290,292,293,294,295,297,301,305,307,309,310,311,312,313,315,316,317,319,321,322,324,325,326,327,328,329,330,332,333,334,335,336,337,338,341,342,343,345,347,348,350,352,354,355,356,357,358,359,360,361,362,364,365,366,367,369,370,371,372,373,374,375,376,378,379,381,382,383,385,386,388,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,412,413,414,415,416,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,454,455,457,458,460,461,462,463,466,467,468,469,471,472,474,475,478,479,480,481,482,483,484],definit:[2,3,6,8,12,13,78,80,116,140,191,203,204,205,206,207,208,216,233,255,293,309,321,324,327,329,331,342,345,356,365,368,376,386,396,419,426,428,429,445,455,457,459,466,468,482,483],defint:475,deform:[],deg2theta:164,deg:478,degener:[3,277],degrad:[8,18,274,348,466],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,143,144,145,146,147,148,149,150,151,152,153,154,155,157,158,164,165,171,172,175,176,183,185,187,190,203,213,220,227,229,230,235,236,241,251,252,255,256,257,268,269,271,275,277,291,292,295,310,311,312,317,333,335,338,341,343,355,381,384,392,467,475,478,484],degress:[145,203],del:471,delai:[3,6,12,358,383,475],deleg:393,delet:[2,3,7,8,12,54,57,60,63,163,168,169,194,203,204,205,206,207,208,211,213,224,227,251,293,310,311,330,332,346,356,358,361,413,457,458,460,468,469,474,479,481,483,484],delete_atom:[],delete_bond:[],delete_el:200,deli:187,delimit:[455,483],deloc:[252,386],delr:409,delt_lo:471,delta:[],delta_1:368,delta_3:368,delta_7:368,delta_conf:3,delta_ij:[409,419],delta_mu:3,delta_pi:368,delta_r:419,delta_sigma:368,delx:187,delz:187,demand:287,demo:11,demon:272,demonstr:[282,409],den:278,dendrim:392,denniston:[9,238,240,241,242,274],denomin:[7,170],denot:[118,220,236,274,285,287,378,391,393,422,426,428],dens:[71,213,386],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,151,163,165,195,196,200,203,206,207,210,216,225,238,241,244,245,274,278,279,283,319,324,350,352,356,363,368,384,409,410,411,419,423,432,434,435,436,457,466,467,475,482],density_continu:428,density_summ:428,depart:[0,7],departur:[249,282],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,143,148,152,153,159,165,166,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,190,191,194,195,196,197,198,201,203,205,206,208,209,210,212,214,216,222,223,226,229,230,231,233,235,236,238,240,241,248,251,253,254,255,256,257,258,266,268,269,271,273,284,287,289,292,294,295,301,307,310,311,312,314,316,318,319,321,323,324,327,328,329,330,332,333,334,335,336,337,338,341,343,348,350,355,356,358,359,360,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,409,410,412,414,415,416,418,419,421,422,423,424,429,430,438,439,440,441,442,443,444,445,446,448,449,450,452,454,457,459,460,463,467,469,471,474,475,477,483,484],dependend:6,depflag:12,dephas:[452,471],depos:217,deposit:[],deprec:[283,421],depth:[51,144,190,319,389,423],dequidt:9,der:[87,107,376,377,406,421,422,449,478],deriv:[6,7,8,9,38,56,63,87,140,159,185,204,214,216,227,235,248,251,253,254,255,256,257,273,279,283,287,316,317,319,324,325,328,354,356,364,368,376,381,386,387,391,400,404,405,409,421,422,438,440,449,478],derjagin:449,derlet:273,descend:191,descent:[7,354],descib:[40,283],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,144,145,149,150,153,156,158,159,163,164,165,167,168,177,182,185,188,189,194,195,196,203,204,205,206,207,208,210,213,214,215,216,217,219,220,228,229,232,233,234,235,236,237,238,240,241,242,246,250,251,252,255,262,270,273,275,280,281,282,283,284,285,292,296,304,307,308,309,310,311,312,313,314,315,316,317,322,324,325,327,332,347,348,350,353,354,355,356,357,361,364,365,367,369,370,371,373,374,375,376,377,378,381,384,386,387,389,390,391,393,398,399,400,401,402,403,404,405,406,407,408,409,412,418,419,420,421,422,423,424,429,430,437,438,439,440,441,442,443,444,446,448,449,450,452,454,455,457,458,460,461,467,470,471,474,483,484,485],descript:[],descriptor:[140,188,394],deserno:348,design:[0,3,6,7,8,9,11,13,14,15,17,118,147,150,164,200,213,219,220,251,252,273,274,293,314,319,365,366,367,370,373,378,380,386,406,407,408,410,411,419,422,440,466],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,112,117,141,147,165,178,187,203,208,214,216,225,227,228,235,236,237,241,251,269,277,278,279,280,283,287,292,295,307,310,311,312,313,318,325,339,344,347,348,350,353,355,356,357,382,384,392,407,408,439,441,443,453,454,455,457,461,466,471,472,474,475,483,484,485],desk:7,desktop:[4,6,7,10,12,190],despit:478,destabil:368,destre:341,destroi:[11,39,211,212],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,143,144,145,148,158,159,160,162,165,166,169,170,173,184,188,190,191,194,195,196,200,203,204,205,206,208,210,212,213,214,215,216,217,225,227,228,229,230,232,233,235,237,238,242,248,249,250,251,252,253,254,255,256,257,261,263,268,269,270,271,274,277,278,279,281,282,284,285,286,292,295,307,310,311,312,313,314,315,317,318,319,320,321,322,323,330,332,334,342,347,348,351,355,356,358,359,362,363,364,365,367,368,370,372,373,374,375,376,377,378,381,382,386,387,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,409,412,413,418,421,422,423,429,430,438,445,448,449,455,457,458,459,460,462,463,466,467,469,472,475,476,483,484,487],detect:[2,3,12,61,63,86,226,278,318,357,377,392,397,452,454,457,468,471,483],determ:362,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,153,154,163,164,165,187,188,190,191,192,193,197,198,199,202,203,204,205,206,207,208,209,210,214,216,217,220,222,227,230,231,233,235,236,241,246,248,249,251,256,257,268,269,271,273,275,279,282,289,290,291,292,293,294,297,299,301,307,310,311,312,314,320,321,324,325,326,327,328,329,330,342,347,348,350,356,358,359,362,364,365,372,377,381,383,384,388,390,393,394,402,409,413,422,423,437,440,444,449,454,457,458,460,462,464,467,471,473,474,476,482,483,484],detil:108,devan:[9,424],devanathan:443,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,232,255,277,282,283,286,364,368,386,411,446,459],devemi:9,deviat:[249,255,273,388],deviator:9,devic:[1,3,12,15,17,232,362],device_typ:362,devin:[284,377],devis:411,dfactor:190,dff:478,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,348],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,286],dhi:[59,187,216,278],dhug:[249,282],dhugoniot:[249,282],dia:409,diagnost:[],diagon:[3,6,83,140,141,142,214,251,279,292,322,426,428],diagonalstyl:429,diagram:[41,118,164,184,210,275],diallo:392,diam:[190,191,278,356],diamet:[3,6,40,113,165,188,190,191,195,196,235,278,292,307,323,325,356,376,389,390,396,400,423,445,449,457,458,467],diamond:[350,386,409],diamter:[40,278],dick:6,dicsuss:248,dictat:[201,249],did:[3,12,355,382,383,384,390,413,441,443,465],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,161,321,347],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,143,144,145,146,148,151,152,153,154,155,157,158,159,165,166,168,173,184,185,187,188,190,191,194,196,199,201,203,205,210,211,212,213,214,215,216,220,226,227,228,229,230,231,232,235,236,238,248,251,252,253,254,256,257,259,261,264,266,267,268,271,273,275,277,279,282,283,284,287,290,292,295,296,304,305,307,310,311,312,315,316,317,319,322,323,324,325,328,332,333,342,344,346,347,348,350,351,353,354,356,357,359,360,361,362,363,364,368,372,373,375,376,377,382,384,386,389,390,391,393,396,398,399,401,402,409,410,411,412,413,415,419,421,422,423,424,425,426,428,429,430,438,439,440,441,443,445,446,449,451,452,454,455,457,459,460,461,462,465,466,467,469,471,472,474,475,476,478,482,483,484,485],differenti:[1,3,6,29,185,347,378,419,442],difficult:[214,275,362,392,466],difficulti:[295,421],diffract:[],diffus:[],digit:[2,3,191,332],dih_table1:185,dih_table2:185,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:212,dihydrid:386,dij:295,dilat:[],dim1:3,dim2:3,dim:[3,59,71,143,146,147,148,151,152,153,154,155,157,165,187,206,216,233,325,350,409,460,482,483,484],dimdim:483,dimems:274,dimens:[],dimension:[3,39,112,118,140,143,145,146,147,148,151,152,153,154,155,157,164,186,203,206,250,274,319,350,353,357,419,457,467],dimensionless:[105,121,122,124,127,129,131,136,140,319,348,429,449],dimentionless:135,dimer:[6,292,409],dimgrai:191,dimstr:[41,210],dinola:[279,310],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,188,309,478],dir1:468,dir2:468,dir:[1,3,4,8,9,11,12,249,273,282,306,419,421,422,455,468,483],dirac:140,direc:419,direct:[],directli:[3,6,8,9,11,12,87,113,140,142,188,189,190,197,222,229,233,238,274,293,311,323,325,326,327,328,350,354,362,363,364,369,371,372,378,381,384,386,398,402,413,416,424,437,455,467,468,469,475,483],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,192,215,234,277,283,286,303,307,316,317,357,361,363,364,368,375,377,378,384,385,387,394,395,406,409,410,411,415,419,420,421,422,429,439,441,442,443,446,455,457,458,459,468,483],disabl:[3,12,16,319,397,455,470,483],disadvantag:[6,210],disallow:[188,216,251],disappear:459,discard:[2,3,41,71,206,210,320,328,454,459,460],discontinu:[9,185,355,404],discourag:409,discov:[13,320],discret:[6,8,40,42,190,191,235,238],discuss:[],disk:[6,84,85,158,186,217,227,278,455],disloc:70,disord:[39,70],disp:[],dispar:423,disperion:[381,402],dispers:[3,6,7,9,163,274,347,348,372,381,402,407,413,422,440,446],displac:[],displace_atom:[],displace_box:59,displacemet:460,displai:[11,13,22,37,44,55,173,184,188,190,334,342,375,438],dispters:3,dissip:[6,228,235,274,316,317,370,382,390,407,408,438],dissolut:211,dist:[6,69,91,108,117,188,275,291,383,437,452,484],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,154,160,163,165,166,167,168,172,187,188,190,191,199,203,206,207,211,212,213,214,216,217,218,221,227,233,238,248,249,250,251,255,263,273,274,278,282,283,290,291,292,295,296,300,304,305,306,307,314,315,317,318,319,322,324,325,326,327,328,329,333,347,348,350,353,355,357,358,359,362,365,366,367,368,369,370,371,372,373,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,392,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,417,418,419,421,422,423,424,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,452,455,457,460,466,467,471,475,478,482,484],distinct:[6,220,289,347,423],distinguish:[6,86,140,241,386,456],distort:363,distrbut:363,distribut:[],distro:[111,375,418,419],ditto:[8,11,12,14,15,16,17,18,115,212,450,455],div:8,divd:117,diverg:[3,12,39,292,317,459,478,485],divid:[3,6,16,41,91,112,117,126,128,141,162,163,173,184,191,203,204,205,210,216,273,315,322,327,347,355,357,387,422,446,466,474,483],divis:[6,238,368,396,406,454,457,475,483],dl_poli:7,dlambda:159,dlammps_async_imd:232,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,190],dlammps_gzip:[3,12,188,190,318,457,458,462],dlammps_jpeg:[3,12,190],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,190],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,188],dlen:467,dlmp_intel_offload:[12,16],dlo:[59,187,216,278],dlopen:6,dlvo:[7,376,449],dm_lb:238,dmax:[307,353],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,144,145,158,160,162,165,166,167,173,184,188,189,190,191,192,194,195,196,201,202,203,204,205,206,207,208,217,227,235,236,246,251,252,256,257,261,268,269,270,271,278,281,292,304,307,310,311,312,321,325,328,330,332,334,342,346,355,356,357,362,363,364,367,375,377,378,384,385,387,392,393,395,396,409,410,411,413,415,418,419,420,429,438,439,441,443,445,446,455,457,458,459,460,462,465,466,467,474,475,483,484,485,486],docuement:423,dodgerblu:191,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,116,117,118,142,144,145,147,148,153,155,159,164,165,166,167,169,171,173,178,184,185,187,188,189,190,191,194,200,201,203,206,209,210,212,213,214,216,220,222,224,227,228,231,233,235,236,238,241,247,251,252,253,254,256,257,268,269,270,271,279,280,281,285,287,290,292,307,310,312,314,315,319,322,323,324,327,328,329,330,335,336,338,339,341,346,347,348,349,350,356,357,358,363,364,365,366,367,368,370,372,373,374,376,377,378,379,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,400,401,403,404,405,407,408,409,410,411,413,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,453,454,455,457,458,459,460,461,464,465,467,468,469,470,471,474,475,478,483,487],doegenomestolif:7,doesn:[3,7,8,12,165,188,201,206,207,304,356,358,362,364,377,385,395,421,422,439,441,442,443,446,457,459],dof:[3,8,112,144,145,158,203,292,484],dof_per_atom:[145,203],dof_per_chunk:[145,203],doff:[356,457],doi:[6,215],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,154,164,167,187,189,190,191,194,201,210,214,216,217,231,234,238,251,252,275,287,292,319,324,325,347,348,357,362,383,413,452,454,457,461,474],domin:[1,386,471],don:[0,8,11,12,13,116,168,197,222,236,281,328,409,455,457],donadio:311,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,159,162,165,168,185,188,190,191,200,201,203,205,206,207,208,210,211,212,213,214,216,217,225,227,232,233,235,236,243,251,256,257,268,269,271,272,274,275,276,281,289,292,293,295,307,310,311,312,314,316,317,330,332,346,347,348,355,357,358,361,362,364,372,384,393,394,395,402,408,409,413,421,437,440,445,452,453,454,455,458,461,462,465,475,476,478,483,484],donor:392,dot:[141,161,197,222,230,250],doti:[368,419],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,216,225,280,328,332,346,348,361,362,368,387,391,421,422,453,457,461,465,470,483,484],dover:200,down:[3,6,7,8,11,39,71,214,227,235,307,323,362,386,413,456,476],downhil:[353,354],download:[5,7,8,9,11,12,13,17,232,394,420],downsid:6,downward:289,dozen:[8,12,107,194,421,422],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:244,dproduct:365,dr_ewald:[118,293],drag:[],dragforc:238,drai:[249,282],drain:[231,323,355],dramat:[59,187,211,212,213,214,216,251,307,310,311,348,362,413,454],drautz:368,draw:190,drawback:281,drawn:[188,190,191,228,452],drayleigh:[249,282],dreid:[],drfourth:105,drho:[113,363,384],drift:[6,103,105,228,229,235,236,247,290,307,466,474,478],drive:[11,12,198,214,216,230,251,273,279,292,326,357],driven:[6,177],driver:[6,12,14,15,194,225,232],drop:[3,191,382],droplet:393,drsquar:105,drude:[],dry:224,dsecriptor:394,dsf:[],dsmc:[],dstyle:278,dt_collis:238,dt_lb:238,dt_md:238,dt_srd:307,dtilt:[59,216],dtneb:471,dtqm:282,dtype:[115,212],dual:[16,17,307,362],dudarev:164,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,126,140,141,143,144,146,148,151,152,153,154,155,157,158,160,164,165,168,169,188,190,194,197,198,205,209,211,212,213,214,215,216,217,222,223,224,225,228,229,232,233,235,236,237,238,241,242,243,247,248,249,250,251,255,263,273,276,278,290,291,292,294,304,306,307,308,310,311,312,313,314,316,317,319,323,324,326,327,328,330,348,353,355,357,358,359,379,382,384,388,389,393,407,408,413,419,421,423,424,437,440,441,443,447,449,450,452,454,457,458,459,466,471,474,475,476,478,483,484],duffi:319,duin:[9,283,288,421,422],duke:348,dummi:[12,29,442],dump1:462,dump2:462,dump2vtk_tri:134,dump:[],dump_atom:8,dump_custom:8,dump_h5md:189,dump_modifi:[],dumpcustom:8,dumptimestep:462,dunbrack:[6,20,171,373,469],dunweg:[235,237],duplic:[2,3,14,15,17,41,42,166,210,229,273,457,482],dupont:[5,7,13],durat:[37,55,143,144,146,147,148,150,151,152,153,154,157,158,184,191,203,227,287,319,342,390,438],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,128,142,147,166,169,185,188,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,247,248,250,251,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,300,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,348,355,357,361,362,382,406,413,422,440,452,453,455,457,460,462,464,465,467,469,471,472,475,476,483,486,487],dvector:8,dvlo:449,dvx:6,dx_lb:238,dy3:164,dyamic:12,dyanam:6,dyanmic:471,dynam:[],dynamo:[5,363,384,409],dyne:482,dyre:403,dysam:460,e28637:29,e_1:368,e_2:368,e_b:387,e_e:386,e_hbond:392,e_i:[6,368,387],e_j:[6,368],e_k:[368,386],e_kl:6,e_lj:[364,381],e_n:[368,386],e_nn:386,e_pr:386,e_rebo:364,e_tors:364,eaa:333,eaat:172,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,134,140,141,142,144,145,146,147,148,149,152,153,154,155,157,158,159,160,161,162,163,164,165,168,169,171,172,173,174,175,176,177,178,179,180,182,183,184,185,187,188,189,190,191,192,193,194,195,196,197,198,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,241,242,243,244,245,247,248,249,250,251,253,254,255,256,257,258,259,260,261,263,264,265,266,267,268,269,270,271,273,274,275,276,277,278,279,280,281,283,284,285,287,289,292,293,294,295,296,300,301,303,304,305,306,307,308,309,310,311,312,314,317,318,319,320,321,322,323,324,325,327,328,329,330,332,333,335,336,337,338,339,341,342,343,346,347,348,350,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,412,413,414,415,416,418,419,421,422,423,424,425,429,430,431,432,433,434,435,436,437,438,439,440,443,444,445,446,447,448,449,450,451,452,454,455,457,458,459,460,461,462,464,465,466,467,469,471,472,474,475,476,478,482,483,484,485,487],eacn:[41,210],eam0d:274,eam3d:274,eam:[],eam_databas:13,eam_gener:13,eangl:475,earli:[41,203,205,206,207,208,210,286,293],earlier:[7,8,12,59,191,357,390,409,413,471],earliest:471,earth:386,easi:[6,7,8,9,11,13,87,141,188,195,196,197,198,206,209,222,230,231,233,235,236,294,301,310,311,312,324,327,329,356,457,460,465,467,484],easier:[8,9,13,16,188,190,274],easili:[8,11,190,191,323,357,454,464,473,483],eastwood:[347,348],eat:172,eatom:330,eaxmpl:6,eba:21,ebb13:172,ebb:21,ebond:[220,236,474,475],ebt:172,ec_ii:409,ec_ij:409,ec_jj:409,echo:[],eco:[421,422],ecoa:[421,422],ecoul:[107,220,236,421,422,475],ecp:[386,457],edg:[2,3,6,41,59,71,118,163,164,167,168,189,190,199,206,233,294,324,327,328,329,330,350,457,460,467],edge_histo:163,edge_threshold:163,edih:475,edim:315,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,478],editor:13,edu:[7,9,11,13,384,407,418,421,422],edward:[9,17],eebt:172,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,109,112,141,143,147,152,153,160,163,169,171,172,174,175,176,177,179,180,182,183,184,185,187,188,190,191,195,196,197,200,201,204,207,208,209,211,212,213,214,216,217,223,226,227,228,229,230,231,232,233,235,236,250,251,253,254,255,256,257,258,266,268,269,271,272,273,275,278,279,281,282,283,284,287,291,292,294,295,306,307,310,311,312,314,315,317,319,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,350,354,355,356,357,358,363,364,366,368,369,370,371,372,373,374,376,377,378,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,425,427,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,459,460,462,466,467,469,475,476,482,483,485],efffect:461,efficaci:39,effici:[0,1,3,6,7,8,10,12,15,17,18,39,58,61,67,112,142,188,189,190,191,214,216,220,229,251,275,277,287,292,295,307,347,348,353,358,362,368,376,378,393,398,402,423,464,487],effort:[5,7,458],efftemp:[96,97,151],efi:[421,422],efield:[],eflux:231,eggebrecht:378,ehb:[421,422],eigensolv:3,eigenvalu:[274,275,347],eigtol:3,eik:159,eim:[],eimp:475,einstein:[287,317],either:[1,2,3,4,6,8,9,11,12,14,15,16,17,22,33,41,44,50,59,63,71,107,113,116,118,140,141,145,147,148,164,165,168,173,178,185,188,189,190,191,194,202,204,205,207,208,210,213,214,215,216,217,227,233,234,238,242,248,249,251,252,255,269,273,289,292,294,295,296,304,307,314,321,325,328,332,334,345,347,348,350,354,355,359,362,368,370,376,384,393,394,396,407,408,409,413,417,419,441,443,445,452,455,457,459,460,461,464,466,469,472,474,483],ejtehadi:[376,389,423],elaplong:[195,196,233,460,475,483],elaps:[3,195,196,197,198,209,216,222,230,231,233,235,236,248,278,294,301,310,311,312,324,325,327,329,430,452,460,462,463,467,471,475,483],elast:[],elastic_t:4,elba:29,electr:[6,194,200,222,236,347,348,387,421,422,450,478,482],electrolyt:[9,449],electron:[3,6,7,9,13,40,96,97,113,118,149,151,156,194,200,219,220,236,237,252,262,270,285,313,319,354,356,363,365,377,381,384,386,387,409,419,420,443,446,450,457,478,482],electron_integr:200,electron_temperatur:200,electron_unit:386,electroneg:[6,283,284,285,377,387],electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,16,18,201,227,283,285,286,320,347,348,376,381,386,398,406,408,422,449],eleftheri:292,elem1:[387,409,429],elem2:[387,409,429],element1:[289,363,384],element2:[289,363,384],element:[3,6,7,8,12,13,63,81,89,103,105,112,117,119,134,140,141,142,143,144,145,146,147,148,152,153,154,155,157,158,161,188,189,190,191,192,194,200,204,205,208,274,289,314,321,363,364,368,377,384,385,386,387,393,394,395,409,410,411,415,419,420,421,422,429,439,441,442,443,446,478,483,486],elementn:[363,384],elementset:200,elev:471,elif:[140,332],elig:[3,201,211,212,224,227,392],elimin:[3,6,71,228,235,236,292,295,316,317,452],elj:381,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,82,144,186],ellipsoid:[3,4,6,7,13,40,42,82,113,130,144,165,186,188,235,253,256,259,260,268,292,307,352,355,389,408,423,438,457,467,485],ellipsoidflag:457,elong:[220,236,475],elp:[421,422],els:[3,7,8,12,71,107,116,117,119,189,190,202,203,204,205,206,207,208,227,251,292,307,319,320,321,330,332,347,393,456,468,483,486],elsewher:[8,248,307,409,420,421,422,469,475,483],elt:409,emac:[],email:[0,3,5,7,8,11,387],emb:[3,9,328],emb_lin_neg:409,embed:[3,5,7,11,12,13,29,88,142,163,319,363,384,387,406,409,410,411,419,438,447,455],embt:172,emi:[7,9],emol:[421,422,475],emphas:390,empir:[200,311,364,386],emploi:[9,274,287,442],empti:[3,57,71,167,292,347,358,397,457,468,469,483],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,83,87,96,97,98,99,100,101,105,109,111,112,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,147,149,151,152,156,157,159,163,171,172,174,175,176,177,178,179,180,182,183,184,185,188,189,191,192,194,195,196,197,198,199,201,207,209,211,212,213,215,216,217,222,223,224,225,226,227,228,229,230,232,233,234,235,236,237,238,239,240,241,242,244,245,247,249,251,252,253,254,255,256,257,258,259,260,261,262,264,266,267,268,269,270,271,273,274,275,277,278,282,283,284,285,286,287,288,289,291,292,294,295,296,297,298,299,300,301,303,304,306,307,310,312,313,314,315,316,317,319,320,322,323,324,325,326,327,328,331,333,335,336,337,338,339,341,342,343,348,355,357,361,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,455,458,459,464,466,476,483,487],enclos:[2,6,12,167,188,280,332,409,453,455,465,483],encod:[13,39,42,188,190,191,281,393],encompass:[3,6,40,57,59,116,166,303,321,438,460],encount:[3,8,12,59,205,361,462,483],encourag:[7,8,286,305],end12i:113,end12x:113,end12z:113,end1i:113,end1x:113,end1z:113,end2i:113,end2x:113,end2z:113,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,57,59,71,113,168,169,172,187,188,190,191,192,195,196,204,205,207,208,213,216,220,228,233,235,236,237,250,251,252,263,279,291,292,296,307,310,311,312,313,315,318,319,322,326,329,330,346,347,356,357,361,362,382,384,389,423,426,428,429,430,444,447,452,455,457,458,459,460,462,464,465,469,473,475,478,483,487],end_of_step:8,endbondtors:[3,172,178,457],endif:8,energet:[213,364,422],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,123,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,188,191,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,333,335,336,337,338,341,343,347,348,353,354,355,357,358,362,363,364,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,421,422,423,424,429,430,431,432,437,438,439,440,441,442,443,445,446,447,448,449,450,452,455,457,462,466,467,469,471,473,474,475,478,482,483,486],energy_update_freq:422,enforc:[6,57,58,104,187,188,189,190,192,194,201,213,216,251,272,274,284,292,295,332,347,398,454,483,484],enforce2d:[],eng:[11,65,69,108,188,225,330,332,377,411],eng_previ:332,engin:[200,216,277,296,316,384,410],engr:[421,422],enhanc:[196,200,452],enlarg:[59,190],enough:[3,40,61,86,165,166,168,210,236,278,282,287,292,320,324,325,328,358,362,378,417,457,461,462],enpub:384,enrti:[],ensembl:[],ensight:6,ensur:[3,6,140,188,201,214,227,228,251,297,318,348,368,383,406,437,439,446],enter:[57,155,387,446,471],enthalpi:[123,253,254,384,474,475,483],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,141,145,164,165,191,194,195,196,203,206,207,210,213,215,224,227,228,231,235,236,247,251,253,254,255,256,257,273,275,277,290,292,305,319,321,332,362,381,402,413,440,457,465,466],entireti:[396,445],entiti:[6,8,40,42,188,292],entri:[3,8,12,38,42,56,65,69,79,92,108,115,118,127,130,131,132,133,134,136,137,138,163,185,191,205,206,207,215,282,330,356,368,385,409,415,422,429,439,440,441,442,443,446,483],entropi:471,entry1:[38,56,191,375,440],entry2:191,entryn:191,enumer:[166,188],enumuer:6,env:362,environ:[1,3,6,11,12,16,17,18,190,229,234,273,362,363,368,375,377,385,386,419,441,454,468,483],epair:[107,191,388,392,421,422,475],epen:[421,422],epfl:[229,234],epp:381,epq:381,eps0:449,eps14:406,epsilon0:443,epsilon:[3,6,36,45,46,50,53,54,87,171,195,196,227,292,307,324,328,353,355,367,373,374,376,378,379,380,381,389,391,392,393,396,397,398,399,400,401,402,403,404,405,406,412,416,423,424,433,439,445,448,449,466,478,482],epsilon_0:450,epsilon_14:373,epsilon_:423,epsilon_d:379,epsilon_i:[389,413,423],epsilon_i_:423,epsilon_i_a:[389,423],epsilon_i_b:[389,423],epsilon_i_c:[389,423],epsilon_ij:413,epsilon_j:[389,413,423],epsilon_j_:423,epsilon_j_a:[389,423],epsilon_j_b:[389,423],epsilon_j_c:[389,423],epsilon_lj:423,epton:418,eqch:160,eqeq:[421,422],eqp:381,eqq:381,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,144,159,161,165,190,191,194,195,196,197,198,201,204,205,208,209,210,214,216,217,222,227,228,230,231,233,235,236,238,241,242,248,249,255,265,273,275,278,280,282,283,284,287,289,291,292,294,296,301,303,310,311,312,315,316,317,319,321,322,324,327,329,330,332,346,350,355,357,358,359,361,362,377,382,388,389,392,407,412,419,421,422,423,425,426,427,429,430,440,445,446,450,453,454,455,457,459,460,464,465,468,471,473,475,483,484],equat:[3,6,7,8,9,91,112,118,164,173,184,194,214,220,221,229,235,236,238,241,249,250,251,252,255,269,273,275,282,283,287,295,307,315,319,322,324,325,327,329,341,347,348,376,381,382,386,387,390,395,407,408,409,413,423,426,428,432,433,435,436,444,450,478],equi:252,equidist:250,equil:[3,283,351,464,487],equilater:467,equilibr:[3,4,5,6,7,9,59,91,165,194,201,204,213,214,227,249,251,252,269,270,282,283,284,285,315,316,317,322,377,378,421,422,453,467],equilibria:322,equilibribum:[211,212],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,148,149,172,174,214,216,227,228,229,236,238,251,255,269,282,287,291,295,296,304,307,314,315,317,322,333,335,338,341,377,409,415,478],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:200,equival:[6,12,13,59,61,124,125,133,138,163,167,191,205,208,214,216,227,235,251,269,279,291,292,327,382,386,441,443,457,460,465,466,475,478],equlibrium:6,equliibr:[283,285],er3:164,eradiu:[40,113,386,457],eras:[294,316],erat:[216,408],erc:378,erfc:[378,398,413],erforc:113,erg:482,erhart:[201,384,441,443],ermscal:365,ernst:9,eror:3,eros:409,erose_form:409,erot:[],errata:[441,443],erratum:324,erron:3,error:[],erta:390,ervel:[113,457],escap:[217,478],especi:[8,11,16,153,165,194,201,210,227,282,287,290,291,362,454],espresso:[9,286],essenti:[8,11,12,27,88,128,146,147,148,151,152,153,154,155,157,174,204,255,274,323,348,364,378,398,443,462,475],essex:29,establish:[87,231],estim:[1,3,6,10,12,38,41,56,91,141,200,210,221,249,307,314,347,348,353,413,422,440,471,475],esu:482,esub:409,eta:[6,238,251,282,283,285,323,385,387,389,419,442,446,482],eta_dot:251,eta_ij:419,eta_ji:387,etag:[40,457],etail:475,etap:251,etap_dot:251,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,143,145,146,147,148,149,151,152,153,154,155,157,159,165,167,168,169,178,188,190,191,194,200,201,202,203,205,206,207,208,211,212,216,217,225,227,228,235,251,278,289,293,319,320,328,332,346,347,355,356,357,358,360,384,385,393,406,408,417,421,422,439,441,443,446,452,455,457,458,459,464,466,467,471,473,474,475,476,478,482,483,485,487],ethernet:18,etol:[355,357,452,471],etot0:282,etot:[6,94,96,97,110,141,151,191,220,236,249,282,474,475],eu2:164,eu3:164,euler:[355,357],eulerian:200,euqat:431,europhi:238,ev_tal:8,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,142,145,155,163,165,188,190,191,195,196,197,198,200,202,203,204,205,206,207,208,209,216,222,228,230,231,233,234,235,236,274,280,283,294,297,301,310,311,312,321,324,327,329,330,332,347,348,353,355,362,413,419,425,427,440,452,453,455,459,460,462,464,465,466,467,471,473,475,483,484],evalut:[332,455],evan:[153,269],evanseck:[6,20,171,373,469],evapor:[],evaul:[8,355],evdwl:[107,421,422,475],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,119,166,167,181,185,188,191,194,195,196,201,202,203,205,206,207,208,210,211,212,214,216,217,220,233,236,249,251,252,274,287,289,292,293,303,307,315,319,322,324,328,330,340,347,353,355,357,362,367,386,387,390,393,413,423,446,447,457,458,460,462,463,464,466,467,469,472,474,475,476,478,487],evenli:[3,41,141,185,210,238,396,447,457],event:[],eventu:[3,6,12,15,167,283,471],ever:[54,56,234,307],evera:[376,389,423,438],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,113,119,128,153,168,188,189,190,191,192,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,221,224,225,227,229,231,232,233,238,239,247,251,252,255,272,273,274,278,279,280,281,282,283,284,285,287,289,290,292,293,295,296,307,309,310,311,312,313,314,315,318,319,320,321,322,330,332,346,348,357,358,359,362,382,383,393,406,421,422,434,451,452,453,457,459,461,462,464,465,466,471,472,473,475,483,487],everyth:[8,107],everywher:[116,400],eviri:386,evolut:[229,238,275,452],evolv:[238,275,320],ewald:[2,3,5,6,7,8,12,88,110,118,141,320,347,348,355,369,371,372,378,381,386,398,402,416,424,438,440,459],ewald_disp:381,ewalddisp:3,exact:[22,41,44,71,122,159,168,173,210,213,228,229,235,236,237,278,287,288,307,319,334,347,375,459,464,471,483,485,487],exactli:[3,6,12,14,17,38,41,56,59,71,91,116,144,149,156,165,185,195,196,205,210,216,221,228,235,236,237,252,262,263,270,274,282,307,312,313,326,362,375,382,384,390,393,396,407,413,440,459,460,467,471,483],exager:478,examin:[6,8,9,17,213,274],examp:[455,483],exampl:[],exce:[3,6,16,17,18,41,58,71,167,203,206,207,210,214,216,221,224,251,274,298,299,307,355,362,457,483],exceed:[3,41,59,210,216,251,307,465],excel:386,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,143,144,145,146,147,148,149,151,152,153,154,155,156,157,158,165,169,171,172,173,174,175,176,177,179,180,182,183,184,185,187,188,191,194,197,203,204,205,209,210,214,216,223,226,227,230,233,235,237,251,252,253,254,255,256,257,258,262,263,266,268,269,270,271,275,284,285,292,294,295,304,307,310,312,313,319,323,327,330,332,333,334,335,336,337,338,341,342,343,347,348,350,352,356,357,358,360,361,362,363,364,366,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,408,410,414,415,416,418,421,422,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,454,455,457,459,460,462,465,466,467,468,469,471,475,478,482,483,484,486],excess:386,exchang:[2,3,6,8,9,61,62,194,200,201,227,235,284,292,315,319,322,347,362,386,472],exchange:347,excit:[9,386],exclud:[3,6,9,12,16,17,63,71,112,140,145,152,153,169,188,203,206,211,212,239,247,277,290,292,314,325,330,355,356,358,370,390,393,407,408,413,437,469],exclus:[1,3,9,12,16,87,362,377,413,466,476],excurs:452,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,166,190,232,286,332,346,349,361,453,455,465,468,471,483],exemplari:228,exemplifi:386,exert:[6,233,236,287,326,327,328,348],exhaust:[200,361,483],exhibit:[251,354,386,466],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,122,165,166,184,189,190,191,194,199,209,212,214,217,227,277,278,280,330,333,335,336,338,342,351,356,362,393,421,447,453,455,457,458,459,468,469,470,483,484,485],exit:[2,3,11,12,41,57,188,210,346,361,455,456,465,474,483],exlanatori:3,exp:[],expand:[],expans:[12,140,188,468,483],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,146,157,163,185,210,222,227,229,248,273,279,281,282,287,292,330,348,358,375,409,413,452,455,457,459,462,466,471,483],expens:[6,10,71,191,273,277,292,319,330,347,348,358,362,455],experi:[6,13,15,17,209,217,232,241,250,279,291,292,353,357,382,413,466,471],experienc:[6,12,240,241],experiment:[227,347,362,471],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,145,153,185,188,190,191,194,203,204,208,210,212,214,216,251,273,281,292,304,330,332,346,347,350,356,357,361,367,384,396,430,445,455,458,459,462,464,467,478,483,487],explan:[3,6,59,113,140,188,203,250,273,393,451,454,455,457,466],explanatori:[3,8,117,188,202,203,205,206,207,292,356,454,483],explantori:[3,288],explic:412,explicit:[6,9,11,22,44,77,87,113,116,159,173,195,196,216,298,299,334,352,364,365,368,373,375,384,386,397,407,444,451,454,458,461],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,143,152,155,163,165,171,172,174,175,176,177,179,180,182,183,185,188,191,197,206,209,216,223,226,228,230,235,251,253,254,255,256,257,258,266,268,269,271,281,282,284,292,294,295,310,312,313,319,323,327,333,335,336,337,338,341,343,356,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,381,382,383,384,385,387,388,389,390,391,392,393,396,397,398,399,400,401,402,403,404,405,406,407,410,413,414,415,416,418,423,424,430,431,432,433,434,435,436,438,439,440,441,442,443,444,445,446,448,449,450,457,459,466,467,469,470,476,478],explictli:[16,470],exploit:[9,15,17,275],explor:[118,164],expon:[3,283,285,384,389,392,406,412,424],exponenti:[87,419,439,446,450,471,483],expos:11,exposit:[200,382,383],express:[6,140,151,165,195,196,214,248,273,283,319,325,332,368,384,386,400,409,429,438,483],expressiont:368,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,194,197,198,201,208,209,215,218,222,225,226,227,229,230,231,233,235,237,249,251,255,263,273,274,290,291,292,294,296,301,304,306,310,311,312,313,314,316,317,319,321,324,328,329,389,409,422,423,429,474,475],extent:[1,3,41,45,57,71,163,167,188,199,206,210,233,326,329,347,350,364,425,427,440,454,457,460],exterior:[3,6,328],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,143,144,146,148,151,152,153,154,155,157,158,164,165,166,167,171,191,205,210,212,251,280,281,282,292,307,355,356,359,360,381,390,393,396,409,413,454,455,457,460,469,478,483],extract:[3,6,11,13,36,63,87,107,115,117,119,195,196,285,357,378,387,409,429,455,462,474],extract_atom:11,extract_comput:[11,455],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,190,214,216,251,317,386,442,478],extrema:406,extrins:200,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[161,321],f_a:[441,442,443],f_ave:117,f_c:442,f_f:443,f_fix_id:282,f_harm:317,f_i:419,f_id:[6,71,117,119,188,194,202,203,204,205,206,207,208,246,309,321,475,483],f_ij:419,f_indent:208,f_int:316,f_jj:91,f_k:419,f_langevin:319,f_max:[282,287],f_msst:249,f_r:[236,441,442,443],f_sigma:368,f_solid:317,f_ss:6,f_temp:236,face:[3,6,57,59,71,153,163,167,199,206,207,324,326,327,328,329,350,389,409,423,457,460],face_threshold:163,facet:163,facil:[0,12],facilit:[6,13],fact:[6,8,16,229,307,317,390,469],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,116,118,140,159,164,167,171,182,188,190,191,195,196,204,210,214,216,217,227,232,235,237,238,249,251,252,255,275,279,291,295,297,299,307,311,315,322,323,324,328,338,348,350,362,364,365,368,369,371,373,378,379,380,382,386,390,393,397,398,409,413,415,416,422,424,430,439,444,454,457,460,461,466,469,471,472,475,478,482,483],factori:[3,455],factoriz:347,fail:[3,11,12,59,169,214,217,347,355,357,380,422,455],failur:[121,426,456,483],fairli:[11,413,466,471],faken:73,falcon:232,fall:[3,6,191,205,278,455,483],fals:[86,330,332,483],fame:8,famili:[446,454],familiar:[0,11],fan:419,far:[3,6,12,17,57,59,61,86,188,191,192,210,211,212,214,217,251,273,291,292,307,324,335,338,353,357,358,445,455,457,462,475],farago:235,farrel:[441,443],farther:188,fashion:[6,8,41,71,165,191,194,195,196,201,206,210,212,217,227,229,233,248,249,251,253,254,255,256,257,265,268,269,270,271,281,282,284,292,296,300,306,309,317,319,323,324,325,327,329,357,393,407,460,469,483,486],fasolino:395,fast:[6,7,9,12,13,17,39,188,260,282,320,347,348,370,407,408,438,440,459,464,466,475,484,487],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,143,152,171,172,174,175,176,177,179,180,182,183,185,188,191,194,197,209,210,216,223,226,230,234,235,251,253,254,255,256,257,258,266,268,269,271,279,283,284,292,294,295,307,310,312,314,316,319,323,327,333,335,336,337,338,341,343,347,348,359,360,362,363,364,366,368,369,370,371,372,373,374,375,376,377,378,381,382,384,385,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,414,415,416,418,423,424,430,438,439,440,441,442,443,445,446,448,449,450,452,466,470,478],fastest:[1,6,14,17,153,206,319,320,362,454],fatal:[3,474],fault:[70,422],faulti:12,fava:389,favor:213,favorit:7,fbmc:314,fcc:[],fcm:[265,483],fdirect:220,fdotr:394,fdti:87,fe2:164,fe3:164,fe_md_boundari:200,featu:8,featur:[],fecr:384,feedback:[7,232],feel:[7,232,233,241,273,328,330,357,413],felling:411,felt:328,femtosecond:482,fene:[],fennel:[378,398],fep:[],ferguson:[6,171,469],fermi:[1,12,15,151,362,443],fermion:[9,386],ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,192,202,203,204,205,206,207,208,236,251,278,281,283,295,321,347,355,356,357,364,454,457,462,466,468,476,483,485],fewer:[1,3,11,15,16,61,241,466],fewest:3,fextern:225,feynman:275,fff:455,ffield:[377,387,421,422],ffmpeg:[3,12,190],ffplai:190,fft:[1,3,7,12,14,15,88,109,110,141,274,347,348,466],fft_inc:[12,348],fft_lib:12,fft_path:12,fftbench:[347,476],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,197,198,222,225,229,275,291,378,398,402,437],field1:[458,462],field2:458,field:[],fifth:[304,415],figur:[1,3,8,11,12,282,454,455],fij:381,file0:273,file1:[11,13,273,318,332,356,462,464,468],file2:[11,13,318,332,356,462,464,468],file:[],file_from:189,filenam:[3,12,13,38,41,56,185,188,190,191,192,200,203,204,205,206,207,208,210,215,273,277,280,283,284,285,288,289,292,293,318,319,344,345,346,357,363,364,368,378,384,385,387,395,409,410,411,415,419,420,421,422,429,439,440,441,442,443,446,453,454,455,458,459,464,468,475,483,485,486,487],filennam:464,filep:[3,188,191,459,464,487],filepo:289,fill:[7,165,190,278,319,350,358,368,422,460],filter:[191,200],final_integr:8,final_integrate_respa:8,finchham:[6,147,380],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,168,185,192,201,213,214,224,227,250,273,279,287,291,353,355,357,358,378,393,398,402,409,438,440,478,483],find_custom:8,fine:[16,17,169,197,222,317,358,362,483],finer:[140,165,483],finest:347,finger:[165,187,248,460],finish:[6,11,41,210,332,344,346,347,359,361,362,445,462,483,484],finit:[],finni:[7,384,438],finvers:220,fiorin:[9,215],fire:[353,354,355,357,471],firebrick:191,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,150,153,159,161,163,164,166,167,168,172,185,188,189,190,191,192,194,203,204,205,206,207,208,210,213,216,227,228,233,238,248,249,250,251,273,275,280,281,282,284,289,292,295,296,304,305,307,308,309,316,317,318,319,321,325,330,332,333,339,350,355,356,357,358,361,362,363,364,367,368,369,371,373,375,377,378,384,386,387,390,391,393,394,395,397,398,402,407,408,409,411,413,415,419,421,422,429,437,439,440,441,442,443,446,450,452,453,454,455,457,458,459,462,464,466,469,470,471,474,475,478,483,484,485,487],fischer:[6,9,19,20,171,373,469],fit:[3,6,9,12,38,56,185,291,307,364,368,395,409,413,433,440,442,465,483],five:[73,151,282,356,368,410,457,471],fix:[],fix_adapt:[159,196,406],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,201,278],fix_evapor:201,fix_flux:200,fix_gcmc:[201,356],fix_gl:229,fix_gld:229,fix_grav:278,fix_id:[3,214,249,251,253,254,255,256,257,279,282],fix_modifi:[],fix_mov:[187,325],fix_nh:8,fix_npt:229,fix_nvt:[201,227],fix_poem:[3,6],fix_pour:[3,217],fix_qbmsst:9,fix_qeq:[3,377],fix_rattl:295,fix_reax_bond:421,fix_rigid:[241,367],fix_saed_vtk:293,fix_setforc:8,fix_shak:295,fix_srd:3,fix_styl:255,fix_temp_rescal:313,fixedpoint:[214,251],fixextern:225,fixid:200,fji:381,flag1:[219,360],flag2:[219,360],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,93,103,104,106,118,160,164,168,188,190,191,192,208,213,215,219,232,235,239,241,247,248,274,281,292,304,306,307,314,318,327,330,345,348,356,360,361,362,364,392,397,409,437,452,454,455,457,458,459,461,462,463,467,483],flag_buck:372,flag_coul:[372,381,402],flag_lj:[381,402],flagfld:[370,407,408],flaghi:[3,370,407,408],flaglog:[370,407,408],flagn:219,flagvf:[370,407,408],flat:[6,319,324,325,329],flavor:[2,7,12],fld:[9,324,370,407,408],flen:365,flex_press:365,flexibl:[3,6,8,166,190,203,206,215,229,252,315,322,386,442,475],flip:[3,6,216,251,326,327],floor:483,flop:12,floralwhit:191,flow:[],fluctuat:[6,64,87,214,227,228,235,238,251,255,273,274,317,319,341],fluid:[],fluid_veloc:242,flush:[3,191,474],flux:[],flv:190,fly:[7,9,12,41,190,194,200,217,220,292,295,320,368,475,478],fmackai:9,fmag:218,fmass:275,fmax:[355,475],fmomentum:220,fmsec:[2,191,235,236,248,251,279,292,310,311,466,477,482,484],fname:346,fno:[12,16],fnorm:[355,475],fnpt:220,fnvt:220,foce:393,fock:365,focu:295,fogarti:[9,285,422],foil:[140,273,429],fold:[305,466],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,144,145,151,153,158,161,163,165,166,171,174,175,176,177,179,180,182,183,185,188,189,190,191,194,200,201,202,203,204,205,206,207,208,210,215,216,217,220,221,225,227,228,229,232,234,235,236,238,241,249,251,255,256,257,268,269,271,274,275,277,280,281,282,283,285,287,289,291,292,293,295,309,310,311,312,315,316,317,318,319,321,322,330,331,335,336,337,338,341,343,345,350,352,355,356,357,362,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,426,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,444,445,446,448,449,450,452,454,455,457,458,459,460,462,464,465,466,469,471,472,473,478,483,484,486],foo:[4,8,11,12,188,190,225,455,468,483],foot:6,footprint:[12,362],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:241,forcefield:[291,392],forcegroup:238,forcezero:353,ford:381,forestgreen:191,forev:71,forget:[236,478],forgiv:251,fork:[12,188],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,9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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":211,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,145,153,154,158,164,165,168,170,184,186,187,188,190,191,192,193,195,196,197,199,200,201,203,206,207,208,211,212,214,215,216,217,221,224,227,228,233,235,236,237,238,239,241,246,249,251,252,255,269,270,274,275,278,279,280,281,282,284,287,289,290,292,293,307,309,314,315,316,317,320,322,324,326,330,342,345,347,348,350,351,353,354,356,358,359,360,362,365,368,370,386,407,408,413,421,422,437,438,452,453,454,457,458,460,462,464,465,466,469,471,473,474,475,476,477,482,484,485,486],"function":483,"long":[369,371,372,373,374,378,380,381,398,402,406,416,424],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[195,196],addforc:197,addit:[12,13],addtorqu:198,adiabat:6,adjust_dt:297,adp:363,airebo:364,alloi:384,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:199,arrai:6,aspher:[6,82,144,253,256,259,260,268],atc:[9,200],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,163,199,201,202,281,483],atom_modifi:39,atom_styl:40,attract:5,aug:0,aveforc:209,awpmd:[9,365],balanc:[41,210],barostat:6,basal:67,beck:366,berendsen:[279,310],between:6,binary2txt:13,bodi:[6,8,42,68,261,367],bond:[8,13,69,211,212,213,288],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:368,born:[369,380],boundari:[7,57],box:[6,58,214],brownian:370,buck:[371,372,380],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,171,373,406],chunk:[6,66,71,75,90,93,104,106,114,145,160,162,203],citat:7,class2:[21,43,172,333,374],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[324,376,449],colvar:[9,13,215],com:[74,75,146],comb3:377,comb:[284,377],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,483],compute_modifi:102,condit:7,conduct:[6,315],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:204,cosin:[23,24,25,26,27,28,174],cossq:335,coul:[369,371,372,373,374,378,379,380,391,398,402,406,416,424],coupl:6,creat:212,create_atom:165,create_bond:166,create_box:167,createatom:13,creation:7,csld:311,csvr:311,cubic:400,cuda:[9,14,109,112,143,152,197,209,223,226,230,251,258,294,295,310,312,323,369,371,373,374,384,390,391,398,399,401,404,414,439,441],custom:8,cut:[49,365,371,374,378,381,386,388,398,399,406,412,416],cvff:336,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[378,398],deform:[148,149,216],delete_atom:168,delete_bond:169,delta:24,deposit:217,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],diagnost:7,diel:379,dielectr:170,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:173,dihedral_styl:[2,171,172,174,175,176,177,178,179,180,181,182,183,184,185],dilat:80,dimens:186,dipol:[6,29,381],direct:220,discuss:6,disp:6,displac:[81,86],displace_atom:187,distribut:[7,12],document:0,dpd:382,drag:218,dreid:[6,392],drude:[6,9,150,219,220,236],dsf:[378,398],dsmc:383,dump:[6,8,188,189,190,192],dump_modifi:191,dynam:283,eam:[13,384],echo:193,edip:385,eff:[9,13,96,97,149,151,156,237,252,262,270,313,386],efield:222,eim:387,elast:6,emac:13,enforce2d:223,ensembl:7,erot:[82,83,84,85],error:3,evapor:224,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],exp:[27,174],expand:[46,401],extend:[8,11],extern:225,fcc:273,featur:[7,8,483],fene:[45,46],fep:[9,13,87,196],field:[6,7],file:6,finit:6,fix:[2,6,8,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,483],fix_modifi:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],flow:6,fluid:238,flux:[91,142],forc:[6,7,142,308],fourier:[30,31,175,337],freez:226,from:[6,11],futur:5,gauss:388,gaybern:389,gcmc:227,gener:[1,6,7,13],get:12,gld:228,gle:229,global:6,gpu:[9,15,366,369,371,373,374,376,378,381,382,384,388,389,391,398,399,400,401,412,414,423,424,430,439,440,441,448,449,450],gran:[325,390],granular:6,graviti:230,gromac:391,group2ndx:331,group:[88,330,483],gyrat:[89,90],h5md:[9,188,189],harmon:[32,47,48,49,176,179,324,338,415],hbond:392,heat:[91,142,231],heatconduct:431,helix:177,hertz:[390,425],histo:205,histori:[5,390],hook:390,hourglass_error:122,how:6,hybrid:[33,50,178,339,393],idealga:432,imag:[188,190],imd:232,implicit:373,improp:[8,92],improper_coeff:334,improper_styl:[2,333,335,336,337,338,339,340,341,342,343],includ:344,inclus:8,indent:233,indic:0,individu:2,induc:6,inertia:93,info:[0,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,345],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:298,integrate_ulsph:299,intel:[9,16,373,389,398,439],interfac:[6,11],internal_energi:123,introduct:7,invers:220,ipi:234,ipp:13,jul:[],jump:346,kate:13,keyword:413,kim:[9,394],kokko:[9,17],kspace:[2,8,9,320],kspace_modifi:347,kspace_styl:[6,348],label:349,lammp:[0,1,2,6,7,8,11,12],langevin:[235,236,237],lattic:350,lcbop:395,librari:[6,11,12],limit:[263,312],line:[12,264,396],linear:405,lineforc:243,list:[2,397],lj1043:324,lj126:324,lj93:324,lj96:399,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:351,lubric:407,lubricateu:408,make:12,mass:352,math:483,matlab:13,meam:[9,409,410,411],measur:1,meso:[244,245],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:412,min_modifi:353,min_styl:354,minim:[8,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,355],misc:9,mod:[319,442],model:[6,7],modifi:8,molecul:356,molfil:[9,188,192],moltempl:13,momentum:[239,247],morri:436,mors:[51,392,414],move:248,move_tri_surf:300,movi:[188,190],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[369,371,373,378,398],msst:249,multi:[6,7,179],multipl:6,nb3b:415,neb:[250,357],neigh_modifi:358,neighbor:359,nemd:6,newton:360,next:361,nharmon:180,noforc:[260,265],non:[6,7],none:[34,52,181,340,417],nongauss:105,nonlinear:53,nph:[251,252,253,254,292],nphug:255,npt:[251,252,256,257,292],nve:[258,259,260,261,262,263,264,265,266,267,292],nvt:[251,252,268,269,270,271,292],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,171,172,174,175,176,177,179,180,182,183,185,230,251,253,254,255,256,257,258,266,268,269,271,284,333,335,336,337,338,341,343,363,364,366,369,370,371,372,373,374,376,377,378,379,381,382,384,387,388,389,390,391,392,393,396,398,399,400,401,402,403,404,405,406,407,410,411,414,415,416,418,423,424,430,439,440,441,442,443,445,446,448,449,450],onewai:272,open:7,oper:483,opl:182,opt:[19,373,384,398,402,414],optim:1,option:[6,8,12],orient:273,orthogon:6,other:6,output:[6,7,8,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],overlai:393,overview:11,packag:[1,9,12,14,15,16,17,18,19,362],pair:[6,107,108],pair_coeff:375,pair_modifi:413,pair_styl:[2,363,364,365,366,367,368,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450],pair_writ:447,pairwis:8,parallel:11,paramet:6,pars:2,partial:152,particl:[6,7,42],partit:451,past:5,per:6,perform:[1,10],peri:418,period:25,phonon:[9,13,274],pimd:275,piston:326,planeforc:276,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:418,poem:[9,277],point:283,polariz:6,poli:[370,407,408],polym:13,polymorph:419,post:7,potenti:[2,6,8],pour:278,pppm:6,prd:452,pre:7,press:279,pressur:112,previou:12,print:[280,453],problem:[3,4],process:[6,7],processor:454,profil:153,properti:[6,113,114,115,281],pymol_aspher:13,python:[9,11,13,455],qbmsst:282,qeq:[283,284,285],qmmm:[9,286],qtb:[9,287],quadrat:183,quantiti:6,quartic:[35,54],quip:420,quit:456,ramp:154,rattl:295,rdf:116,read_data:457,read_dump:458,read_restart:459,reax:[9,13,285,288,289,421,422],reaxc:9,rebo:364,recent:290,reduc:117,refer:483,reflect:327,region:[8,117,155,156,328,460,483],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,226,227,228,229,230,231,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,287,288,289,290,292,293,294,296,297,298,299,300,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,341,342,343,344,345,346,347,348,350,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,479,480,481,483,484,485,486,487],relax:214,replic:461,replica:[6,7],report:3,requir:12,rerun:462,rescal:[312,313],reset:221,reset_timestep:463,resquar:423,restart2data:13,restart:[6,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,464],restrain:291,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],rho:126,rhosum:434,rigid:[6,83,98,241,292],ring:341,rotat:157,rule:2,run:[6,11,12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329,465],run_styl:466,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,424],self:306,serial:11,set:[6,467],setforc:294,setvel:301,shake:295,share:[11,12],shell:[6,468],shield:283,shift:[26,27,48,49,174],simpl:31,simul:6,size:6,slater:283,slice:119,sllod:[269,270],small:292,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,296,297,298,299,300,301,303,425,426,427,428],smooth:[404,405],sna:140,snad:140,snap:429,snapshot:6,snav:140,soft:[406,430],solver:2,sourc:7,spatial:[206,207],spc:6,speci:289,special:[7,413,483],special_bond:469,sph:[9,431,432,433,434,435,436],sphere:[84,85,158,207,241,254,257,266,271],spheric:6,spline:[410,411],spring:[304,305,306,317],squar:28,srd:[307,329],srp:437,standard:9,start:[12,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],state:309,stationari:245,stop:[195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,216,217,218,220,221,222,223,224,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,321,322,323,324,325,326,327,328,329],store:[308,309],strategi:1,streitz:378,stress:[141,142],structur:2,style:[1,2,6,8],submit:8,suffix:470,summari:6,swap:[201,213],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,479,480,481,482,483,484,485,486,487],system:6,tabl:[0,6,38,56,185,440,441],tad:471,taitwat:[435,436],talli:142,temp:[143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,310,311,312,313],temper:472,temperatur:6,tersoff:[441,442,443],test:11,tfmc:314,thermal:[6,315],thermo:[6,473],thermo_modifi:474,thermo_styl:475,thermodynam:[6,8],thermostat:6,thole:444,time:[6,208],timer:476,timestep:477,tip3p:6,tip4p:[6,378,398,402,406],tip:12,tlsph:426,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:318,tool:[12,13],torqu:160,transform:220,tri:[267,445],tri_surfac:427,triangle_mesh_vertic:134,triclin:6,tstat:382,ttm:319,tune:320,type:7,ulsph:428,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:343,uncomput:479,undump:480,unfix:481,unit:482,user:[9,12,14,16,18],vacf:161,valu:[6,483],variabl:[6,8,483],variou:1,vashishta:446,vcm:162,vector:[6,321,483],veloc:484,version:[0,5,12],via:12,vim:13,viscos:[6,322],viscou:[242,323],visual:6,vol:139,voronoi:[9,163],vtk:293,wall:[6,324,325,326,327,328,329],wall_surfac:303,warn:3,water:6,weight:205,what:[7,12],wolf:[369,378],wrapper:11,write:6,write_data:485,write_dump:486,write_restart:487,xmgrace:13,xmovi:13,xrd:164,xtc:9,yukawa:[448,449],zbl:[443,450]}}) 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