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Merge branch 'master' into kim-v2-update

This commit is contained in:
Ryan S. Elliott 2018-08-24 14:28:33 -05:00
parent dd2a1e4787 413fdbbf23
commit 796b6b2d9c
190 changed files with 901 additions and 868 deletions
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15
README
View File

@ -36,7 +36,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started:
doc/Manual.html the LAMMPS manual
doc/Section_intro.html hi-level introduction to LAMMPS
doc/Section_start.html how to build and use LAMMPS
doc/Developer.pdf LAMMPS developer guide
http://lammps.sandia.gov/doc/Manual.html the LAMMPS manual
http://lammps.sandia.gov/doc/Intro.html hi-level introduction
http://lammps.sandia.gov/doc/Build.html how to build LAMMPS
http://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS
http://lammps.sandia.gov/doc/Developer.pdf LAMMPS developer guide
You can also create these doc pages locally:
% cd doc
% make html # creates HTML pages in doc/html
% make pdf # creates Manual.pdf and Developer.pdf

11
cmake/CMakeLists.txt
View File

@ -276,11 +276,14 @@ endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
if(NOT LAPACK_FOUND)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
else()
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
endif()
@ -377,6 +380,9 @@ endif()
if(PKG_LATTE)
option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
if(DOWNLOAD_LATTE)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
message(STATUS "LATTE not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
@ -479,6 +485,9 @@ if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
if(DOWNLOAD_MSCG)
if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")

10
cmake/README.md
View File

@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl>
</td>
</tr>
<tr>
<td><code>BUILD_EXE</code></td>
<td>control whether to build LAMMPS executable</td>
<td>
<dl>
<dt><code>on</code> (default)</dt>
<dt><code>off</code></dt>
</dl>
</td>
</tr>
<tr>
<td><code>BUILD_SHARED_LIBS</code></td>
<td>control whether to build LAMMPS as a shared-library</td>

9
doc/Makefile
View File

@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
# ------------------------------------------
@ -42,6 +42,8 @@ help:
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
@ -106,6 +108,11 @@ epub: $(OBJECTS)
@rm -rf epub
@echo "Build finished. The ePUB manual file is created."
mobi: epub
@rm -f LAMMPS.mobi
@ebook-convert LAMMPS.epub LAMMPS.mobi
@echo "Conversion finished. The MOBI manual file is created."
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \

4
doc/src/Build.txt
View File

@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
Build_settings
Build_package
Build_extras
Build_windows
END_RST -->
@ -39,7 +40,8 @@ END_RST -->
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
"Packages with extra build options"_Build_extras.html :all(b)
"Packages with extra build options"_Build_extras.html
"Notes for building LAMMPS on Windows"_Build_windows.html :all(b)
If you have problems building LAMMPS, it is often due to software
issues on your local machine. If you can, find a local expert to

12
doc/src/Build_basics.txt
View File

@ -61,7 +61,7 @@ library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
are found, and the name of the library files (MPI_LIB).
For a serial build, you need to specify the 3 varaibles, as shown
For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
@ -145,7 +145,7 @@ By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any "accelerator
packages"_Speed_packages.html you have included in the build.
You can tell CMake to look for a specific compiler with these varaible
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
@ -216,8 +216,8 @@ LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the "Howto couple"_Howto_couple.html doc
page for more info on coupling LAMMPS to other codes. See the
"Python"_Python doc page for more info on wrapping and running LAMMPS
from Python via its library interface.
"Python"_Python_head.html doc page for more info on wrapping and
running LAMMPS from Python via its library interface.
[CMake variables]:
@ -247,7 +247,7 @@ Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directroy, since they are always built as shared
the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
@ -299,7 +299,7 @@ Install LAMMPS after a build :h4,link(install)
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
that you may need super-user priveleges (e.g. sudo) if the directory
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
[CMake variable]:

19
doc/src/Build_cmake.txt
View File

@ -13,12 +13,10 @@ This page is a short summary of how to use CMake to build LAMMPS.
Details on CMake variables that enable specific LAMMPS build options
are given on the pages linked to from the "Build"_Build.html doc page.
Richard Berger (Temple U) has also written a more comprehensive guide
Richard Berger (Temple U) has also written a "more comprehensive
guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start:
"Bulding LAMMPS using
CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md
good place to start.
:line
@ -42,7 +40,7 @@ executable called "lmp" and a library called "liblammps.a" in the
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
LAMMPS or need to recompile LAMMPS repeatedly, installation of the
LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
After compilation, you can optionally copy the LAMMPS executable and
@ -52,7 +50,7 @@ make install # optional, copy LAMMPS executable & library elsewhere :pre
:line
There are 3 variants of CMake: a command-line verison (cmake), a text mode
There are 3 variants of CMake: a command-line version (cmake), a text mode
UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
any of them interchangeably to configure and create the LAMMPS build
environment. On Linux all the versions produce a Makefile as their
@ -81,8 +79,9 @@ directory to un-install all packages. The purge removes all the *.h
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
LAMMPS. If you include the GPU or KOKKOS packages, CMake version 3.2
or later is required. Installation instructions for CMake are below.
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
later version. CMake will print a message telling you if a later
version is required. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from
@ -189,7 +188,7 @@ module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name :pre
Most Linux distributions offer precompiled cmake packages through
Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
"https://cmake.org/download/"_https://cmake.org/download/.

58
doc/src/Build_extras.txt
View File

@ -48,7 +48,7 @@ This is the list of packages that may require additional steps.
"USER-QMMM"_#user-qmmm,
"USER-QUIP"_#user-quip,
"USER-SMD"_#user-smd,
"USER-VTK"_#user-vtk :tb(c=6,ea=c)
"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
:line
@ -175,8 +175,15 @@ package?" page.
[CMake build]:
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
-D KIM_LIBRARY=path # path to KIM shared library (only needed if a custom location)
-D KIM_INCLUDE_DIR=path # path to KIM include directory (only needed if a custom location) :pre
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), KIM_LIBRARY is the
filename (plus path) of the KIM library file, not the directory the
library file is in. KIM_INCLUDE_DIR is the directory the KIM include
file is in.
[Traditional make]:
@ -296,7 +303,13 @@ library.
[CMake build]:
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # path to LATTE shared library (only needed if a custom location) :pre
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) :pre
If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and
built inside the CMake build directory. If the LATTE library is
already on your system (in a location CMake cannot find it),
LATTE_LIBRARY is the filename (plus path) of the LATTE library file,
not the directory the library file is in.
[Traditional make]:
@ -327,7 +340,7 @@ NOTE: the use of the MEAM package is discouraged, as it has been
superseded by the USER-MEAMC package, which is a direct translation of
the Fortran code in the MEAM library to C++. The code in USER-MEAMC
should be functionally equivalent to the MEAM package, fully supports
use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
not), and has optimizations that make it significantly faster than the
MEAM package.
@ -371,8 +384,15 @@ lib/mscg/README and MSCG/Install files for more details.
[CMake build]:
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # path to MSCG shared library (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # path to MSCG include directory (only needed if a custom location) :pre
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre
If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
inside the CMake build directory. If the MSCG library is already on
your system (in a location CMake cannot find it), MSCG_LIBRARY is the
filename (plus path) of the MSCG library file, not the directory the
library file is in. MSCG_INCLUDE_DIR is the directory the MSCG
include file is in.
[Traditional make]:
@ -450,7 +470,7 @@ lib/python/README for more details.
-D PYTHON_EXECUTABLE=path # path to Python executable to use :pre
Without this setting, CMake will ues the default Python on your
Without this setting, CMake will guess the default Python on your
system. To use a different Python version, you can either create a
virtualenv, activate it and then run cmake. Or you can set the
PYTHON_EXECUTABLE variable to specify which Python interpreter should
@ -515,8 +535,15 @@ library"_voro_home.
[CMake build]:
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # (only needed if at custom location) path to VORO shared library
-D VORO_INCLUDE_DIR=path # (only needed if at custom location) path to VORO include directory :pre
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre
If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
built inside the CMake build directory. If the Voro++ library is
already on your system (in a location CMake cannot find it),
VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
not the directory the library file is in. VORO_INCLUDE_DIR is the
directory the Voro++ include file is in.
[Traditional make]:
@ -660,7 +687,7 @@ the HDF5 library.
No additional settings are needed besides "-D PKG_USER-H5MD=yes".
This should autodetect the H5MD library on your system. Several
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is
installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user
@ -750,7 +777,7 @@ on your system.
No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
This should autodetect the NETCDF library if it is installed on your
This should auto-detect the NETCDF library if it is installed on your
system at standard locations. Several advanced CMake NETCDF options
exist if you need to specify where it was installed. Use the ccmake
(terminal window) or cmake-gui (graphical) tools to see these options
@ -877,7 +904,10 @@ Eigen3 is a template library, so you do not need to build it.
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre
Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library.
If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
inside the CMake build directory. If the Eigen3 library is already on
your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
is the directory the Eigen3++ include file is in.
[Traditional make]:
@ -906,7 +936,7 @@ your system.
No additional settings are needed besides "-D PKG_USER-VTK=yes".
This should autodetect the VTK library if it is installed on your
This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist if
you need to specify where it was installed. Use the ccmake (terminal
window) or cmake-gui (graphical) tools to see these options and set

10
doc/src/Build_make.txt
View File

@ -35,16 +35,16 @@ This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
do development on LAMMPS or need to recompile LAMMPS repeatedly, the
do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
uninstalling packages), you must recompile and relink the LAMMPS
uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
recompiled.
re-compiled.
NOTE: When you build LAMMPS for the first time, a long list of *.d
files will be printed out rapidly. This is not an error; it is the
@ -71,8 +71,8 @@ Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags
for optimized performance. Please note, however, that some of these
customized machine Makefile are contributed by users. Since both
compilers, OS configs, and LAMMPS itself keep changing, their settings
may become outdated:
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac

2
doc/src/Build_package.txt
View File

@ -59,7 +59,7 @@ packages:
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c)
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
The mechanism for including packages is simple but different for CMake
versus make.

10
doc/src/Build_settings.txt
View File

@ -80,8 +80,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run using the "kspace_style
pppm"_kspace_style.html command. The "Run output"_doc page gives more
details.
pppm"_kspace_style.html command. The "Run output"_Run_output.html
doc page gives more details.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
@ -101,7 +101,7 @@ Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precesion means they are 8-byte doubles. Note
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT_SINGLE
@ -193,7 +193,7 @@ Output of JPG, PNG, and movie files :h4,link(graphics)
The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command
ouputs movie files in MPEG format. Using these options requires the
outputs movie files in MPEG format. Using these options requires the
following settings:
[CMake variables]:
@ -206,7 +206,7 @@ following settings:
# default = yes if CMake can find ffmpeg, else no :pre
Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executuable files, you can set these
the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file

97
doc/src/Build_windows.txt Normal file
View File

@ -0,0 +1,97 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Notes for building LAMMPS on Windows :h3
"General remarks"_#generic
"Running Linux on Windows"_#linux
"Using GNU GCC ported to Windows"_#gnu
"Using a cross-compiler"_#cross :ul
:line
General remarks :h4,link(generic)
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
Thus portability to other platforms is desired, but not always achieved.
The LAMMPS developers strongly rely on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences with some low-level functionality.
Running Linux on Windows :h4,link(linux)
So before trying to build LAMMPS on Windows, please consider if using
the pre-compiled Windows binary packages are sufficient for your needs
(as an aside, those packages themselves are build on a Linux machine
using cross-compilers). If it is necessary for your to compile LAMMPS
on a Windows machine (e.g. because it is your main desktop), please also
consider using a virtual machine software and run a Linux virtual machine,
or - if have a recently updated Windows 10 installation - consider using
the Windows subsystem for Linux, which allows to run a bash shell from
Ubuntu and from there on, you can pretty much use that shell like you
are running on an Ubuntu Linux machine (e.g. installing software via
apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
Using GNU GCC ported to Windows :h4,link(gnu)
One option for compiling LAMMPS on Windows natively, that has been known
to work in the past is to install a bash shell, unix shell utilities,
perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
provides a unix/linux interface to low-level Windows functions, so LAMMPS
can be compiled on Windows. The necessary (minor) modifications to LAMMPS
are included, but may not always up-to-date for recently added functionality
and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. The CMake build system is untested
for this; you will have to request that makefiles are generated and
manually set the compiler.
When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
this up automatically, but is untested.
In case of problems, you are recommended to contact somebody with
experience in using cygwin. If you do come across portability problems
requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS github project.
Using a cross-compiler :h4,link(cross)
If you need to provide custom LAMMPS binaries for Windows, but do not
need to do the compilation on Windows, please consider using a Linux
to Windows cross-compiler. This is how currently the Windows binary
packages are created by the LAMMPS developers. Because of that, this is
probably the currently best tested and supported way to build LAMMPS
executables for Windows. There are makefiles provided for the
traditional build system, but CMake has also been successfully tested
using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines.
Please keep in mind, though, that this only applies to compiling LAMMPS.
Whether the resulting binaries do work correctly is no tested by the
LAMMPS developers. We instead rely on the feedback of the users
of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However
this is subject to time constraints and focus on HPC platforms.
Native Visual C++ support :h4,link(native)
Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio
style build environment, but the LAMMPS code itself is not fully ported
to support Visual C++. Volunteers to take on this task are welcome.

2
doc/src/Commands_all.txt
View File

@ -19,7 +19,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
All commands :h3
An alphabetic list of all LAMMPS commmands.
An alphabetic list of all LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,

2
doc/src/Commands_bond.txt
View File

@ -95,7 +95,7 @@ OPT.
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.htm;,
"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,

4
doc/src/Commands_parse.txt
View File

@ -14,7 +14,7 @@ LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
Here are 6 rulse for how each line in the input script is parsed by
Here are 6 rules for how each line in the input script is parsed by
LAMMPS:
(1) If the last printable character on the line is a "&" character,
@ -71,7 +71,7 @@ floating-point value. The format string is used to output the result
of the variable expression evaluation. If a format string is not
specified a high-precision "%.20g" is used as the default.
This can be useful for formatting print output to a desired precion:
This can be useful for formatting print output to a desired precision:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre

10
doc/src/Errors_messages.txt
View File

@ -743,7 +743,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt
Single precision cannot be used with MSM. :dd
@ -5078,7 +5078,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/point requires atom attribute q} :dt
@ -5092,7 +5092,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/shielded requires atom attribute q} :dt
@ -5110,7 +5110,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
recompile. :dd
re-compile. :dd
{Fix qeq/slater requires atom attribute q} :dt
@ -5541,7 +5541,7 @@ See the package gpu command. :dd
{GPUs are requested but Kokkos has not been compiled for CUDA} :dt
Recompile Kokkos with CUDA support to use GPUs. :dd
Re-compile Kokkos with CUDA support to use GPUs. :dd
{Ghost velocity forward comm not yet implemented with Kokkos} :dt

2
doc/src/Errors_warnings.txt
View File

@ -13,7 +13,7 @@ This is an alphabetic list of the WARNING messages LAMMPS prints out
and the reason why. If the explanation here is not sufficient, the
documentation for the offending command may help. Warning messages
also list the source file and line number where the warning was
generated. For example, a message lile this:
generated. For example, a message like this:
WARNING: Bond atom missing in box size check (domain.cpp:187) :pre

158
doc/src/Howto.txt
View File

@ -8,27 +8,44 @@ Section"_Examples.html :c
:line
How to discussions :h2
Howto discussions :h2
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
"glossary"_http://lammps.sandia.gov website page also lists MD
terminology with links to corresponding LAMMPS manual pages.
The example input scripts included in the examples dir of the LAMMPS
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples dir of the LAMMPS
distribution and highlighted on the "Examples"_Examples.html doc page
also show how to setup and run various kinds of simulations.
Tutorials howto :h3
<!-- RST
.. toctree::
:name: tutorials
:maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
END_RST -->
<!-- HTML_ONLY -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
<!-- END_HTML_ONLY -->
General howto :h3
<!-- RST
.. toctree::
:name: general
:maxdepth: 1
Howto_restart
@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
Howto_library
Howto_couple
.. toctree::
:maxdepth: 1
END_RST -->
Howto_output
Howto_chunk
<!-- HTML_ONLY -->
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
<!-- END_HTML_ONLY -->
Settings howto :h3
<!-- RST
.. toctree::
:name: settings
:maxdepth: 1
Howto_2d
Howto_triclinic
Howto_walls
Howto_nemd
Howto_granular
Howto_spherical
Howto_dispersion
.. toctree::
:maxdepth: 1
Howto_temperature
Howto_thermostat
Howto_barostat
Howto_walls
Howto_nemd
Howto_dispersion
END_RST -->
<!-- HTML_ONLY -->
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Thermostats"_Howto_thermostat.html
"Barostats"_Howto_barostat.html
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
<!-- END_HTML_ONLY -->
Analysis howto :h3
<!-- RST
.. toctree::
:name: analysis
:maxdepth: 1
Howto_output
Howto_chunk
Howto_temperature
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
END_RST -->
<!-- HTML_ONLY -->
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
"Calculate temperature"_Howto_temperature.html
"Calculate elastic constants"_Howto_elastic.html
"Calculate thermal conductivity"_Howto_kappa.html
"Calculate viscosity"_Howto_viscosity.html
"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
<!-- END_HTML_ONLY -->
Force fields howto :h3
<!-- RST
.. toctree::
:name: force
:maxdepth: 1
Howto_bioFF
@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
Howto_tip4p
Howto_spc
END_RST -->
<!-- HTML_ONLY -->
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)
<!-- END_HTML_ONLY -->
Packages howto :h3
<!-- RST
.. toctree::
:name: packages
:maxdepth: 1
Howto_spherical
Howto_granular
Howto_body
Howto_polarizable
Howto_coreshell
@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
END_RST -->
<!-- HTML_ONLY -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
"2d simulations"_Howto_2d.html
"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
"Walls"_Howto_walls.html
"NEMD simulations"_Howto_nemd.html
"Granular models"_Howto_granular.html
"Finite-size spherical and aspherical particles"_Howto_spherical.html
"Long-range dispersion settings"_Howto_dispersion.html :all(b)
"Calculate temperature"_Howto_temperature.html
"Thermostats"_Howto_thermostat.html
"Barostats"_Howto_barostat.html
"Calculate elastic constants"_Howto_elastic.html
"Calculate thermal conductivity"_Howto_kappa.html
"Calculate viscosity"_Howto_viscosity.html
"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
"TIP3P water model"_Howto_tip3p.html
"TIP4P water model"_Howto_tip4p.html
"SPC water model"_Howto_spc.html :all(b)
"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html

6
doc/src/Howto_barostat.txt
View File

@ -64,11 +64,11 @@ Thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes pressure
values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default pressure is
setup by the thermo command itself. It is NOT the presure associated
setup by the thermo command itself. It is NOT the pressure associated
with any barostatting fix you have defined or with any compute you
have defined that calculates a presure. The doc pages for the
have defined that calculates a pressure. The doc pages for the
barostatting fixes explain the ID of the pressure compute they create.
Thus if you want to view these pressurse, you need to specify them
Thus if you want to view these pressures, you need to specify them
explicitly via the "thermo_style custom"_thermo_style.html command.
Or you can use the "thermo_modify"_thermo_modify.html command to
re-define what pressure compute is used for default thermodynamic

2
doc/src/Howto_body.txt
View File

@ -337,7 +337,7 @@ the sphere that surrounds each vertex. The diameter value can be
different for each body particle. These floating-point values can be
listed on as many lines as you wish; see the
"read_data"_read_data.html command for more details. Because the
maxmimum vertices per face is hard-coded to be 4
maximum number of vertices per face is hard-coded to be 4
(i.e. quadrilaterals), faces with more than 4 vertices need to be
split into triangles or quadrilaterals. For triangular faces, the
last vertex index should be set to -1.

2
doc/src/Howto_diffusion.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Calculate a diffusion coefficient :h3
Calculate diffusion coefficients :h3
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE

2
doc/src/Howto_dispersion.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Long-raage dispersion settings :h3
Long-range dispersion settings :h3
The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,

8
doc/src/Howto_library.txt
View File

@ -171,16 +171,16 @@ void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each callling processor. The scatter
same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to invididual atoms, which may be
owned by different processos.
passed by all calling processors, to individual atoms, which may be
owned by different processors.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
resulting vector is not ordered by atom ID. Atom IDs can be requetsed
resulting vector is not ordered by atom ID. Atom IDs can be requested
by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).

2
doc/src/Howto_pylammps.txt
View File

@ -73,7 +73,7 @@ that package into your current Python installation.
cd $LAMMPS_DIR/python
python install.py :pre
NOTE: Recompiling the shared library requires reinstalling the Python package
NOTE: Recompiling the shared library requires re-installing the Python package
Installation inside of a virtualenv :h5

2
doc/src/Howto_spherical.txt
View File

@ -159,7 +159,7 @@ ellipsoidal particles:
The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
calculation and thermostatting. The "fix langevin"_fix_langevin
calculation and thermostatting. The "fix langevin"_fix_langevin.html
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the

6
doc/src/Howto_spins.txt
View File

@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Magnetic spins :h3
The magnetic spin simualtions are enabled by the SPIN package, whose
The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
The model representents the simulation of atomic magnetic spins coupled
The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
@ -43,7 +43,7 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
All the computed magnetic properties can be outputed by two main
All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or

2
doc/src/Howto_temperature.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
Calcalate temperature :h3
Calculate temperature :h3
Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy

9
doc/src/Install_patch.txt
View File

@ -17,10 +17,11 @@ how to stay current are on the "Install git"_Install_git.html and
If you prefer to download a tarball, as described on the "Install
git"_Install_tarball.html doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the "bug and feature page"_bug of the
website, along with a list of changed files and details about what is
in the new patch release. This page explains how to apply the patch
file to your local LAMMPS directory.
a patch file is posted on the "bug and feature
page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local
LAMMPS directory.
NOTE: You should not apply patch files to a local Git or SVN repo of
LAMMPS, only to an unpacked tarball. Use Git and SVN commands to

365
doc/src/Intro_authors.txt
View File

@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
LAMMPS authors :h3
Authors of LAMMPS :h3
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
@ -15,7 +15,8 @@ University:
"Steve Plimpton"_sjp, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Stan Moore, stamoor at sandia.gov
Axel Kohlmeyer, akohlmey at gmail.com :ul
Axel Kohlmeyer, akohlmey at gmail.com
Richard Berger, richard.berger at temple.edu :ul
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
@ -24,26 +25,31 @@ and Ray Shan, now at Materials Design.
:line
The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
The "Authors page"_http://lammps.sandia.gov/authors.html of the
"LAMMPS website"_lws has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to
LAMMPS.
Richard Berger (Temple U), Python interface, GitHub site, Sphinx doc pages
:line
The following folks deserve special recognition. Many of the packages
they have written are unique for an MD code and LAMMPS would not be as
general-purpose as it is without their expertise and efforts.
Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF
Mike Brown (Intel), GPU and USER-INTEL packages
Colin Denniston (U Western Ontario), USER-LB package
Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages
Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
Mike Parks (Sandia), PERI package for Peridynamics
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
Christian Trott (Sandia), USER-CUDA and KOKKOS packages
Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
:line
@ -58,322 +64,3 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak and Roy Pollock (LLNL) :ul
:line
Here is a timeline for when various individuals contributed to a new
feature or command or tool added to LAMMPS:
Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U)
Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
May18 : fix bond/react : Jake Gissinger (CU Boulder)
Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U)
Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
Dec17 : fix python/move : Richard Berger (Temple U)
Nov17 : pair extep : Jaap Kroes (Radboud U)
Oct17 : USER-UEF package : David Nicholson (MIT)
Oct17 : fix rhok : Ulf Pederson (Roskilde U)
Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
Sep17 : fix latte : Christian Negre (LANL)
Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
Aug17 : USER-MESO package : Zhen Li (Brown University)
Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
Jun17 : compute cnp/atom : Paulo Branicio (USC)
May17 : fix python and pair python : Richard Berger (Temple U)
May17 : pair edip/multi : Chao Jiang (U Wisconsin)
May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
Mar17 : fix filter/corotate : Lukas Fath (KIT)
Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
Jan17 : fix mscg : Lauren Abbott (Sandia)
Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
Sep16 : kspace pppm/kk : Stan Moore (Sandia)
Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
Aug16 : fix controller : Aidan Thompson (Sandia)
Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
Jul16 : dihedral spherical : Andrew Jewett
Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
Jun16 : fix orient/bcc : Tegar Wicaksono (UBC)
Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
Apr16 : bond write : Axel Kohlmeyer (Temple U)
Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
Dec15 : fix qeq/fire : Ray Shan (Sandia)
Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
Oct15 : displace_atoms variable option : Reese Jones (Sandia)
Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
Aug15 : timer command : Axel Kohlmeyer (Temple U)
Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
Feb15 : fix tfmc : Kristof Bal (U of Antwerp)
Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF)
Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
Aug14 : USER-INTEL package : Mike Brown (Intel)
May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
Sep13 : xmgrace tool : Vikas Varshney
Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
Aug13 : pair nm and variants : Julien Devemy (ICCF)
Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia)
Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
Jun13 : fix tune/kspace : Paul Crozier (Sandia)
Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
May13 : compute msd/nongauss : Rob Hoy
May13 : pair list : Axel Kohlmeyer (Temple U)
May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
Apr13 : dump_modify nfile and fileper : Christopher Knight
Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
Feb13 : fix species : Ray Shan (Sandia)
Jan13 : compute voronoi/atom : Daniel Schwen
Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
May12 : read_dump : Tim Sirk (ARL)
May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
Feb12 : pair_style beck : Jon Zimmerman (Sandia)
Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
Jan12 : dihedral_style table : Andrew Jewett (UCSB)
Jan12 : angle_style dipole : Mario Orsi
Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
Sep11 : pair_style edip : Luca Ferraro (CASPUR)
Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
Aug11 : fix restrain : Craig Tenney (Sandia)
Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
Aug11 : pair_style dipole/sf : Mario Orsi
Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \
Axel Kohlmeyer (Temple U)
Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
Chandra Veer Singh (Cornell)
Jun11 : Windows build option via Microsoft Visual Studio : \
Ilya Valuev (JIHT, Moscow, Russia)
Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
Jun11 : dump image : Nathan Fabian (Sandia)
May11 : pppm GPU single and double : Mike Brown (ORNL)
May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
- : fix adapt and compute ti for thermodynamic integration for \
free energies : Sai Jayaraman (Sandia)
- : pair_style born and gauss : Sai Jayaraman (Sandia)
- : stochastic rotation dynamics (SRD) via fix srd : \
Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
- : ipp Perl script tool : Reese Jones (Sandia)
- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \
Paul Saxe (Materials Design) and Reese Jones (Sandia)
- : pair_style peri/lps : Mike Parks (Sandia)
- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
- : public SVN & Git repositories for LAMMPS : \
Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
- : compute heat/flux : German Samolyuk (ORNL) and \
Mario Pinto (Computational Research Lab, Pune, India)
- : pair_style yukawa/colloid : Randy Schunk (Sandia)
- : fix wall/colloid : Jeremy Lechman (Sandia)
2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
- : concentration-dependent EAM potential : \
Alexander Stukowski (Technical University of Darmstadt)
- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
- : min_style hftn : Todd Plantenga (Sandia)
- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
- : dump cfg : Liang Wan (Chinese Academy of Sciences)
- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
- : fix langevin tally : Carolyn Phillips (U Michigan)
- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
Philip Howell (Siemens), Vikas Varsney (AFRL)
- : region cone : Pim Schravendijk
- : pair_style born/coul/long : Ahmed Ismail (Sandia)
- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
- : peridynamics : Mike Parks (Sandia)
- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
- : GROMACS pair potentials : Mark Stevens (Sandia)
- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
- : pair_style lubricate : Randy Schunk (Sandia)
- : compute ackland/atom : Gerolf Ziegenhain
- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
Pieter in 't Veld (Sandia)
- : AI-REBO bond-order potential : Ase Henry (MIT)
- : making LAMMPS a true "object" that can be instantiated \
multiple times, e.g. as a library : Ben FrantzDale (RPI)
- : pymol_asphere viz tool : Mike Brown (Sandia)
2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
- : tensile and shear deformations : Pieter in 't Veld (Sandia)
- : GayBerne potential : Mike Brown (Sandia)
- : ellipsoidal particles : Mike Brown (Sandia)
- : colloid potentials : Pieter in 't Veld (Sandia)
- : fix heat : Paul Crozier and Ed Webb (Sandia)
- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
- : MEAM potential : Greg Wagner (Sandia)
- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
James Fischer (High Performance Technologies), \
David Richie and Vincent Natoli (Stone Ridge Technologies)
2006 : fix wall/lj126 : Mark Stevens (Sandia)
- : Stillinger-Weber and Tersoff potentials : \
Aidan Thompson and Xiaowang Zhou (Sandia)
- : region prism : Pieter in 't Veld (Sandia)
- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
- : OPLS dihedral potential: Mark Stevens (Sandia)
- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
- : faster pair hybrid potential: James Fischer \
(High Performance Technologies, Inc), Vincent Natoli and \
David Richie (Stone Ridge Technology)
- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
- : grain boundary orientation fix : Koenraad Janssens and \
David Olmsted (Sandia)
- : pair_style lj/smooth potential : Craig Maloney (UCSB)
- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
(Johns Hopkins U) and Paul Crozier (Sandia)
- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Mark Stevens (Sandia)
- : Finnis/Sinclair EAM: Tim Lau (MIT)
- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
Frank van Swol (Sandia)
- : TIP4P potential (4-site water): Ahmed Ismail and \
Amalie Frischknecht (Sandia)
2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
- : compressed dump files: Erik Luijten (U Illinois)
- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
- : electric field fix: Christina Payne (Vanderbilt U)
- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
Vikas Varshney (U Akron)
- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
- : Morse bond potential: Jeff Greathouse (Sandia)
- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
- : force tables for long-range Coulombics: Paul Crozier (Sandia)
2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany)
- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia)
- : parallel tempering: Mark Sears (Sandia)
earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
- : HTFN energy minimizer: Todd Plantenga (Sandia)
- : class 2 force fields: Eric Simon (Cray)
- : NVT/NPT integrators: Mark Stevens (Sandia)
- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)

4
doc/src/Intro_overview.txt
View File

@ -17,7 +17,7 @@ variety of interatomic potentials (force fields) and boundary
conditions. It can model 2d or 3d systems with only a few particles
up to millions or billions.
LAMMPS can be built and run on a laptop or destop machine, but is
LAMMPS can be built and run on a laptop or desktop machine, but is
designed for parallel computers. It will run on any parallel machine
that supports the "MPI"_mpi message-passing library. This includes
shared-memory boxes and distributed-memory clusters and
@ -45,7 +45,7 @@ nature; some long-range models are included as well.
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
too large. This is in contrast to methods used for modeling plasmas
too large. This is in contrast to methods used for modeling plasma
or gravitational bodies (e.g. galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques to

6
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="16 Aug 2018 version">
<META NAME="docnumber" CONTENT="22 Aug 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
16 Aug 2018 version :c,h2
22 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
@ -66,7 +66,7 @@ every LAMMPS command.
.. toctree::
:maxdepth: 2
:numbered:
:numbered: 3
:caption: User Documentation
:name: userdoc
:includehidden:

20
doc/src/Manual_build.txt
View File

@ -10,15 +10,16 @@ Section"_Manual.html :c
Building the LAMMPS manual :h2
Depending on how you obtained LAMMPS, the doc directory has
2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
Depending on how you obtained LAMMPS, the doc directory has 2 or 3
sub-directories and optionally 2 PDF files and 2 e-book format files:
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
tools # tools and settings for building the documentation
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB format :pre
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format :pre
If you downloaded LAMMPS as a tarball from the web site, all these
directories and files should be included.
@ -40,7 +41,7 @@ HTML files already exist. This requires various tools including
Sphinx, which the build process will attempt to download and install
on your system, if not already available. See more details below.
(c) You can genererate an older, simpler, less-fancy style of HTML
(c) You can generate an older, simpler, less-fancy style of HTML
documentation by typing "make old". This will create an "old"
directory. This can be useful if (b) does not work on your box for
some reason, or you want to quickly view the HTML version of a doc
@ -61,6 +62,7 @@ make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data :pre
@ -68,7 +70,7 @@ make clean-all # remove entire build folder and any cached data :pre
Installing prerequisites for HTML build :h3
To run the HTML documention build toolchain, Python 3 and virtualenv
To run the HTML documentation build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
Ubuntu :h4
@ -81,7 +83,7 @@ sudo yum install python3-virtualenv :pre
Fedora (since version 22) :h4
sudo dnf install python3-virtualenv pre
sudo dnf install python3-virtualenv :pre
MacOS X :h4
@ -115,10 +117,8 @@ ePUB :h4
Same as for HTML. This uses the same tools and configuration
files as the HTML tree.
For converting the generated ePUB file to a mobi format file
For converting the generated ePUB file to a MOBI format file
(for e-book readers like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
You first create the ePUB file with 'make epub' and then do:
ebook-convert LAMMPS.epub LAMMPS.mobi :pre
You first create the ePUB file and then convert it with 'make mobi'

2
doc/src/Modify_overview.txt
View File

@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Overview :h3
The best way to add a new feature to LAMMPS is to find a similar
featureand look at the corresponding source and header files to figure
feature and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual

26
doc/src/Packages_details.txt
View File

@ -297,7 +297,7 @@ lib/gpu/README
"Section 2.6 -sf gpu"_Run_options.html
"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Commands all"_lc pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@ -382,6 +382,11 @@ switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
lib/kokkos/README for a list of compilers and their respective
platforms, that are known to work.
[Authors:] The KOKKOS package was created primarily by Christian Trott
and Stan Moore (Sandia), with contributions from other folks as well.
@ -407,7 +412,7 @@ lib/kokkos/README
"Section 2.6 -sf kk"_Run_options.html
"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@ -846,7 +851,7 @@ multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
verlet/split algorithm for performing long-range Coulombics on one set
of processors, and the remainder of the force field calcalation on
of processors, and the remainder of the force field calculation on
another set.
[Supporting info:]
@ -869,7 +874,7 @@ RIGID package :link(PKG-RIGID),h4
[Contents:]
Fixes which enforce rigid constraints on collections of atoms or
particles. This includes SHAKE and RATTLE, as well as varous
particles. This includes SHAKE and RATTLE, as well as various
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
@ -1365,7 +1370,7 @@ which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
supported, performance will be suboptimal.
supported, performance will be sub-optimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
@ -1387,7 +1392,7 @@ src/USER-INTEL/README
"Section 2.6 -sf intel"_Run_options.html
"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@ -1577,8 +1582,6 @@ molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation
tools.
:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
To use this package you must have the desired VMD plugins available on
your system.
@ -1588,7 +1591,7 @@ plugin via the "dump molfile"_dump_molfile.html command. Plugins can
be obtained from a VMD installation which has to match the platform
that you are using to compile LAMMPS for. By adding plugins to VMD,
support for new file formats can be added to LAMMPS (or VMD or other
programs that use them) without having to recompile the application
programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found
at
"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
@ -1630,6 +1633,7 @@ tools:
"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org)
:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
:link(atomeye,http://www.libatoms.org)
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@ -1693,7 +1697,7 @@ src/USER-OMP/README
"Section 2.6 -sf omp"_Run_options.html
"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@ -1993,3 +1997,5 @@ src/USER-VTK: filenames -> commands
src/USER-VTK/README
lib/vtk/README
"dump vtk"_dump_vtk.html :ul

52
doc/src/Packages_standard.txt
View File

@ -25,42 +25,42 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
dash = no library
no = no library
sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no
"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no
"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no
"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no
"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys
"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no
"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no
"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no
"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no
"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no
"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no
"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l)

58
doc/src/Packages_user.txt
View File

@ -32,7 +32,7 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
dash = no library
no = no library
sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
@ -40,35 +40,35 @@ ext = external library: you will need to download and install it on your machine
Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no
"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no
"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no
"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no
"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no
"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)

4
doc/src/Python_call.txt
View File

@ -59,9 +59,9 @@ and callbacks to LAMMPS.
The "fix python/invoke"_fix_python_invoke.html command can execute
Python code at selected timesteps during a simulation run.
The "pair_style python"_pair_python command allows you to define
The "pair_style python"_pair_python.html command allows you to define
pairwise potentials as python code which encodes a single pairwise
interaction. This is useful for rapid-developement and debugging of a
interaction. This is useful for rapid development and debugging of a
new potential.
To use any of these commands, you only need to build LAMMPS with the

4
doc/src/Python_head.txt
View File

@ -62,11 +62,11 @@ library interface provided in src/library.h and src/library.h. That
interface is exposed to Python either when calling LAMMPS from Python
or when calling Python from a LAMMPS input script and then calling
back to LAMMPS from Python code. The library interface is designed to
be easy to add funcionality to. Thus the Python interface to LAMMPS
be easy to add functionality to. Thus the Python interface to LAMMPS
is also easy to extend as well.
If you create interesting Python scripts that run LAMMPS or
interesting Python functions that can be called from a LAMMPS input
script, that you think would be genearlly useful, please post them as
script, that you think would be generally useful, please post them as
a pull request to our "GitHub site"_https://github.com/lammps/lammps,
and they can be added to the LAMMPS distribution or webpage.

10
doc/src/Python_library.txt
View File

@ -186,20 +186,20 @@ keyword as a float.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
The set_variable() methosd sets an existing string-style variable to a
The set_variable() method sets an existing string-style variable to a
new string value, so that subsequent LAMMPS commands can access the
variable.
The reset_box() emthods resets the size and shape of the simulation
The reset_box() method resets the size and shape of the simulation
box, e.g. as part of restoring a previously extracted and saved state
of a simulation.
The gather methods collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each callling processor. The scatter
same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to invididual atoms, which may be
owned by different processos.
passed by all calling processors, to individual atoms, which may be
owned by different processors.
Note that the data returned by the gather methods,
e.g. gather_atoms("x"), is different from the data structure returned

2
doc/src/Run_basics.txt
View File

@ -75,7 +75,7 @@ setenv OMP_NUM_THREADS 2 # csh or tcsh :pre
This can also be done via the "package"_package.html command or via
the "-pk command-line switch"_Run_options.html which invokes the
package command. See the "package"_package.html command or
"Speed"_Speed.html doc pages for more details about which accerlarator
"Speed"_Speed.html doc pages for more details about which accelerator
packages and which commands support multi-threading.
:line

4
doc/src/Run_windows.txt
View File

@ -33,8 +33,8 @@ in parallel, follow these steps.
Download and install a compatible MPI library binary package:
for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the

6
doc/src/Speed_bench.txt
View File

@ -11,7 +11,7 @@ Benchmarks :h3
Current LAMMPS performance is discussed on the "Benchmarks
page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
where timings and parallel efficiencies are listed. The page has
where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
@ -77,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated.
Performance on a parallel machine can also be predicted from one-core
or one-node timings if the parallel efficiency can be estimated. The
communication bandwidth and latency of a particular parallel machine
affects the efficiency. On most machines LAMMPS will give parallel
efficiencies on these benchmarks above 50% so long as the number of
affects the efficiency. On most machines LAMMPS will give a parallel
efficiency on these benchmarks above 50% so long as the number of
atoms/core is a few 100 or greater, and closer to 100% for large
numbers of atoms/core. This is for all-MPI mode with one MPI task per
core. For nodes with accelerator options or hardware (OpenMP, GPU,

119
doc/src/Speed_compare.txt
View File

@ -9,65 +9,108 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Comparison of various accelerator packages :h3
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.
run on GPUs, optimize for vector units on CPUs and run on Intel
Xeon Phi (co-)processors.
All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
All of these packages can accelerate a LAMMPS calculation taking
advantage of hardware features, but they do it in different ways
and acceleration is not always guaranteed.
As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
one package may be faster than the other. We give some guidelines
below, but the best way to determine which package is faster for your
input script is to try multiple of them on your machine and experiment
with available performance tuning settings. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
Both, the GPU and the KOKKOS package allows you to assign multiple
MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
can lead to a speedup through better utilization of the GPU (by
overlapping computation and data transfer) and more efficient
computation of the non-GPU accelerated parts of LAMMPS through MPI
parallelization, as all system data is maintained and updated on
the host. For KOKKOS, there is less to no benefit from this, due
to its different memory management model, which tries to retain
data on the GPU.
:ulb,l
The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The
KOKKOS/CUDA package only does this on timesteps when a CPU calculation
is required (e.g. to invoke a fix or compute that is non-GPU-ized).
Hence, if you can formulate your input script to only use GPU-ized
fixes and computes, and avoid doing I/O too often (thermo output, dump
file snapshots, restart files), then the data transfer cost of the
KOKKOS/CUDA package can be very low, causing it to run faster than the
GPU package. :l
The GPU package moves per-atom data (coordinates, forces, and
(optionally) neighbor list data, if not computed on the GPU) between
the CPU and GPU at every timestep. The KOKKOS/CUDA package only does
this on timesteps when a CPU calculation is required (e.g. to invoke
a fix or compute that is non-GPU-ized). Hence, if you can formulate
your input script to only use GPU-ized fixes and computes, and avoid
doing I/O too often (thermo output, dump file snapshots, restart files),
then the data transfer cost of the KOKKOS/CUDA package can be very low,
causing it to run faster than the GPU package. :l
The GPU package is often faster than the KOKKOS/CUDA package, if the
number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
The GPU package is often faster than the KOKKOS/CUDA package, when the
number of atoms per GPU is on the smaller side. The crossover point,
in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
depends strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. If the GPU package is running with several MPI processes
Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
etc) on the CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l
spread across more CPUs and hence the GPU package can run faster in these
cases. :l
When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l
When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
performance depends to some extent on the available bandwidth between
the CPUs and the GPU. This can differ significantly based on the
available bus technology, capability of the host CPU and mainboard,
the wiring of the buses and whether switches are used to increase the
number of available bus slots, or if GPUs are housed in an external
enclosure. This can become quite complex. :l
To achieve significant acceleration through GPUs, both KOKKOS and GPU
package require capable GPUs with fast on-device memory and efficient
data transfer rates. This requests capable upper mid-level to high-end
(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
result in a slowdown instead. :l
For the GPU package, specifically when running in parallel with MPI,
if it often more efficient to exclude the PPPM kspace style from GPU
acceleration and instead run it - concurrently with a GPU accelerated
pair style - on the CPU. This can often be easily achieved with placing
a {suffix off} command before and a {suffix on} command after the
{kspace_style pppm} command. :l
The KOKKOS/OpenMP and USER-OMP package have different thread management
strategies, which should result in USER-OMP being more efficient for a
small number of threads with increasing overhead as the number of threads
per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
case, but have lower performance with few threads. :l
The USER-INTEL package contains many options and settings for achieving
additional performance on Intel hardware (CPU and accelerator cards), but
to unlock this potential, an Intel compiler is required. The package code
will compile with GNU gcc, but it will not be as efficient. :l
:ule
[Differences between the two packages:]
[Differences between the GPU and KOKKOS packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. :ulb,l
The GPU package accelerates only pair force, neighbor list, and (parts
of) PPPM calculations. The KOKKOS package attempts to run most of the
calculation on the GPU, but can transparently support non-accelerated
code (with a performance penalty due to having data transfers between
host and GPU). :ulb,l
The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
The GPU package can be compiled for CUDA or OpenCL and thus supports
both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
resulting in equal or better performance over OpenCL. :l
OpenCL in the GPU package does theoretically also support Intel CPUs or
Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
is superior. :l
:ule

54
doc/src/Speed_gpu.txt
View File

@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
GPU package :h3
The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
versions of many pair styles, including the 3-body Stillinger-Weber
pair style, and for "kspace_style pppm"_kspace_style.html for
long-range Coulombics. It has the following general features:
The GPU package was developed by Mike Brown while at SNL and ORNL
and his collaborators, particularly Trung Nguyen (now at Northwestern).
It provides GPU versions of many pair styles and for parts of the
"kspace_style pppm"_kspace_style.html for long-range Coulombics.
It has the following general features:
It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
e.g. within a node of a parallel machine. :ulb,l
Atom-based data (e.g. coordinates, forces) moves back-and-forth
Atom-based data (e.g. coordinates, forces) are moved back-and-forth
between the CPU(s) and GPU every timestep. :l
Neighbor lists can be built on the CPU or on the GPU :l
@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l
Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU. :l
Force computations of different style (pair vs. bond/angle/dihedral/improper)
can be performed concurrently on the GPU and CPU(s), respectively. :l
It allows for GPU computations to be performed in single or double
precision, or in mixed-mode precision, where pairwise forces are
@ -39,21 +39,32 @@ force vectors. :l
LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU
hardware. :l
same functionality is supported on a variety of hardware. :l
:ule
[Required hardware/software:]
To use this package, you currently need to have an NVIDIA GPU and
install the NVIDIA CUDA software on your system:
To compile and use this package in CUDA mode, you currently need
to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
toolkit software on your system (this is primarily tested on Linux
and completely unsupported on Windows):
Check if you have an NVIDIA GPU: cat
/proc/driver/nvidia/gpus/0/information Go to
http://www.nvidia.com/object/cuda_get.html Install a driver and
toolkit appropriate for your system (SDK is not necessary) Run
lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
below) to list supported devices and properties :ul
Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
Go to http://www.nvidia.com/object/cuda_get.html :l
Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
list supported devices and properties :ule,l
To compile and use this package in OpenCL mode, you currently need
to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
installed. There can be multiple of them for the same or different hardware
(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
as 'platforms'. The GPU library will select the [first] suitable platform,
but this can be overridden using the device option of the "package"_package.html
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
platforms and devices with a suitable ICD available.
[Building LAMMPS with the GPU package:]
@ -120,7 +131,10 @@ GPUs/node to use, as well as other options.
The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
precision used on the GPU (double, single, mixed).
precision used on the GPU (double, single, mixed). Using the GPU package
in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the GPU package on various
@ -146,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
performance. Neighbor lists can be built on the GPU or CPU. Force
calculations can be dynamically balanced across the CPU cores and
GPUs. GPU-specific settings can be made which can be optimized
for different hardware. See the "packakge"_package.html command
for different hardware. See the "package"_package.html command
doc page for details. :l
As described by the "package gpu"_package.html command, GPU

4
doc/src/Speed_intel.txt
View File

@ -68,7 +68,7 @@ In most molecular dynamics software, parallelization parameters
to changing the order of operations with finite-precision
calculations. The USER-INTEL package is deterministic. This means
that the results should be reproducible from run to run with the
{same} parallel configurations and when using determinstic
{same} parallel configurations and when using deterministic
libraries or library settings (MPI, OpenMP, FFT). However, there
are differences in the USER-INTEL package that can change the
order of operations compared to LAMMPS without acceleration:
@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html" to the beginning of the input script for
grid numa"_processors.html to the beginning of the input script for
better scalability.
When running on many nodes, performance might be better when using

16
doc/src/Speed_kokkos.txt
View File

@ -93,12 +93,12 @@ The "t Nt" option specifies how many OpenMP threads per MPI task to
use with a node. The default is Nt = 1, which is MPI-only mode. 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 hyperthreading is enabled, then the product of MPI tasks *
OpenMP threads/task should not exceed the physical number of cores *
hardware threads. The "-k on" switch also issues a "package kokkos"
command (with no additional arguments) which sets various KOKKOS
options to default values, as discussed on the "package"_package.html
command doc page.
suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
tasks * OpenMP threads/task should not exceed the physical number of
cores * hardware threads. The "-k on" switch also issues a
"package kokkos" command (with no additional arguments) which sets
various KOKKOS options to default values, as discussed on the
"package"_package.html command doc page.
The "-sf kk" "command-line switch"_Run_options.html will automatically
append the "/kk" suffix to styles that support it. In this manner no
@ -149,7 +149,7 @@ Intel Knight's Landing (KNL) Xeon Phi:
KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
reserved for the OS, and only 64 or 66 cores are used. Each core has 4
hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
cores to run on. The product of MPI tasks * OpenMP threads/task should
not exceed this limit, otherwise performance will suffer. Note that
with the KOKKOS package you do not need to specify how many KNLs there
@ -228,7 +228,7 @@ for details and default settings. Experimenting with its options can
provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
NOTE: For good performance of the KOKKOS package on GPUs, you must
have Kepler generation GPUs (or later). The Kokkos library exploits

2
doc/src/Speed_measure.txt
View File

@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.

2
doc/src/Speed_omp.txt
View File

@ -29,7 +29,7 @@ instructions.
[Run with the USER-OMP package from the command line:]
These example asume one or more 16-core nodes.
These examples assume one or more 16-core nodes.
env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS
lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels

2
doc/src/Speed_packages.txt
View File

@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available for a particular
style, find the style name in the "Commands_all"_Commands_all.html
style, find the style name in the "Commands_all"_lc
style pages (fix,compute,pair,etc) and see what suffixes are listed
(g,i,k,o,t) with it. The doc pages for individual commands
(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list

135
doc/src/Tools.txt
View File

@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
reside in that directory. Most of them are larger packages in their
own sub-directories with their own Makefiles and/or README files.
"amber2lmp"_#amber
"binary2txt"_#binary
"ch2lmp"_#charmm
"chain"_#chain
"colvars"_#colvars
"createatoms"_#createatoms
"doxygen"_#doxygen
"drude"_#drude
"eam database"_#eamdb
"eam generate"_#eamgn
"eff"_#eff
"emacs"_#emacs
"fep"_#fep
"i-pi"_#ipi
"ipp"_#ipp
"kate"_#kate
"lmp2arc"_#arc
"lmp2cfg"_#cfg
"matlab"_#matlab
"micelle2d"_#micelle
"moltemplate"_#moltemplate
"msi2lmp"_#msi
"phonon"_#phonon
"polybond"_#polybond
"pymol_asphere"_#pymol
"python"_#pythontools
"reax"_#reax_tool
"smd"_#smd
"vim"_#vim
"xmgrace"_#xmgrace :ul
:line
Pre-processing tools :h3
"amber2lmp"_#amber,
"ch2lmp"_#charmm,
"chain"_#chain,
"createatoms"_#createatoms,
"drude"_#drude,
"eam database"_#eamdb,
"eam generate"_#eamgn,
"eff"_#eff,
"ipp"_#ipp,
"micelle2d"_#micelle,
"moltemplate"_#moltemplate,
"msi2lmp"_#msi,
"polybond"_#polybond :tb(c=6,ea=c,a=l)
Post-processing tools :h3
"amber2lmp"_#amber,
"binary2txt"_#binary,
"ch2lmp"_#charmm,
"colvars"_#colvars,
"eff"_#eff,
"fep"_#fep,
"lmp2arc"_#arc,
"lmp2cfg"_#cfg,
"matlab"_#matlab,
"phonon"_#phonon,
"pymol_asphere"_#pymol,
"python"_#pythontools,
"reax"_#reax_tool,
"smd"_#smd,
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
Miscellaneous tools :h3
"doxygen"_#doxygen,
"emacs"_#emacs,
"i-pi"_#ipi,
"kate"_#kate,
"vim"_#vim :tb(c=5,ea=c,a=l)
:line
amber2lmp tool :h3,link(amber)
Tool descriptions :h3
amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@ -91,7 +106,7 @@ necessary modifications yourself.
:line
binary2txt tool :h3,link(binary)
binary2txt tool :h4,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@ -104,7 +119,7 @@ since binary files are not compatible across all platforms.
:line
ch2lmp tool :h3,link(charmm)
ch2lmp tool :h4,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@ -129,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
chain tool :h3,link(chain)
chain tool :h4,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.html.
:line
colvars tools :h3,link(colvars)
colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@ -168,7 +183,7 @@ gmail.com) at ICTP, Italy.
:line
createatoms tool :h3,link(createatoms)
createatoms tool :h4,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@ -181,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
doxygen tool :h3,link(doxygen)
doxygen tool :h4,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@ -193,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
drude tool :h3,link(drude)
drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@ -206,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
eam database tool :h3,link(eamdb)
eam database tool :h4,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@ -222,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
eam generate tool :h3,link(eamgn)
eam generate tool :h4,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@ -235,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
eff tool :h3,link(eff)
eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@ -246,7 +261,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
emacs tool :h3,link(emacs)
emacs tool :h4,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
@ -257,7 +272,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
fep tool :h3,link(fep)
fep tool :h4,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@ -270,7 +285,7 @@ See README file in the tools/fep directory.
:line
i-pi tool :h3,link(ipi)
i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@ -287,7 +302,7 @@ calculations with LAMMPS.
:line
ipp tool :h3,link(ipp)
ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@ -301,7 +316,7 @@ tools/createatoms tool's input file.
:line
kate tool :h3,link(kate)
kate tool :h4,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@ -312,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
lmp2arc tool :h3,link(arc)
lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@ -328,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
lmp2cfg tool :h3,link(cfg)
lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@ -339,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
matlab tool :h3,link(matlab)
matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@ -357,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
micelle2d tool :h3,link(micelle)
micelle2d tool :h4,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@ -374,7 +389,7 @@ definition file. This tool was used to create the system for the
:line
moltemplate tool :h3,link(moltemplate)
moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@ -388,7 +403,7 @@ supports it. It has its own WWW page at
:line
msi2lmp tool :h3,link(msi)
msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@ -405,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
phonon tool :h3,link(phonon)
phonon tool :h4,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@ -420,7 +435,7 @@ University.
:line
polybond tool :h3,link(polybond)
polybond tool :h4,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@ -434,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
pymol_asphere tool :h3,link(pymol)
pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@ -452,7 +467,7 @@ This tool was written by Mike Brown at Sandia.
:line
python tool :h3,link(pythontools)
python tool :h4,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@ -468,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
reax tool :h3,link(reax_tool)
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@ -479,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
smd tool :h3,link(smd)
smd tool :h4,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@ -495,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
vim tool :h3,link(vim)
vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@ -506,7 +521,7 @@ ziegenhain.com)
:line
xmgrace tool :h3,link(xmgrace)
xmgrace tool :h4,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting

2
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_add_species.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_atom_element_map.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_atom_weight.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_atomic_charge.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_boundary.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_boundary_dynamics.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_boundary_faceset.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_boundary_integral.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_consistent_fe_initialization.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_contour_integral.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_control.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_control_momentum.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_control_thermal.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_decomposition.html
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@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_electron_integration.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_equilibrium_start.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_extrinsic_exchange.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_fe_md_boundary.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_fem_mesh.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_filter_scale.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_filter_type.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_fix_atc.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_fix_flux.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_fix_nodes.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_computes.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_fields.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_gradients.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_kernel.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_on_the_fly.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_hardy_rates.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_initial.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_internal_atom_integrate.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_internal_element_set.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_internal_quadrature.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_kernel_function.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_localized_lambda.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_lumped_lambda_solve.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mask_direction.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mass_matrix.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_material.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mesh_add_to_nodeset.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mesh_create.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mesh_create_elementset.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mesh_create_faceset_box.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
doc/src/USER/atc/man_mesh_create_faceset_plane.html
View File

@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

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<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

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<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

2
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<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
<a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
<a href="../../Section_commands.html#comm">Commands</a>
<a href="../../Commands_all.html">Commands</a>
</center>
<hr>

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