tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

collapse multiple empty lines into a single empty line

Browse Source
This commit is contained in:
Axel Kohlmeyer
2020-03-10 15:56:11 -04:00
parent e643e88913
commit ae9255e057
718 changed files with 0 additions and 7932 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
doc/src/Build.rst
View File

@ -8,7 +8,6 @@ for use with GNU make or gmake, or a build environment generated by CMake
alternative you can download a package with pre-built executables
as described on the :doc:`Install <Install>` doc page.
.. toctree::
:maxdepth: 1

17
doc/src/Build_basics.rst
View File

@ -10,10 +10,8 @@ CMake and make:
* :ref:`Build the LAMMPS documentation <doc>`
* :ref:`Install LAMMPS after a build <install>`
----------
.. _serial:
Serial vs parallel build
@ -57,7 +55,6 @@ The build with traditional makefiles has to be done inside the source folder `sr
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Any "make machine" command will look up the make settings from a file
Makefile.machine, create a folder Obj\_machine with all objects and
generated files and an executable called *lmp\_machine*\ . The standard
@ -154,10 +151,8 @@ while dropping all 'shared()' directives. The script
'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
this conversion.
----------
.. _compile:
Choice of compiler and compile/link options
@ -204,7 +199,6 @@ for all the C++ files:
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
A few example command lines are:
.. code-block:: bash
@ -347,7 +341,6 @@ build may generate an error. This means you will need to install a
shared library version of the auxiliary library. The build instructions
for the library should tell you how to do this.
As an example, here is how to build and install the `MPICH library
<mpich_>`_, a popular open-source version of MPI, as a shared library
in the default /usr/local/lib location:
@ -377,7 +370,6 @@ recommended to ensure the integrity of the system software installation.
----------
.. _doc:
Build the LAMMPS documentation
@ -412,7 +404,6 @@ LAMMPS source distribution.
make package_check # check for complete and consistent package lists
make spelling # spell-check the manual
Thus "make html" will create a "doc/html" directory with the HTML format
manual pages so that you can browse them with a web browser locally on
your system.
@ -423,7 +414,6 @@ your system.
current LAMMPS version (HTML and PDF files), from the website
`download page <http://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :
It is also possible to create the HTML version of the manual within
@ -436,10 +426,8 @@ the "install" step when installing LAMMPS after the CMake build via
-D BUILD_DOC=value # yes or no (default)
----------
.. _tools:
Build LAMMPS tools
@ -450,7 +438,6 @@ using CMake or Make.
**CMake build3**\ :
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default)
@ -460,7 +447,6 @@ The generated binaries will also become part of the LAMMPS installation
**Traditional make**\ :
.. code-block:: bash
cd lammps/tools
@ -470,10 +456,8 @@ The generated binaries will also become part of the LAMMPS installation
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
----------
.. _install:
Install LAMMPS after a build
@ -487,7 +471,6 @@ you want to copy files to is protected.
**CMake build**\ :
.. code-block:: bash
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake

20
doc/src/Build_cmake.rst
View File

@ -9,17 +9,14 @@ Richard Berger (Temple U) has also written a `more comprehensive guide <https://
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start.
----------
Building LAMMPS with CMake is a two-step process. First you use CMake
to create a build environment in a new directory. On Linux systems,
this will be based on makefiles for use with make. Then you use the
make command to build LAMMPS, which uses the created
Makefile(s). Example:
.. code-block:: bash
cd lammps # change to the LAMMPS distribution directory
@ -51,7 +48,6 @@ even more.
After compilation, you may optionally install the LAMMPS executable into
your system with:
.. code-block:: bash
make install # optional, copy LAMMPS executable & library elsewhere
@ -62,10 +58,8 @@ manpages, potential and force field files. The location of the installation
tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
to ${HOME}/.local
----------
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
@ -106,13 +100,10 @@ ccmake or cmake-gui) again from the same build directory and alter
various options; see details below. Or you can remove the entire build
folder, recreate the directory and start over.
----------
**Command-line version of CMake**\ :
.. code-block:: bash
cmake [options ...] /path/to/lammps/cmake # build from any dir
@ -124,7 +115,6 @@ cmake directory which contains the CMakeLists.txt file.
The argument can be preceeded or followed by various CMake
command-line options. Several useful ones are:
.. code-block:: bash
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
@ -168,13 +158,10 @@ In these cases it is usually better to first remove all the
files/directories in the build directory, or start with a fresh build
directory.
----------
**Curses version (terminal-style menu) of CMake**\ :
.. code-block:: bash
ccmake ../cmake
@ -186,13 +173,10 @@ required to edit some of the entries of CMake configuration variables
in between. Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
more information.
----------
**GUI version of CMake**\ :
.. code-block:: bash
cmake-gui ../cmake
@ -205,15 +189,12 @@ edit some of the entries of CMake configuration variables in between.
Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
for more information.
----------
**Installing CMake**
Check if your machine already has CMake installed:
.. code-block:: bash
which cmake # do you have it?
@ -223,7 +204,6 @@ Check if your machine already has CMake installed:
On clusters or supercomputers which use environment modules to manage
software packages, do this:
.. code-block:: bash
module list # is a module for cmake already loaded?

14
doc/src/Build_development.rst
View File

@ -4,10 +4,8 @@ Development build options (CMake only)
The CMake build of LAMMPS has a few extra options which are useful during
development, testing or debugging.
----------
.. _compilation:
Verify compilation flags
@ -17,22 +15,18 @@ Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
compilation you can use the following option.
.. code-block:: bash
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
.. code-block:: bash
make VERBOSE=1
----------
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
@ -47,17 +41,14 @@ The following settings allow you enable these features if your compiler supports
it. Please note that they come with a performance hit. However, they are
usually faster than using tools like Valgrind.
.. code-block:: bash
-D ENABLE_SANITIZE_ADDRESS=value # enable Address Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_UNDEFINED=value # enable Undefined Behaviour Sanitizer, value = no (default) or yes
-D ENABLE_SANITIZE_THREAD=value # enable Thread Sanitizer, value = no (default) or yes
----------
.. _testing:
Code Coverage and Testing
@ -71,7 +62,6 @@ developers can run the tests directly on their workstation.
this is incomplete and only represents a small subset of tests that we run
.. code-block:: bash
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
@ -80,7 +70,6 @@ developers can run the tests directly on their workstation.
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
.. code-block:: bash
make test
@ -92,14 +81,12 @@ faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
.. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
This will also add the following targets to generate coverage reports after running the LAMMPS executable:
.. code-block:: bash
make test # run tests first!
@ -108,7 +95,6 @@ This will also add the following targets to generate coverage reports after runn
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
.. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git

101
doc/src/Build_extras.rst
View File

@ -4,7 +4,6 @@ Packages with extra build options
When building with some packages, additional steps may be required,
in addition to:
.. code-block:: bash
$ cmake -D PKG_NAME=yes
@ -57,7 +56,6 @@ This is the list of packages that may require additional steps.
----------
.. _compress:
COMPRESS package
@ -70,7 +68,6 @@ available on your system.
If CMake cannot find the library, you can set these variables:
.. code-block:: bash
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
@ -82,10 +79,8 @@ If make cannot find the library, you can edit the file
lib/compress/Makefile.lammps to specify the paths and library
name.
----------
.. _gpu:
GPU package
@ -96,7 +91,6 @@ which GPU hardware to build for.
**CMake build**\ :
.. code-block:: bash
-D GPU_API=value # value = opencl (default) or cuda
@ -146,7 +140,6 @@ You can also build the library in one step from the lammps/src dir,
using a command like these, which simply invoke the lib/gpu/Install.py
script with the specified args:
.. code-block:: bash
$ make lib-gpu # print help message
@ -188,10 +181,8 @@ lib/gpu/Makefile.lammps may need to be edited.
package uses the library settings from the lib/gpu/Makefile.machine
used to build the GPU library.
----------
.. _kim:
KIM package
@ -214,7 +205,6 @@ minutes to hours) to build. Of course you only need to do that once.)
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
@ -251,7 +241,6 @@ follow the instructions in lib/kim/README. You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the lib/kim/Install.py script with the specified args.
.. code-block:: bash
$ make lib-kim # print help message
@ -272,7 +261,6 @@ using. For example:
----------
.. _kokkos:
KOKKOS package
@ -323,7 +311,6 @@ case-sensitive values, e.g. BDW, not bdw.
For multicore CPUs using OpenMP, set these 2 variables.
.. code-block:: bash
-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above
@ -331,7 +318,6 @@ For multicore CPUs using OpenMP, set these 2 variables.
For Intel KNLs using OpenMP, set these 2 variables:
.. code-block:: bash
-D KOKKOS_ARCH=KNL
@ -339,7 +325,6 @@ For Intel KNLs using OpenMP, set these 2 variables:
For NVIDIA GPUs using CUDA, set these 4 variables:
.. code-block:: bash
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
@ -352,7 +337,6 @@ The wrapper value is the Cuda nvcc compiler wrapper provided in the
Kokkos library: lib/kokkos/bin/nvcc\_wrapper. The setting should
include the full path name to the wrapper, e.g.
.. code-block:: bash
-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper
@ -365,7 +349,6 @@ src/MAKE/OPTIONS/Makefile.kokkos\* files for examples.
For multicore CPUs using OpenMP:
.. code-block:: make
KOKKOS_DEVICES = OpenMP
@ -373,7 +356,6 @@ For multicore CPUs using OpenMP:
For Intel KNLs using OpenMP:
.. code-block:: make
KOKKOS_DEVICES = OpenMP
@ -381,7 +363,6 @@ For Intel KNLs using OpenMP:
For NVIDIA GPUs using CUDA:
.. code-block:: make
KOKKOS_DEVICES = Cuda
@ -396,17 +377,14 @@ The 2 lines define a nvcc wrapper compiler, which will use nvcc for
compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
files.
.. code-block:: make
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx
----------
.. _latte:
LATTE package
@ -417,7 +395,6 @@ library.
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
@ -437,7 +414,6 @@ one step from the lammps/src dir, using a command like these, which
simply invokes the lib/latte/Install.py script with the specified
args:
.. code-block:: bash
$ make lib-latte # print help message
@ -452,10 +428,8 @@ dir. When LAMMPS itself is built it will use these links. You should
also check that the Makefile.lammps file you create is appropriate for
the compiler you use on your system to build LATTE.
----------
.. _message:
MESSAGE package
@ -467,7 +441,6 @@ be installed on your system.
**CMake build**\ :
.. code-block:: bash
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
@ -482,7 +455,6 @@ follow the instructions in lib/message/README. You can also do it in
one step from the lammps/src dir, using a command like these, which
simply invoke the lib/message/Install.py script with the specified args:
.. code-block:: bash
$ make lib-message # print help message
@ -494,10 +466,8 @@ and lib/message/Makefile.lammps. The latter is copied from an
existing Makefile.lammps.\* and has settings to link with the ZeroMQ
library if requested in the build.
----------
.. _mscg:
MSCG package
@ -511,7 +481,6 @@ lib/mscg/README and MSCG/Install files for more details.
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
@ -532,7 +501,6 @@ follow the instructions in lib/mscg/README. You can also do it in one
step from the lammps/src dir, using a command like these, which simply
invoke the lib/mscg/Install.py script with the specified args:
.. code-block:: bash
$ make lib-mscg # print help message
@ -547,10 +515,8 @@ be created in lib/mscg to point to the MS-CG src/installation dir.
When LAMMPS is built in src it will use these links. You should not
need to edit the lib/mscg/Makefile.lammps file.
----------
.. _opt:
OPT package
@ -567,10 +533,8 @@ package when using Intel compilers. It should be added to the CCFLAGS
line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
an example.
----------
.. _poems:
POEMS package
@ -588,7 +552,6 @@ lib/poems/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/poems/Install.py script with the specified args:
.. code-block:: bash
$ make lib-poems # print help message
@ -604,10 +567,8 @@ necessary, you can edit/create a new lib/poems/Makefile.machine file
for your system, which should define an EXTRAMAKE variable to specify
a corresponding Makefile.lammps.machine file.
----------
.. _python:
PYTHON package
@ -620,7 +581,6 @@ lib/python/README for more details.
**CMake build**\ :
.. code-block:: bash
-D PYTHON_EXECUTABLE=path # path to Python executable to use
@ -639,10 +599,8 @@ process to find Python. You should only need to create a new
Makefile.lammps.\* file (and copy it to Makefile.lammps) if the LAMMPS
build fails.
----------
.. _voronoi:
VORONOI package
@ -652,11 +610,8 @@ To build with this package, you must download and build the `Voro++ library <vor
.. _voro-home: http://math.lbl.gov/voro++
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
@ -678,7 +633,6 @@ one step from the lammps/src dir, using a command like these, which
simply invoke the lib/voronoi/Install.py script with the specified
args:
.. code-block:: bash
$ make lib-voronoi # print help message
@ -691,10 +645,8 @@ created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the lib/voronoi/Makefile.lammps file.
----------
.. _user-adios:
USER-ADIOS package
@ -709,7 +661,6 @@ installation and the instructions below are followed for the respective build sy
**CMake build**\ :
.. code-block:: bash
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
@ -719,22 +670,18 @@ installation and the instructions below are followed for the respective build sy
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
.. code-block:: bash
$ make yes-user-adios
otherwise, set ADIOS2\_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
----------
.. _user-atc:
USER-ATC package
@ -755,7 +702,6 @@ lib/atc/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/atc/Install.py script with the specified args:
.. code-block:: bash
$ make lib-atc # print help message
@ -777,7 +723,6 @@ can either exist on your system, or you can use the files provided in
lib/linalg. In the latter case you also need to build the library in
lib/linalg with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
@ -785,10 +730,8 @@ lib/linalg with a command like these:
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
.. _user-awpmd:
USER-AWPMD package
@ -806,7 +749,6 @@ lib/awpmd/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/awpmd/Install.py script with the specified args:
.. code-block:: bash
$ make lib-awpmd # print help message
@ -828,7 +770,6 @@ these can either exist on your system, or you can use the files
provided in lib/linalg. In the latter case you also need to build the
library in lib/linalg with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
@ -836,10 +777,8 @@ library in lib/linalg with a command like these:
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
.. _user-colvars:
USER-COLVARS package
@ -880,7 +819,6 @@ LAMMPS. This is best carried out from the LAMMPS src directory using a
command like these, which simply invoke the lib/colvars/Install.py script with
the specified args:
.. code-block:: bash
$ make lib-colvars # print help message
@ -905,10 +843,8 @@ The build should produce two files: the library lib/colvars/libcolvars.a
lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does
not need to be edited.
----------
.. _user-plumed:
USER-PLUMED package
@ -923,7 +859,6 @@ The USER-PLUMED package has been tested to work with Plumed versions
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
with a different version of the Plumed kernel.
PLUMED can be linked into MD codes in three different modes: static,
shared, and runtime. With the "static" mode, all the code that PLUMED
requires is linked statically into LAMMPS. LAMMPS is then fully
@ -959,7 +894,6 @@ must ensure that GSL is installed in locations that are specified in
your environment. There are then two additional commands that control
the manner in which PLUMED is obtained and linked into LAMMPS.
.. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
@ -995,7 +929,6 @@ discussion of PLUMED linkage modes, please see above.
Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args:
.. code-block:: bash
$ make lib-plumed # print help message
@ -1011,7 +944,6 @@ suitable for LAMMPS to compile and link PLUMED using the desired linkage
mode. After this step is completed, you can install the USER-PLUMED
package and compile LAMMPS in the usual manner:
.. code-block:: bash
$ make yes-user-plumed
@ -1031,10 +963,8 @@ lib-plumed" with the desired settings **and** do a re-install if the
USER-PLUMED package with "make yes-user-plumed" to update the required
makefile settings with the changes in the lib/plumed folder.
----------
.. _user-h5md:
USER-H5MD package
@ -1062,7 +992,6 @@ lib/h5md/README. You can also do it in one step from the lammps/src
dir, using a command like these, which simply invoke the
lib/h5md/Install.py script with the specified args:
.. code-block:: bash
$ make lib-h5md # print help message
@ -1076,10 +1005,8 @@ lib/h5md/Makefile.machine file for your system, which should define an
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
file.
----------
.. _user-intel:
USER-INTEL package
@ -1093,7 +1020,6 @@ on the :doc:`Speed intel <Speed_intel>` doc page.
**CMake build**\ :
.. code-block:: bash
-D INTEL_ARCH=value # value = cpu (default) or knl
@ -1120,7 +1046,6 @@ additional information.
For CPUs:
.. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
@ -1130,7 +1055,6 @@ For CPUs:
For KNLs:
.. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
@ -1138,10 +1062,8 @@ For KNLs:
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
----------
.. _user-molfile:
USER-MOLFILE package
@ -1149,7 +1071,6 @@ USER-MOLFILE package
**CMake build**\ :
.. code-block:: bash
-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed
@ -1176,10 +1097,8 @@ default headers, but these are not compatible with all VMD versions,
so it is often best to change this setting to the location of the
same include files of the local VMD installation in use.
----------
.. _user-netcdf:
USER-NETCDF package
@ -1205,10 +1124,8 @@ and library files which LAMMPS needs to build with this package. If
the settings are not valid for your system, you will need to edit the
Makefile.lammps file. See lib/netcdf/README for details.
----------
.. _user-omp:
USER-OMP package
@ -1227,7 +1144,6 @@ styles supporting OpenMP) the following compile and link flags must
be added to your Makefile.machine file.
See src/MAKE/OPTIONS/Makefile.omp for an example.
.. parsed-literal::
CCFLAGS: -fopenmp # for GNU and Clang Compilers
@ -1239,10 +1155,8 @@ For other platforms and compilers, please consult the documentation
about OpenMP support for your compiler. Please see the note about
how to address compatibility :ref:`issues with the 'default(none)' directive <default-none-issues>` of some compilers.
----------
.. _user-qmmm:
USER-QMMM package
@ -1282,7 +1196,6 @@ go back to the lib/qmmm folder and follow the instructions on the
README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder. You need to make certain, that
**Traditional make**\ :
Before building LAMMPS, you must build the QMMM library in lib/qmmm.
@ -1291,7 +1204,6 @@ explained in lib/qmmm/README. You can also do it in one step from the
lammps/src dir, using a command like these, which simply invoke the
lib/qmmm/Install.py script with the specified args:
.. code-block:: bash
$ make lib-qmmm # print help message
@ -1316,7 +1228,6 @@ lib/qmmm folder.
----------
.. _user-quip:
USER-QUIP package
@ -1330,7 +1241,6 @@ lib/quip/README file for details on how to do this.
**CMake build**\ :
.. code-block:: bash
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
@ -1349,10 +1259,8 @@ LAMMPS with this package. You should only need to edit
Makefile.lammps if the LAMMPS build can not use its settings to
successfully build on your system.
----------
.. _user-scafacos:
USER-SCAFACOS package
@ -1362,11 +1270,8 @@ To build with this package, you must download and build the `ScaFaCoS Coulomb so
.. _scafacos-home: http://www.scafacos.de
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes
@ -1397,10 +1302,8 @@ created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the lib/scafacos/Makefile.lammps file.
----------
.. _user-smd:
USER-SMD package
@ -1411,7 +1314,6 @@ Eigen3 is a template library, so you do not need to build it.
**CMake build**\ :
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
@ -1429,7 +1331,6 @@ instructions in lib/smd/README. You can also do it in one step from
the lammps/src dir, using a command like these, which simply invoke
the lib/smd/Install.py script with the specified args:
.. code-block:: bash
$ make lib-smd # print help message
@ -1441,10 +1342,8 @@ lib/smd to point to the Eigen dir. When LAMMPS builds it will use
this link. You should not need to edit the lib/smd/Makefile.lammps
file.
----------
.. _user-vtk:
USER-VTK package

6
doc/src/Build_link.rst
View File

@ -31,7 +31,6 @@ these 2 files:
----------
**Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with
@ -54,7 +53,6 @@ link the coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
This assumes that LAMMPS has been compiled in the folder
@ -193,7 +191,6 @@ would add something like this to your ~/.profile file:
For the csh or tcsh shells, you would equivalently add something like this
to your ~/.cshrc file:
.. code-block:: csh
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
@ -212,7 +209,6 @@ You can verify whether all required shared libraries are found with the
libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash
@ -226,10 +222,8 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS

2
doc/src/Build_make.rst
View File

@ -73,7 +73,6 @@ in the LAMMPS distribution. Typing "make machine" uses
use Makefile.serial and Makefile.mpi, respectively. Other makefiles
are in these directories:
.. parsed-literal::
OPTIONS # Makefiles which enable specific options
@ -93,7 +92,6 @@ customized machine Makefile are contributed by users. Since both
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
.. code-block:: bash
make mac # build serial LAMMPS on a Mac

9
doc/src/Build_package.rst
View File

@ -47,14 +47,12 @@ versus make.
**CMake build**\ :
.. code-block:: bash
-D PKG_NAME=value # yes or no (default)
Examples:
.. code-block:: bash
-D PKG_MANYBODY=yes
@ -76,7 +74,6 @@ once with CMake.
**Traditional make**\ :
.. code-block:: bash
cd lammps/src
@ -87,7 +84,6 @@ once with CMake.
Examples:
.. code-block:: bash
make no-rigid
@ -132,10 +128,8 @@ src directory.
That is no longer the case, so that CMake will build as-is without the
need to un-install those packages.
----------
**CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line,
@ -169,7 +163,6 @@ one of them as a starting point and customize it to your needs.
**Example:**
.. code-block:: bash
# build LAMMPS with most commonly used packages, but then remove
@ -186,10 +179,8 @@ one of them as a starting point and customize it to your needs.
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake .
----------
**Make shortcuts for installing many packages**\ :
The following commands are useful for managing package source files

33
doc/src/Build_settings.rst
View File

@ -14,10 +14,8 @@ explain how to do this for building both with CMake and make.
* :ref:`Workaround for long long integers <longlong>`
* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
----------
.. _cxx11:
C++11 standard compliance
@ -35,7 +33,6 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
----------
.. _fft:
FFT library
@ -49,7 +46,6 @@ LAMMPS can use them if they are available on your system.
**CMake variables**\ :
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
@ -69,7 +65,6 @@ OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
used. If CMake cannot detect the FFT library, you can set these variables
to assist:
.. code-block:: bash
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
@ -81,7 +76,6 @@ to assist:
**Makefile.machine settings**\ :
.. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
@ -93,7 +87,6 @@ to assist:
# default is FFT\_PACK\_ARRAY if not specified
.. code-block:: make
FFT_INC = -I/usr/local/include
@ -159,7 +152,6 @@ library a second time with support for single-precision.
For FFTW3, do the following, which should produce the additional
library libfftw3f.a or libfftw3f.so.
.. code-block:: bash
make clean
@ -172,10 +164,8 @@ Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
----------
.. _size:
Size of LAMMPS data types
@ -187,14 +177,12 @@ adequate.
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
@ -249,10 +237,8 @@ compiled with the same size setting, or the link will fail. A CMake
build does this automatically. When building with make, the setting
in whichever lib/gpu/Makefile is used must be the same as above.
----------
.. _graphics:
Output of JPG, PNG, and movie files
@ -265,7 +251,6 @@ following settings:
**CMake variables**\ :
.. code-block:: bash
-D WITH_JPEG=value # yes or no
@ -279,7 +264,6 @@ Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
.. code-block:: bash
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
@ -292,7 +276,6 @@ variables:
**Makefile.machine settings**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
@ -321,10 +304,8 @@ supports the "popen" function in the standard runtime library.
communication library and lead to simulations using ffmpeg to hang or
crash.
----------
.. _gzip:
Read or write compressed files
@ -336,7 +317,6 @@ gzip compression by several LAMMPS commands, including
**CMake variables**\ :
.. code-block:: bash
-D WITH_GZIP=value # yes or no
@ -345,7 +325,6 @@ gzip compression by several LAMMPS commands, including
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
@ -365,10 +344,8 @@ found by LAMMPS during a run.
I/O is also available using a compression library instead, which is
what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
----------
.. _align:
Memory allocation alignment
@ -385,7 +362,6 @@ aligned on 64-byte boundaries.
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
@ -397,7 +373,6 @@ and this setting ignored.
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
@ -408,10 +383,8 @@ be used on Windows, as it does use different function calls for
allocating aligned memory, that are not compatible with how LAMMPS
manages its dynamical memory.
----------
.. _longlong:
Workaround for long long integers
@ -424,22 +397,18 @@ those systems:
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
----------
.. _exceptions:
Exception handling when using LAMMPS as a library
@ -453,14 +422,12 @@ e.g. to Python. Of course the calling code has to be set up to
**CMake variable**\ :
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS

2
doc/src/Build_windows.rst
View File

@ -6,10 +6,8 @@ Notes for building LAMMPS on Windows
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using a cross-compiler <cross>`
----------
.. _generic:
General remarks

1
doc/src/Commands.rst
View File

@ -4,7 +4,6 @@ Commands
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
.. toctree::
:maxdepth: 1

1
doc/src/Commands_bond.rst
View File

@ -99,7 +99,6 @@ have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
.. table_from_list::
:columns: 4

2
doc/src/Commands_input.rst
View File

@ -16,7 +16,6 @@ simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
.. code-block:: LAMMPS
timestep 0.5
@ -25,7 +24,6 @@ Thus this sequence of commands:
does something different than this sequence:
.. code-block:: LAMMPS
run 100

1
doc/src/Commands_parse.rst
View File

@ -86,7 +86,6 @@ LAMMPS:
This can be useful for formatting print output to a desired precision:
.. code-block:: LAMMPS
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"

1
doc/src/Errors.rst
View File

@ -7,7 +7,6 @@ and warnings doc pages give complete lists of all the messages the
code may generate (except those generated by USER packages), with
additional details for many of them.
.. toctree::
:maxdepth: 1

2
doc/src/Errors_common.rst
View File

@ -63,7 +63,6 @@ is an integer or floating-point number, respectively, and reject the
input with an error message (for instance, when an integer is required,
but a floating-point number 1.0 is provided):
.. parsed-literal::
ERROR: Expected integer parameter instead of '1.0' in input script or data file
@ -81,7 +80,6 @@ reading the input and before parsing commands,
the documentation of the corresponding command explicitly says it is.
Otherwise, you will receive an error message of this kind:
.. parsed-literal::
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file

5
doc/src/Errors_messages.rst
View File

@ -7,7 +7,6 @@ documentation for the offending command may help. Error messages also
list the source file and line number where the error was generated.
For example, a message like this:
.. parsed-literal::
ERROR: Illegal velocity command (velocity.cpp:78)
@ -21,12 +20,8 @@ code or contact the author of the package.
Doc page with :doc:`WARNING messages <Errors_warnings>`
----------
*1-3 bond count is inconsistent*
An inconsistency was detected when computing the number of 1-3
neighbors for each atom. This likely means something is wrong with

5
doc/src/Errors_warnings.rst
View File

@ -7,7 +7,6 @@ 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 like this:
.. parsed-literal::
WARNING: Bond atom missing in box size check (domain.cpp:187)
@ -21,12 +20,8 @@ code or contact the author of the package.
Doc page with :doc:`ERROR messages <Errors_messages>`
----------
*Adjusting Coulombic cutoff for MSM, new cutoff = %g*
The adjust/cutoff command is turned on and the Coulombic cutoff has been
adjusted to match the user-specified accuracy.

6
doc/src/Examples.rst
View File

@ -38,10 +38,8 @@ particular quantity.
Lists of both kinds of directories are given below.
----------
Lowercase directories
---------------------
@ -157,7 +155,6 @@ Lowercase directories
Here is how you can run and visualize one of the sample problems:
.. parsed-literal::
cd indent
@ -180,15 +177,12 @@ like ImageMagick or QuickTime or various Windows-based tools. See the
Imagemagick command would create a GIF file suitable for viewing in a
browser.
.. parsed-literal::
% convert -loop 1 \*.jpg foo.gif
----------
Uppercase directories
---------------------

6
doc/src/Howto.rst
View File

@ -12,7 +12,6 @@ also show how to setup and run various kinds of simulations.
Tutorials howto
===============
.. toctree::
:name: tutorials
:maxdepth: 1
@ -24,7 +23,6 @@ Tutorials howto
General howto
=============
.. toctree::
:name: general_howto
:maxdepth: 1
@ -40,7 +38,6 @@ General howto
Settings howto
==============
.. toctree::
:name: settings_howto
:maxdepth: 1
@ -56,7 +53,6 @@ Settings howto
Analysis howto
==============
.. toctree::
:name: analysis_howto
:maxdepth: 1
@ -72,7 +68,6 @@ Analysis howto
Force fields howto
==================
.. toctree::
:name: force_howto
:maxdepth: 1
@ -85,7 +80,6 @@ Force fields howto
Packages howto
==============
.. toctree::
:name: packages_howto
:maxdepth: 1

1
doc/src/Howto_2d.rst
View File

@ -11,7 +11,6 @@ simulation box, set the z dimensions narrow, but finite, so that the
create\_atoms command will tile the 3d simulation box with a single z
plane of atoms - e.g.
.. code-block:: LAMMPS
:doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25

26
doc/src/Howto_bash.rst
View File

@ -3,10 +3,8 @@ Using LAMMPS with Bash on Windows
**written by Richard Berger**
----------
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager
@ -82,10 +80,8 @@ Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
.. image:: JPG/bow_tutorial_10.png
----------
Compiling LAMMPS in Bash on Windows
-----------------------------------
@ -97,7 +93,6 @@ Installing prerequisite packages
First upgrade all existing packages using
.. code-block:: bash
sudo apt update
@ -106,7 +101,6 @@ First upgrade all existing packages using
Next install the following packages, which include compilers and libraries
needed for various LAMMPS features:
.. code-block:: bash
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
@ -126,7 +120,6 @@ Obtain a copy of the LAMMPS code and go into it using "cd"
Option 1: Downloading LAMMPS tarball using wget
"""""""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
@ -136,7 +129,6 @@ Option 1: Downloading LAMMPS tarball using wget
Option 2: Obtaining LAMMPS code from GitHub
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
git clone https://github.com/lammps/lammps.git
@ -150,7 +142,6 @@ At this point you can compile LAMMPS like on Ubuntu Linux.
Compiling serial version
""""""""""""""""""""""""
.. code-block:: bash
cd src/
@ -161,7 +152,6 @@ This will create an executable called lmp\_serial in the src/ directory
Compiling MPI version
"""""""""""""""""""""
.. code-block:: bash
cd src/
@ -169,20 +159,16 @@ Compiling MPI version
This will create an executable called lmp\_mpi in the src/ directory
----------
Finally, please note the absolute path of your src folder. You can get this using
.. code-block:: bash
pwd
or
.. code-block:: bash
echo $PWD
@ -190,22 +176,18 @@ or
To run any examples you need the location of the executable. For now, let us
save this location in a temporary variable
.. code-block:: bash
LAMMPS_DIR=$PWD
----------
Running an example script
^^^^^^^^^^^^^^^^^^^^^^^^^
Once compiled you can execute some of the LAMMPS examples. Switch into the
examples/melt folder
.. code-block:: bash
cd ../examples/melt
@ -214,14 +196,12 @@ The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mp
version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either
version as follows:
.. code-block:: bash
$LAMMPS_DIR/lmp_serial -in in.melt
or
.. code-block:: bash
mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
@ -235,21 +215,18 @@ Adding your executable directory to your PATH
You can avoid having to type the full path of your LAMMPS binary by adding its
parent folder to the PATH environment variable as follows:
.. code-block:: bash
export PATH=$LAMMPS_DIR:$PATH
Input scripts can then be run like this:
.. code-block:: bash
lmp_serial -in in.melt
or
.. code-block:: bash
mpirun -np 4 lmp_mpi -in in.melt
@ -258,7 +235,6 @@ However, this PATH variable will not persist if you close your bash window.
To persist this setting edit the $HOME/.bashrc file using your favorite editor
and add this line
.. code-block:: bash
export PATH=/full/path/to/your/lammps/src:$PATH
@ -267,14 +243,12 @@ and add this line
For an executable lmp\_serial with a full path
.. code-block:: bash
/home/richard/lammps/src/lmp_serial
the PATH variable should be
.. code-block:: bash
export PATH=/home/richard/lammps/src:$PATH

14
doc/src/Howto_bioFF.rst
View File

@ -20,12 +20,8 @@ force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
command's documentation for the formula it computes.
@ -114,33 +110,23 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` dreiding
----------
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
.. _howto-Cornell:
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
.. _howto-Sun:
**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
.. _howto-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

30
doc/src/Howto_body.rst
View File

@ -33,10 +33,8 @@ style are described below.
More styles may be added in the future. See the :doc:`Modify body <Modify_body>` doc page for details on how to add a new body
style to the code.
----------
**When to use body particles:**
You should not use body particles to model a rigid body made of
@ -104,10 +102,8 @@ particles of different styles
The pair styles defined for use with specific body styles are listed
in the sections below.
----------
**Specifics of body style nparticle:**
The *nparticle* body style represents body particles as a rigid body
@ -119,7 +115,6 @@ duplicates its functionality.
The atom\_style body command for this body style takes two additional
arguments:
.. parsed-literal::
atom_style body nparticle Nmin Nmax
@ -133,7 +128,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 1 M
@ -170,7 +164,6 @@ For output purposes via the :doc:`compute body/local <compute_body_local>` and :
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of sub-particle
@ -188,10 +181,8 @@ collection of spheres, one for each sub-particle. The size of each
sphere is determined by the *bflag1* parameter for the *body* keyword.
The *bflag2* argument is ignored.
----------
**Specifics of body style rounded/polygon:**
The *rounded/polygon* body style represents body particles as a 2d
@ -207,7 +198,6 @@ described in :ref:`Fraige <body-Fraige>`.
Similar to body style *nparticle*\ , the atom\_style body command for
this body style takes two additional arguments:
.. parsed-literal::
atom_style body rounded/polygon Nmin Nmax
@ -221,7 +211,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 1 M
@ -262,7 +251,6 @@ orientation of the square is aligned with the xy coordinate axes which
is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
.. parsed-literal::
3 1 27
@ -281,7 +269,6 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
by circles of diameter 0.5, is specified as follows:
.. parsed-literal::
1 1 13
@ -293,7 +280,6 @@ by circles of diameter 0.5, is specified as follows:
A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
.. parsed-literal::
1 1 10
@ -308,10 +294,8 @@ interactions. The :doc:`fix wall/body/polygon <fix_wall_body_polygon>`
command can be used with this body style to compute the interaction of
body particles with a wall.
----------
**Specifics of body style rounded/polyhedron:**
The *rounded/polyhedron* body style represents body particles as a 3d
@ -330,7 +314,6 @@ This body style is for 3d discrete element models, as described in
Similar to body style *rounded/polygon*\ , the atom\_style body command
for this body style takes two additional arguments:
.. parsed-literal::
atom_style body rounded/polyhedron Nmin Nmax
@ -344,7 +327,6 @@ When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
in the *Bodies* section of the data file:
.. parsed-literal::
atom-ID 3 M
@ -401,7 +383,6 @@ The orientation of the cube is aligned with the xyz coordinate axes
which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz
iyz = 0.667 0.667 0.667 0 0 0.
.. parsed-literal::
1 3 79
@ -438,7 +419,6 @@ iyz = 0.667 0.667 0.667 0 0 0.
A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
by circles of diameter 0.5, is specified as follows:
.. parsed-literal::
1 1 13
@ -450,7 +430,6 @@ by circles of diameter 0.5, is specified as follows:
A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
.. parsed-literal::
1 1 10
@ -465,15 +444,12 @@ be used with this body style to compute body/body interactions. The
used with this body style to compute the interaction of body particles
with a wall.
----------
For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of vertex
@ -495,20 +471,14 @@ tangent to the spheres). The drawn diameter of each line segment is
determined by the *bflag1* parameter for the *body* keyword. The
*bflag2* argument is ignored.
----------
.. _body-Fraige:
**(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).
.. _body-Wang:
**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).

5
doc/src/Howto_chunk.rst
View File

@ -150,7 +150,6 @@ properties:
(1) Average velocity in each of 1000 2d spatial bins:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
@ -159,7 +158,6 @@ properties:
(2) Temperature in each spatial bin, after subtracting a flow
velocity:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
@ -168,7 +166,6 @@ velocity:
(3) Center of mass of each molecule:
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
@ -177,7 +174,6 @@ velocity:
(4) Total force on each molecule and ave/max across all molecules:
.. code-block:: LAMMPS
compute cc1 all chunk/atom molecule
@ -189,7 +185,6 @@ velocity:
(5) Histogram of cluster sizes:
.. code-block:: LAMMPS
compute cluster all cluster/atom 1.0

2
doc/src/Howto_client_server.rst
View File

@ -134,7 +134,6 @@ together to exchange MPI messages between them.
For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes:
.. code-block:: bash
% mpirun -np 1 lmp_mpi -log log.client < in.client &
@ -150,7 +149,6 @@ For message exchange in *mpi/one* mode:
Launch both codes in a single mpirun command:
.. code-block:: bash
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server

14
doc/src/Howto_coreshell.rst
View File

@ -24,7 +24,6 @@ shell of a core/shell pair should be bonded to each other with a
harmonic bond that provides the spring force. For example, a data file
for NaCl, as found in examples/coreshell, has this format:
.. parsed-literal::
432 atoms # core and shell atoms
@ -87,7 +86,6 @@ Ewald solvers can be used.
For the NaCL example problem, these pair style and bond style settings
are used:
.. code-block:: LAMMPS
pair_style born/coul/long/cs 20.0 20.0
@ -131,7 +129,6 @@ this temperature be output for the overall system.
For the NaCl example, this can be done as follows:
.. code-block:: LAMMPS
group cores type 1 2
@ -150,7 +147,6 @@ the default :doc:`temperature <compute_temp>` and specifying it as a
second argument in :doc:`fix modify <fix_modify>` and
:doc:`thermo_modify <thermo_modify>` resulting in:
.. code-block:: LAMMPS
(...)
@ -174,7 +170,6 @@ the pairs. This can be done by using the *bias* keyword of the
:doc:`velocity create <velocity>` command and assigning the :doc:`compute temp/cs <compute_temp_cs>` command to the *temp* keyword of the
:doc:`velocity <velocity>` command, e.g.
.. code-block:: LAMMPS
velocity all create 1427 134 bias yes temp CSequ
@ -211,7 +206,6 @@ pairs as chunks.
For example if core/shell pairs are the only molecules:
.. code-block:: LAMMPS
read_data NaCl_CS_x0.1_prop.data
@ -222,7 +216,6 @@ For example if core/shell pairs are the only molecules:
For example if core/shell pairs and other molecules are present:
.. code-block:: LAMMPS
fix csinfo all property/atom i_CSID # property/atom command
@ -232,7 +225,6 @@ For example if core/shell pairs and other molecules are present:
The additional section in the date file would be formatted like this:
.. parsed-literal::
CS-Info # header of additional section
@ -247,20 +239,14 @@ The additional section in the date file would be formatted like this:
8 4
(...)
----------
.. _MitchellFincham:
**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
5, 1031-1038 (1993).
.. _MitchellFincham2:
**(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
6, 393-404 (1994).

15
doc/src/Howto_couple.rst
View File

@ -12,10 +12,8 @@ LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you will have to think about in the
context of your application.
----------
(1) Define a new :doc:`fix <fix>` command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
@ -27,12 +25,8 @@ LAMMPS.
.. _poems: http://www.rpi.edu/~anderk5/lab
----------
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
@ -53,10 +47,8 @@ command writes and reads.
See the :doc:`Modify command <Modify_command>` doc page for info on how
to add a new command to LAMMPS.
----------
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
@ -78,15 +70,10 @@ examples/COUPLE/README for more details:
a kinetic Monte Carlo model for grain growth using MD to calculate
strain induced across grain boundaries
.. _quest: http://dft.sandia.gov/Quest
.. _spparks: http://www.sandia.gov/~sjplimp/spparks.html
The :doc:`Build basics <Build_basics>` doc page describes how to build
LAMMPS as a library. Once this is done, you can interface with LAMMPS
either via C++, C, Fortran, or Python (or any other language that
@ -113,10 +100,8 @@ LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
----------
(4) Couple LAMMPS with another code in a client/server mode. This is
described on the :doc:`Howto client/server <Howto_client_server>` doc
page.

4
doc/src/Howto_drude.rst
View File

@ -56,12 +56,8 @@ with a Coulomb pair style. It may be useful to use *coul/long/cs* or
similar from the CORESHELL package if the core and Drude particle come
too close, which can cause numerical issues.
----------
.. _howto-Lamoureux:
**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

50
doc/src/Howto_drude2.rst
View File

@ -30,7 +30,6 @@ zero. The (half-)stiffness of the :doc:`harmonic bond <bond_harmonic>`
:math:`K_D = k_D/2` and the Drude charge :math:`q_D` are related to the atom
polarizability :math:`\alpha` by
.. math::
K_D = \frac 1 2\, \frac {q_D^2} \alpha
@ -46,7 +45,6 @@ fields:
* Alternately :ref:`Schroeder and Steinhauser <Schroeder>` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.
* In both these force fields hydrogen atoms are treated as non-polarizable.
The motion of of the Drude particles can be calculated by minimizing
the energy of the induced dipoles at each timestep, by an iterative,
self-consistent procedure. The Drude particles can be massless and
@ -85,7 +83,6 @@ You can use the *polarizer* tool (Python script distributed with the
USER-DRUDE package) to convert a non-polarizable data file (here
*data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
.. parsed-literal::
polarizer -q -f phenol.dff data.102494.lmp data-p.lmp
@ -96,7 +93,6 @@ from *phenol.dff*\ , as well as the DC-DP bond constants. The file
*phenol.dff* contains the polarizabilities of the atom types
and the mass of the Drude particles, for instance:
.. parsed-literal::
# units: kJ/mol, A, deg
@ -113,7 +109,6 @@ have to be specified as comments at the end of lines of the *Masses*
section. You probably need to edit it to add these names. It should
look like
.. parsed-literal::
Masses
@ -124,10 +119,8 @@ look like
4 1.008 # HA
5 1.008 # HO
----------
**Basic input file**
The atom style should be set to (or derive from) *full*\ , so that you
@ -138,7 +131,6 @@ script (the use of these lines will be explained below). In order for
LAMMPS to recognize that you are using Drude oscillators, you should
use the fix *drude*\ . The command is
.. code-block:: LAMMPS
fix DRUDE all drude C C C N N D D D
@ -159,7 +151,6 @@ command. With our phenol, there is 1 more special neighbor for which
space is required. Otherwise LAMMPS crashes and gives the required
value.
.. code-block:: LAMMPS
read_data data-p.lmp extra/special/per/atom 1
@ -173,7 +164,6 @@ include Coulomb interactions, for instance *lj/cut/coul/long* with
*kspace\_style pppm*. For example, with a cutoff of 10. and a precision
1.e-4:
.. code-block:: LAMMPS
pair_style lj/cut/coul/long 10.0
@ -184,14 +174,12 @@ to be added for the DPs. Since the DPs have no Lennard-Jones
interactions, their :math:`\epsilon` is 0. so the only *pair\_coeff* line
that needs to be added is
.. code-block:: LAMMPS
pair_coeff * 6* 0.0 0.0 # All-DPs
Now for the thermalization, the simplest choice is to use the :doc:`fix langevin/drude <fix_langevin_drude>`.
.. code-block:: LAMMPS
fix LANG all langevin/drude 300. 100 12435 1. 20 13977
@ -205,7 +193,6 @@ atoms need to be in this fix's group. LAMMPS will thermostat the DPs
together with their DC. For this, ghost atoms need to know their
velocities. Thus you need to add the following command:
.. code-block:: LAMMPS
comm_modify vel yes
@ -217,7 +204,6 @@ can add the *zero yes* option at the end of the fix line.
If the fix *shake* is used to constrain the C-H bonds, it should be
invoked after the fix *langevin/drude* for more accuracy.
.. code-block:: LAMMPS
fix SHAKE ATOMS shake 0.0001 20 0 t 4 5
@ -231,7 +217,6 @@ Since the fix *langevin/drude* does not perform time integration (just
modification of forces but no position/velocity updates), the fix
*nve* should be used in conjunction.
.. code-block:: LAMMPS
fix NVE all nve
@ -240,7 +225,6 @@ Finally, do not forget to update the atom type elements if you use
them in a *dump\_modify ... element ...* command, by adding the element
type of the DPs. Here for instance
.. code-block:: LAMMPS
dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
@ -254,7 +238,6 @@ standard atoms in his default compute. If you want to output the
temperatures of the DC-DP pair centers of mass and of the DPs relative
to their DCs, you should use the :doc:`compute temp\_drude <compute_temp_drude>`
.. code-block:: LAMMPS
compute TDRUDE all temp/drude
@ -263,15 +246,12 @@ And then output the correct temperatures of the Drude oscillators
using *thermo\_style custom* with respectively *c\_TDRUDE[1]* and
*c\_TDRUDE[2]*. These should be close to 300.0 and 1.0 on average.
.. code-block:: LAMMPS
thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
----------
**Thole screening**
Dipolar interactions represented by point charges on springs may not
@ -289,7 +269,6 @@ the interactions between the charges representing the induced dipoles.
It is to be used as *hybrid/overlay* with any standard *coul* pair
style. In our example, we would use
.. code-block:: LAMMPS
pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
@ -305,7 +284,6 @@ explicitly defined. The output of the *polarizer* script can be used
to complete the *pair\_coeff* section of the input file. In our
example, this will look like:
.. code-block:: LAMMPS
pair_coeff 1 1 lj/cut/coul/long 0.0700 3.550
@ -349,7 +327,6 @@ For the *thole* pair style the coefficients are
specified by the pair\_style command)
#. the cutoff (optional, default value defined by the pair\_style command)
The special neighbors have charge-charge and charge-dipole
interactions screened by the *coul* factors of the *special\_bonds*
command (0.0, 0.0, and 0.5 in the example above). Without using the
@ -361,16 +338,13 @@ example 1-2 neighbors: using the pair\_style *thole*\ , their dipoles
will see each other (despite the *coul* factor being 0.) and the
interactions between these dipoles will be damped by Thole's function.
----------
**Thermostats and barostats**
Using a Nose-Hoover barostat with the *langevin/drude* thermostat is
straightforward using fix *nph* instead of *nve*\ . For example:
.. code-block:: LAMMPS
fix NPH all nph iso 1. 1. 500
@ -385,7 +359,6 @@ with respect to their DC. The *fix drude/transform/inverse* performs
the reverse transformation. For a NVT simulation, with the DCs and
atoms at 300 K and the DPs at 1 K relative to their DC one would use
.. code-block:: LAMMPS
fix DIRECT all drude/transform/direct
@ -395,7 +368,6 @@ atoms at 300 K and the DPs at 1 K relative to their DC one would use
For our phenol example, the groups would be defined as
.. code-block:: LAMMPS
group ATOMS type 1 2 3 4 5 # DCs and non-polarizable atoms
@ -409,7 +381,6 @@ times and for the forces also). To avoid the flying ice cube artifact
center of mass of the whole system drifts faster and faster, the *fix
momentum* can be used. For instance:
.. code-block:: LAMMPS
fix MOMENTUM all momentum 100 linear 1 1 1
@ -424,7 +395,6 @@ the temperature to correspond to the fix group only. We must then use
the *fix\_modify* command for this. In the end, the block of
instructions for thermostatting and barostatting will look like
.. code-block:: LAMMPS
compute TATOMS ATOMS temp
@ -434,10 +404,8 @@ instructions for thermostatting and barostatting will look like
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse
----------
**Rigid bodies**
You may want to simulate molecules as rigid bodies (but polarizable).
@ -448,7 +416,6 @@ review the different thermostats and ensemble combinations.
NVT ensemble using Langevin thermostat:
.. code-block:: LAMMPS
comm_modify vel yes
@ -458,7 +425,6 @@ NVT ensemble using Langevin thermostat:
NVT ensemble using Nose-Hoover thermostat:
.. code-block:: LAMMPS
fix DIRECT all drude/transform/direct
@ -468,7 +434,6 @@ NVT ensemble using Nose-Hoover thermostat:
NPT ensemble with Langevin thermostat:
.. code-block:: LAMMPS
comm_modify vel yes
@ -478,7 +443,6 @@ NPT ensemble with Langevin thermostat:
NPT ensemble using Nose-Hoover thermostat:
.. code-block:: LAMMPS
compute TATOM ATOMS temp
@ -488,45 +452,31 @@ NPT ensemble using Nose-Hoover thermostat:
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse
----------
.. _Lamoureux2:
**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
.. _Schroeder:
**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133,
154511 (2010).
.. _Jiang2:
**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
J Phys Chem Lett, 2, 87-92 (2011).
.. _Thole2:
**(Thole)** Chem Phys, 59, 341 (1981).
.. _Noskov2:
**(Noskov)** Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
.. _SWM4-NDP:
**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
Let, 418, 245-249 (2006)

4
doc/src/Howto_elastic.rst
View File

@ -33,12 +33,8 @@ tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
----------
.. _Shinoda1:
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

27
doc/src/Howto_github.rst
View File

@ -22,10 +22,8 @@ and will reduce the time until the integration is complete. For more
information on the requirements to have your code included into LAMMPS
please see the :doc:`Modify contribute <Modify_contribute>` doc page.
----------
**Making an account**
First of all, you need a GitHub account. This is fairly simple, just
@ -34,10 +32,8 @@ the "Sign up for GitHub" button. Once your account is created, you
can sign in by clicking the button in the top left and filling in your
username or e-mail address and password.
----------
**Forking the repository**
To get changes into LAMMPS, you need to first fork the `lammps/lammps`
@ -63,10 +59,8 @@ At the same time, you can set things up, so you can include changes from
upstream into your repository and thus keep it in sync with the ongoing
LAMMPS development.
----------
**Adding changes to your own fork**
Additions to the upstream version of LAMMPS are handled using *feature
@ -81,14 +75,12 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
First of all, create a clone of your version on github on your local
machine via HTTPS:
.. code-block:: bash
$ git clone https://github.com/<your user name>/lammps.git <some name>
or, if you have set up your GitHub account for using SSH keys, via SSH:
.. code-block:: bash
$ git clone git@github.com:<your user name>/lammps.git
@ -108,7 +100,6 @@ test them without interfering with the repository on GitHub.
To pull changes from upstream into this copy, you can go to the directory
and use git pull:
.. code-block:: bash
$ cd mylammps
@ -117,7 +108,6 @@ and use git pull:
You can also add this URL as a remote:
.. code-block:: bash
$ git remote add lammps_upstream https://www.github.com/lammps/lammps
@ -127,7 +117,6 @@ branch for the feature you want to work on. This tutorial contains the
workflow that updated this tutorial, and hence we will call the branch
"github-tutorial-update":
.. code-block:: bash
$ git checkout -b github-tutorial-update master
@ -140,7 +129,6 @@ unrelated feature, you should switch branches!
After everything is done, add the files to the branch and commit them:
.. code-block:: bash
$ git add doc/src/Howto_github.txt
@ -165,14 +153,12 @@ After everything is done, add the files to the branch and commit them:
After adding all files, the change set can be committed with some
useful message that explains the change.
.. code-block:: bash
$ git commit -m 'Finally updated the github tutorial'
After the commit, the changes can be pushed to the same branch on GitHub:
.. code-block:: bash
$ git push
@ -181,7 +167,6 @@ Git will ask you for your user name and password on GitHub if you have
not configured anything. If your local branch is not present on GitHub yet,
it will ask you to add it by running
.. code-block:: bash
$ git push --set-upstream origin github-tutorial-update
@ -192,22 +177,18 @@ password, the feature branch should be added to your fork on GitHub.
If you want to make really sure you push to the right repository
(which is good practice), you can provide it explicitly:
.. code-block:: bash
$ git push origin
or using an explicit URL:
.. code-block:: bash
$ git push git@github.com:Pakketeretet2/lammps.git
----------
**Filing a pull request**
Up to this point in the tutorial, all changes were to *your* clones of
@ -255,10 +236,8 @@ Now just write some nice comments and click on "Create pull request".
.. image:: JPG/tutorial_create_new_pull_request2.png
:align: center
----------
**After filing a pull request**
.. note::
@ -408,7 +387,6 @@ Because the changes are OK with us, we are going to merge by clicking on
Now, since in the meantime our local text for the tutorial also changed,
we need to pull Axel's change back into our branch, and merge them:
.. code-block:: bash
$ git add Howto_github.txt
@ -425,7 +403,6 @@ With Axel's changes merged in and some final text updates, our feature
branch is now perfect as far as we are concerned, so we are going to
commit and push again:
.. code-block:: bash
$ git add Howto_github.txt
@ -438,10 +415,8 @@ This merge also shows up on the lammps GitHub page:
.. image:: JPG/tutorial_reverse_pull_request7.png
:align: center
----------
**After a merge**
When everything is fine, the feature branch is merged into the master branch:
@ -456,7 +431,6 @@ It is in principle safe to delete them from your own fork. This helps
keep it a bit more tidy. Note that you first have to switch to another
branch!
.. code-block:: bash
$ git checkout master
@ -472,7 +446,6 @@ first delete and then pull, everything should still be fine.
Finally, if you delete the branch locally, you might want to push this
to your remote(s) as well:
.. code-block:: bash
$ git push origin :github-tutorial-update

6
doc/src/Howto_kappa.rst
View File

@ -62,20 +62,14 @@ auto-correlation. See the doc page for the :doc:`compute heat/flux <compute_hea
that calculates the thermal conductivity of solid Ar via the GK
formalism.
----------
.. _howto-Ikeshoji:
**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
.. _howto-Wirnsberger:
**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).

5
doc/src/Howto_library.rst
View File

@ -58,7 +58,6 @@ details.
The added functions can access or change any internal LAMMPS data you
wish.
.. code-block:: c
void lammps_open(int, char **, MPI_Comm, void **)
@ -136,7 +135,6 @@ information from LAMMPS and setting value within LAMMPS. Again, see
the documentation in the src/library.cpp file for details, including
which quantities can be queried by name:
.. code-block:: c
int lammps_extract_setting(void *, char *)
@ -163,7 +161,6 @@ is not listed. For the other extract functions, the underlying
storage may be reallocated as LAMMPS runs, so you need to re-call the
function to assure a current pointer or returned value(s).
.. code-block:: c
double lammps_get_thermo(void *, char *)
@ -187,7 +184,6 @@ The lammps\_reset\_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
saved state of a simulation.
.. code-block:: c
void lammps_gather_atoms(void *, char *, int, int, void *)
@ -230,7 +226,6 @@ those values to each atom in the system. The
lammps\_scatter\_atoms\_subset() function takes a subset of IDs as an
argument and only scatters those values to the owning atoms.
.. code-block:: c
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,

2
doc/src/Howto_manifold.rst
View File

@ -46,7 +46,5 @@ to the relevant fixes.
.. _Paquay1:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.

4
doc/src/Howto_multiple.rst
View File

@ -8,7 +8,6 @@ If "multiple simulations" means continue a previous simulation for
more timesteps, then you simply use the :doc:`run <run>` command
multiple times. For example, this script
.. code-block:: LAMMPS
units lj
@ -27,7 +26,6 @@ If you wish to run totally different simulations, one after the other,
the :doc:`clear <clear>` command can be used in between them to
re-initialize LAMMPS. For example, this script
.. code-block:: LAMMPS
units lj
@ -48,7 +46,6 @@ For large numbers of independent simulations, you can use
multiple times with different settings. For example, this
script, named in.polymer
.. code-block:: LAMMPS
variable d index run1 run2 run3 run4 run5 run6 run7 run8
@ -65,7 +62,6 @@ file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
.. code-block:: LAMMPS
variable a loop 8

4
doc/src/Howto_nemd.rst
View File

@ -43,13 +43,9 @@ NEMD simulations can also be used to measure transport properties of a fluid
through a pore or channel. Simulations of steady-state flow can be performed
using the :doc:`fix flow/gauss <fix_flow_gauss>` command.
----------
.. _Daivis-nemd:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

1
doc/src/Howto_output.rst
View File

@ -12,7 +12,6 @@ There are four basic kinds of LAMMPS output:
screen.
* :doc:`Restart files <restart>`.
A simulation prints one set of thermodynamic output and (optionally)
restart files. It can generate any number of dump files and fix
output files, depending on what :doc:`dump <dump>` and :doc:`fix <fix>`

33
doc/src/Howto_pylammps.rst
View File

@ -56,7 +56,6 @@ output support enabled.
Step 1a: For the CMake based build system, the steps are:
.. code-block:: bash
mkdir $LAMMPS_DIR/build-shared
@ -68,7 +67,6 @@ Step 1a: For the CMake based build system, the steps are:
Step 1b: For the legacy, make based build system, the steps are:
.. code-block:: bash
cd $LAMMPS_DIR/src
@ -85,7 +83,6 @@ Step 2: Installing the LAMMPS Python package
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation with:
.. code-block:: bash
make install-python
@ -110,7 +107,6 @@ Benefits of using a virtualenv
**Prerequisite (e.g. on Ubuntu)**
.. code-block:: bash
apt-get install python-virtualenv
@ -118,7 +114,6 @@ Benefits of using a virtualenv
Creating a virtualenv with lammps installed
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
# create virtualenv named 'testing'
@ -132,7 +127,6 @@ When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPYTHON_EXECUTABLE=$(which python)
@ -154,7 +148,6 @@ Creating a new instance of PyLammps
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new *lammps* instance is created.
.. code-block:: Python
from lammps import PyLammps
@ -162,7 +155,6 @@ module. By using the default constructor, a new *lammps* instance is created.
You can also initialize PyLammps on top of this existing *lammps* object:
.. code-block:: Python
from lammps import lammps, PyLammps
@ -177,7 +169,6 @@ the command method of the lammps object instance.
For instance, let's take the following LAMMPS command:
.. code-block:: LAMMPS
region box block 0 10 0 5 -0.5 0.5
@ -185,7 +176,6 @@ For instance, let's take the following LAMMPS command:
In the original interface this command can be executed with the following
Python code if *L* was a lammps instance:
.. code-block:: Python
L.command("region box block 0 10 0 5 -0.5 0.5")
@ -193,7 +183,6 @@ Python code if *L* was a lammps instance:
With the PyLammps interface, any command can be split up into arbitrary parts
separated by white-space, passed as individual arguments to a region method.
.. code-block:: Python
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
@ -206,7 +195,6 @@ The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
.. code-block:: Python
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
@ -214,7 +202,6 @@ manually by creating formatted strings.
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
@ -225,8 +212,6 @@ System state
In addition to dispatching commands directly through the PyLammps object, it
also provides several properties which allow you to query the system state.
L.system
Is a dictionary describing the system such as the bounding box or number of atoms
@ -260,8 +245,6 @@ L.dump
L.groups
List of groups present in the current system
Working with LAMMPS variables
-----------------------------
@ -269,7 +252,6 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
L.variable("a index 2")
@ -279,7 +261,6 @@ A dictionary of all variables is returned by L.variables
you can access an individual variable by retrieving a variable object from the
L.variables dictionary by name
.. code-block:: Python
a = L.variables['a']
@ -287,7 +268,6 @@ L.variables dictionary by name
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
print(a.value)
@ -300,7 +280,6 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
variables, compute or fix data.
.. code-block:: Python
result = L.eval("ke") # kinetic energy
@ -315,7 +294,6 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
position, velocity, force, etc.).
.. code-block:: Python
# access first atom
@ -329,7 +307,6 @@ position, velocity, force, etc.).
Some properties can also be used to set:
.. code-block:: Python
# set position in 2D simulation
@ -347,7 +324,6 @@ after a run via the L.runs list. This list contains a growing list of run data.
The first element is the output of the first run, the second element that of
the second run.
.. code-block:: Python
L.run(1000)
@ -359,7 +335,6 @@ the second run.
Each run contains a dictionary of all trajectories. Each trajectory is
accessible through its thermo name:
.. code-block:: Python
L.runs[0].thermo.Step # list of time steps in first run
@ -367,7 +342,6 @@ accessible through its thermo name:
Together with matplotlib plotting data out of LAMMPS becomes simple:
.. code-block:: Python
import matplotlib.plot as plt
@ -406,7 +380,6 @@ tutorials and showcasing your latest research.
To launch an instance of Jupyter simply run the following command inside your
Python environment (this assumes you followed the Quick Start instructions):
.. code-block:: bash
jupyter notebook
@ -429,7 +402,6 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: Python
phi = [d \* math.pi / 180 for d in range(360)]
@ -463,7 +435,6 @@ Initially, a 2D system is created in a state with minimal energy.
It is then disordered by moving each atom by a random delta.
.. code-block:: Python
random.seed(27848)
@ -483,7 +454,6 @@ It is then disordered by moving each atom by a random delta.
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: Python
estart = L.eval("pe")
@ -536,7 +506,6 @@ Using PyLammps and mpi4py (Experimental)
PyLammps can be run in parallel using mpi4py. This python package can be installed using
.. code-block:: bash
pip install mpi4py
@ -544,7 +513,6 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. code-block:: Python
from mpi4py import MPI
@ -561,7 +529,6 @@ executes it in parallel. You can find in.melt in the examples/melt folder.
To run this script (melt.py) in parallel using 4 MPI processes we invoke the
following mpirun command:
.. code-block:: bash
mpirun -np 4 python melt.py

1
doc/src/Howto_replica.rst
View File

@ -37,7 +37,6 @@ replica. The processors assigned to each replica are determined at
run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
which in this context are the same as replicas. E.g. these commands:
.. code-block:: bash
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper

4
doc/src/Howto_restart.rst
View File

@ -21,7 +21,6 @@ Look at the *in.chain* input script provided in the *bench* directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
.. code-block:: LAMMPS
restart 50 tmp.restart
@ -32,7 +31,6 @@ and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
.. code-block:: LAMMPS
read_restart tmp.restart.50
@ -62,14 +60,12 @@ uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
.. code-block:: LAMMPS
lmp_g++ -r tmp.restart.50 tmp.restart.data
Then, this script could be used to re-run the last 50 steps:
.. code-block:: LAMMPS
units lj

4
doc/src/Howto_spc.rst
View File

@ -40,13 +40,9 @@ the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _howto-Berendsen:
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).

1
doc/src/Howto_spherical.rst
View File

@ -38,7 +38,6 @@ The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command
like
.. code-block:: LAMMPS
atom_style hybrid sphere dipole

4
doc/src/Howto_spins.rst
View File

@ -56,13 +56,9 @@ the magnetic energy. The second command is :doc:`compute property/atom <compute_
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
----------
.. _Tranchida:
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).

4
doc/src/Howto_thermostat.rst
View File

@ -82,13 +82,9 @@ specify them explicitly via the :doc:`thermo_style custom <thermo_style>` comman
:doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output.
----------
.. _Daivis-thermostat:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

8
doc/src/Howto_tip3p.rst
View File

@ -51,26 +51,18 @@ details:
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _howto-tip3p:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
.. _Jorgensen1:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _Price1:
**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).

4
doc/src/Howto_tip4p.rst
View File

@ -99,13 +99,9 @@ and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _Jorgensen5:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

2
doc/src/Howto_triclinic.rst
View File

@ -200,7 +200,6 @@ an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:
.. parsed-literal::
ITEM: BOX BOUNDS xy xz yz
@ -212,7 +211,6 @@ This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
.. parsed-literal::
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)

5
doc/src/Howto_viscosity.rst
View File

@ -62,7 +62,6 @@ simulation box.
Here is an example input script that calculates the viscosity of
liquid Ar via the GK formalism:
.. code-block:: LAMMPS
# Sample LAMMPS input script for viscosity of liquid Ar
@ -131,13 +130,9 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
----------
.. _Daivis-viscosity:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

4
doc/src/Howto_viz.rst
View File

@ -27,10 +27,6 @@ snapshots.
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
.. _ensight: http://www.ensight.com
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A

1
doc/src/Install.rst
View File

@ -8,7 +8,6 @@ have more flexibility as to what features to include or exclude in the
build. If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
need the source code.
.. toctree::
:maxdepth: 1

4
doc/src/Install_git.rst
View File

@ -16,7 +16,6 @@ commands explained below to communicate with the git servers on
GitHub. For people still using subversion (svn), GitHub also
provides `limited support for subversion clients <svn_>`_.
.. warning::
As of October 2016, the official home of public LAMMPS development is
@ -35,7 +34,6 @@ You can follow LAMMPS development on 3 different git branches:
To access the git repositories on your box, use the clone command to
create a local copy of the LAMMPS repository with a command like:
.. code-block:: bash
$ git clone -b unstable https://github.com/lammps/lammps.git mylammps
@ -57,7 +55,6 @@ LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
up-to-date by typing the following git commands from within the
"mylammps" directory:
.. code-block:: bash
$ git checkout unstable # not needed if you always stay in this branch
@ -92,7 +89,6 @@ Once you have updated your local files with a "git pull" (or "git
checkout"), you still need to re-build LAMMPS if any source files have
changed. To do this, you should cd to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files

2
doc/src/Install_linux.rst
View File

@ -206,7 +206,6 @@ Gentoo Linux executable
LAMMPS is part of Gentoo's main package tree and can be installed by
typing:
.. code-block:: bash
% emerge --ask lammps
@ -216,7 +215,6 @@ built on the your machine.
Certain LAMMPS packages can be enable via USE flags, type
.. code-block:: bash
% equery uses lammps

4
doc/src/Install_mac.rst
View File

@ -10,7 +10,6 @@ GPU, KOKKOS, LATTE, MSCG, MESSAGE, MPIIO POEMS VORONOI.
After installing Homebrew, you can install LAMMPS on your system with
the following commands:
.. code-block:: bash
% brew install lammps
@ -21,7 +20,6 @@ the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
Once LAMMPS is installed, you can test the installation with the
Lennard-Jones benchmark file:
.. code-block:: bash
% brew test lammps -v
@ -31,7 +29,6 @@ results in Homebrew also installing the `kim-api` binaries when LAMMPS is
installed. In order to use potentials from `openkim.org <openkim_>`_, you can
install the `openkim-models` package
.. code-block:: bash
% brew install openkim-models
@ -44,5 +41,4 @@ If you have problems with the installation you can post issues to
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.
.. _openkim: https://openkim.org

1
doc/src/Install_tarball.rst
View File

@ -52,7 +52,6 @@ the next patch release tarball.
----------
If you download a current LAMMPS tarball, one way to stay current as
new patch tarballs are released, is to download a patch file which you
can apply to your local directory to update it for each new patch

1
doc/src/Intro.rst
View File

@ -3,7 +3,6 @@ Introduction
These pages provide a brief introduction to LAMMPS.
.. toctree::
:maxdepth: 1

7
doc/src/Intro_authors.rst
View File

@ -13,23 +13,18 @@ University:
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: http://lammps.sandia.gov
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
----------
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.
----------
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.
@ -49,10 +44,8 @@ general-purpose as it is without their expertise and efforts.
* Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD
* Greg Wagner (Northwestern U), MEAM package for MEAM potential
----------
As discussed on the `History page <http://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original

6
doc/src/Intro_features.rst
View File

@ -16,10 +16,8 @@ classes of functionality:
10. :ref:`Pre- and post-processing <prepost>`
11. :ref:`Specialized features (beyond MD itself) <special>`
----------
.. _general:
General features
@ -191,12 +189,8 @@ Pre- and post-processing
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
.. _python: http://www.python.org
.. _special:
Specialized features

6
doc/src/Intro_opensource.rst
View File

@ -15,16 +15,10 @@ distribution.
.. _gnu: http://www.gnu.org/copyleft/gpl.html
.. _gnuorg: http://www.gnu.org
.. _opensource: http://www.opensource.org
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they

10
doc/src/Manual_build.rst
View File

@ -5,7 +5,6 @@ Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
.. parsed-literal::
src # content files for LAMMPS documentation
@ -49,11 +48,9 @@ b. You can build the HTML or PDF files yourself, by typing "make html"
----------
The generation of all documentation is managed by the Makefile in
the doc directory.
.. code-block:: bash
Documentation Build Options:
@ -74,7 +71,6 @@ the doc directory.
----------
Installing prerequisites for HTML build
=======================================
@ -84,7 +80,6 @@ have to be installed. Here are instructions for common setups:
Ubuntu
------
.. code-block:: bash
sudo apt-get install python-virtualenv
@ -92,7 +87,6 @@ Ubuntu
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
------------------------------------------------------------------------------------
.. code-block:: bash
sudo yum install python3-virtualenv
@ -100,7 +94,6 @@ Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version
Fedora (since version 22)
-------------------------
.. code-block:: bash
sudo dnf install python3-virtualenv
@ -121,17 +114,14 @@ virtualenv
Once Python 3 is installed, open a Terminal and type
.. code-block:: bash
pip3 install virtualenv
This will install virtualenv from the Python Package Index.
----------
Installing prerequisites for epub build
=======================================

1
doc/src/Modify.rst
View File

@ -10,7 +10,6 @@ If you add a new feature to LAMMPS and think it will be of interest to
general users, we encourage you to submit it for inclusion in LAMMPS
as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, after reading the :doc:`Modify contribute <Modify_contribute>` doc page.
.. toctree::
:maxdepth: 1

2
doc/src/Modify_atom.rst
View File

@ -98,7 +98,6 @@ The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find\_custom() method that is
useful in this context:
.. parsed-literal::
int index = atom->find_custom(char \*name, int &flag);
@ -109,7 +108,6 @@ that it exists and its index is returned. The method also sets flag =
The vector of values associated with the attribute can then be
accessed using the returned index as
.. parsed-literal::
int \*ivector = atom->ivector[index];

1
doc/src/Modify_contribute.rst
View File

@ -203,7 +203,6 @@ packages in the src directory for examples. If you are uncertain, please ask.
usage. That kind of citation should just be in the doc page you
provide.
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example

3
doc/src/Modify_overview.rst
View File

@ -31,14 +31,12 @@ potentials described in the classic 1997 :ref:`paper <Foo>` by Foo, et al.
If you wish to invoke those potentials in a LAMMPS input script with a
command like
.. code-block:: LAMMPS
pair_style foo 0.1 3.5
then your pair\_foo.h file should be structured as follows:
.. code-block:: c++
#ifdef PAIR_CLASS
@ -103,5 +101,4 @@ functionality:
.. _Foo:
**(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

1
doc/src/Modify_variable.rst
View File

@ -9,7 +9,6 @@ via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or
"equal" can compute complex equations that involve the following types
of arguments:
.. parsed-literal::
thermo keywords = ke, vol, atoms, ...

1
doc/src/Packages.rst
View File

@ -11,7 +11,6 @@ distribution. The :doc:`Build package <Build_package>` doc page gives
general info on how to install and un-install packages as part of the
LAMMPS build process.
.. toctree::
:maxdepth: 1

173
doc/src/Packages_details.rst
View File

@ -60,7 +60,6 @@ page gives those details.
* :ref:`SRD <PKG-SRD>`
* :ref:`VORONOI <PKG-VORONOI>`
.. table_from_list::
:columns: 6
@ -106,10 +105,8 @@ page gives those details.
* :ref:`USER-VTK <PKG-USER-VTK>`
* :ref:`USER-YAFF <PKG-USER-YAFF>`
----------
.. _PKG-ASPHERE:
ASPHERE package
@ -133,10 +130,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* http://lammps.sandia.gov/movies.html#line
* http://lammps.sandia.gov/movies.html#tri
----------
.. _PKG-BODY:
BODY package
@ -158,10 +153,8 @@ overview.
* :doc:`pair_style body/nparticle <pair_body_nparticle>`
* examples/body
----------
.. _PKG-CLASS2:
CLASS2 package
@ -181,10 +174,8 @@ CLASS2 molecular force field.
* :doc:`improper_style class2 <improper_class2>`
* :doc:`pair_style lj/class2 <pair_class2>`
----------
.. _PKG-COLLOID:
COLLOID package
@ -213,10 +204,8 @@ Higdon's group at UIUC.
* examples/colloid
* examples/srd
----------
.. _PKG-COMPRESS:
COMPRESS package
@ -246,10 +235,8 @@ This package has :ref:`specific installation instructions <compress>` on the :do
* :doc:`dump custom/gz <dump>`
* :doc:`dump xyz/gz <dump>`
----------
.. _PKG-CORESHELL:
CORESHELL package
@ -276,10 +263,8 @@ this package.
* :doc:`pair_style lj/cut/coul/long/cs <pair_lj>`
* examples/coreshell
----------
.. _PKG-DIPOLE:
DIPOLE package
@ -299,10 +284,8 @@ short-range or long-range interactions.
* :doc:`pair_style lj/long/dipole/long <pair_dipole>`
* examples/dipole
----------
.. _PKG-GPU:
GPU package
@ -341,10 +324,8 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
for styles followed by (g)
* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
----------
.. _PKG-GRANULAR:
GRANULAR package
@ -373,10 +354,8 @@ potentials.
* http://lammps.sandia.gov/movies.html#brazil
* http://lammps.sandia.gov/movies.html#granregion
----------
.. _PKG-KIM:
KIM package
@ -430,10 +409,8 @@ This package has :ref:`specific installation instructions <kim>` on the :doc:`Bu
* lib/kim/README
* examples/kim
----------
.. _PKG-KOKKOS:
KOKKOS package
@ -486,10 +463,8 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
----------
.. _PKG-KSPACE:
KSPACE package
@ -523,10 +498,8 @@ different FFT options for your LAMPMS build.
* examples/peptide
* bench/in.rhodo
----------
.. _PKG-LATTE:
LATTE package
@ -544,8 +517,6 @@ description is given with the :doc:`fix latte <fix_latte>` command.
.. _latte-home: https://github.com/lanl/LATTE
**Authors:** Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
itself is developed at Los Alamos National Laboratory by Marc
Cawkwell, Anders Niklasson, and Christian Negre.
@ -563,10 +534,8 @@ This package has :ref:`specific installation instructions <latte>` on the :doc:`
* examples/latte
* `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
----------
.. _PKG-MANYBODY:
MANYBODY package
@ -589,10 +558,8 @@ A variety of many-body and bond-order potentials. These include
* examples/vashishta
* bench/in.eam
----------
.. _PKG-MC:
MC package
@ -616,10 +583,8 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`pair_style dsmc <pair_dsmc>`
* http://lammps.sandia.gov/movies.html#gcmc
----------
.. _PKG-MESSAGE:
MESSAGE package
@ -644,10 +609,8 @@ This package has :ref:`specific installation instructions <message>` on the :doc
* :doc:`server mc <server_mc>`
* examples/message
----------
.. _PKG-MISC:
MISC package
@ -678,10 +641,8 @@ listing, "ls src/MISC", to see the list of commands.
* http://lammps.sandia.gov/pictures.html#ttm
* http://lammps.sandia.gov/movies.html#evaporation
----------
.. _PKG-MOLECULE:
MOLECULE package
@ -712,10 +673,8 @@ force fields, and a TIP4P water model.
* bench/in.chain
* bench/in.rhodo
----------
.. _PKG-MPIIO:
MPIIO package
@ -736,10 +695,8 @@ written and read in parallel.
* :doc:`write_restart <write_restart>`
* :doc:`read_restart <read_restart>`
----------
.. _PKG-mscg:
MSCG package
@ -752,8 +709,6 @@ Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <m
.. _mscg-home: https://github.com/uchicago-voth/MSCG-release
To use this package you must have the MS-CG library available on your
system.
@ -772,10 +727,8 @@ This package has :ref:`specific installation instructions <mscg>` on the :doc:`B
* lib/mscg/README
* examples/mscg
----------
.. _PKG-OPT:
OPT package
@ -808,10 +761,8 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
----------
.. _PKG-PERI:
PERI package
@ -841,10 +792,8 @@ Foster (UTSA).
* examples/peri
* http://lammps.sandia.gov/movies.html#peri
----------
.. _PKG-POEMS:
POEMS package
@ -872,10 +821,8 @@ This package has :ref:`specific installation instructions <poems>` on the :doc:`
* :doc:`fix poems <fix_poems>`
* examples/rigid
----------
.. _PKG-PYTHON:
PYTHON package
@ -907,10 +854,8 @@ This package has :ref:`specific installation instructions <python>` on the :doc:
* lib/python/README
* examples/python
----------
.. _PKG-QEQ:
QEQ package
@ -929,10 +874,8 @@ part of their formulation.
* examples/qeq
* examples/streitz
----------
.. _PKG-REPLICA:
REPLICA package
@ -962,10 +905,8 @@ another set.
* examples/prd
* examples/tad
----------
.. _PKG-RIGID:
RIGID package
@ -991,10 +932,8 @@ Also several computes which calculate properties of rigid bodies.
* http://lammps.sandia.gov/movies.html#box
* http://lammps.sandia.gov/movies.html#star
----------
.. _PKG-SHOCK:
SHOCK package
@ -1015,10 +954,8 @@ a material.
* examples/hugoniostat
* examples/msst
----------
.. _PKG-SNAP:
SNAP package
@ -1042,10 +979,8 @@ computes which analyze attributes of the potential.
* :doc:`compute snav/atom <compute_sna_atom>`
* examples/snap
----------
.. _PKG-SPIN:
SPIN package
@ -1074,10 +1009,8 @@ the usual manner via MD. Various pair, fix, and compute styles.
* :doc:`neb/spin <neb_spin>`
* examples/SPIN
----------
.. _PKG-SRD:
SRD package
@ -1100,10 +1033,8 @@ colloidal particles.
* http://lammps.sandia.gov/movies.html#line
* http://lammps.sandia.gov/movies.html#poly
----------
.. _PKG-VORONOI:
VORONOI package
@ -1118,8 +1049,6 @@ neighbors.
.. _voro-home: http://math.lbl.gov/voro++
To use this package you must have the Voro++ library available on your
system.
@ -1139,10 +1068,8 @@ This package has :ref:`specific installation instructions <voronoi>` on the :doc
* :doc:`compute voronoi/atom <compute_voronoi_atom>`
* examples/voronoi
----------
.. _PKG-USER-ADIOS:
USER-ADIOS package
@ -1171,11 +1098,8 @@ This package has :ref:`specific installation instructions <user-adios>` on the :
* :doc:`dump custom/adios <dump_adios>`
* :doc:`read_dump <read_dump>`
----------
.. _PKG-USER-ATC:
USER-ATC package
@ -1201,10 +1125,8 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* examples/USER/atc
* http://lammps.sandia.gov/pictures.html#atc
----------
.. _PKG-USER-AWPMD:
USER-AWPMD package
@ -1230,10 +1152,8 @@ This package has :ref:`specific installation instructions <user-awpmd>` on the :
* :doc:`pair_style awpmd/cut <pair_awpmd>`
* examples/USER/awpmd
----------
.. _PKG-USER-BOCS:
USER-BOCS package
@ -1265,10 +1185,8 @@ J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
Example inputs are in the examples/USER/bocs folder.
----------
.. _PKG-USER-CGDNA:
USER-CGDNA package
@ -1295,10 +1213,8 @@ rigid-body integrators with improved stability.
* :doc:`bond_style oxrna2/\* <bond_oxdna>`
* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
----------
.. _PKG-USER-CGSDK:
USER-CGSDK package
@ -1322,10 +1238,8 @@ acids.
* examples/USER/cgsdk
* http://lammps.sandia.gov/pictures.html#cg
----------
.. _PKG-USER-COLVARS:
USER-COLVARS package
@ -1359,10 +1273,8 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
* :doc:`fix colvars <fix_colvars>`
* examples/USER/colvars
----------
.. _PKG-USER-PLUMED:
USER-PLUMED package
@ -1381,8 +1293,6 @@ Tribello.
.. _PLUMED: http://www.plumed.org
**Install:**
This package has :ref:`specific installation instructions <user-plumed>` on the :doc:`Build extras <Build_extras>` doc page.
@ -1394,10 +1304,8 @@ This package has :ref:`specific installation instructions <user-plumed>` on the
* :doc:`fix plumed <fix_plumed>`
* examples/USER/plumed
----------
.. _PKG-USER-DIFFRACTION:
USER-DIFFRACTION package
@ -1418,10 +1326,8 @@ intensities based on kinematic diffraction theory.
* :doc:`fix saed/vtk <fix_saed_vtk>`
* examples/USER/diffraction
----------
.. _PKG-USER-DPD:
USER-DPD package
@ -1461,10 +1367,8 @@ Brennan (ARL).
* :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
* examples/USER/dpd
----------
.. _PKG-USER-DRUDE:
USER-DRUDE package
@ -1495,10 +1399,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
* examples/USER/drude
* tools/drude
----------
.. _PKG-USER-EFF:
USER-EFF package
@ -1533,10 +1435,8 @@ tools/eff; see its README file.
* tools/eff
* http://lammps.sandia.gov/movies.html#eff
----------
.. _PKG-USER-FEP:
USER-FEP package
@ -1562,10 +1462,8 @@ for using this package in tools/fep; see its README file.
* tools/fep/README
* tools/fep
----------
.. _PKG-USER-H5MD:
USER-H5MD package
@ -1581,8 +1479,6 @@ LAMMPS snapshots in this format.
.. _HDF5: http://www.hdfgroup.org/HDF5
To use this package you must have the HDF5 library available on your
system.
@ -1600,10 +1496,8 @@ This package has :ref:`specific installation instructions <user-h5md>` on the :d
* lib/h5md/README
* :doc:`dump h5md <dump_h5md>`
----------
.. _PKG-USER-INTEL:
USER-INTEL package
@ -1649,10 +1543,8 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
* src/USER-INTEL/TEST
* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
----------
.. _PKG-USER-LB:
USER-LB package
@ -1675,10 +1567,8 @@ Ontario).
* :doc:`fix lb/viscous <fix_lb_viscous>`
* examples/USER/lb
----------
.. _PKG-USER-MGPT:
USER-MGPT package
@ -1704,10 +1594,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
* :doc:`pair_style mgpt <pair_mgpt>`
* examples/USER/mgpt
----------
.. _PKG-USER-MISC:
USER-MISC package
@ -1729,10 +1617,8 @@ src/USER-MISC/README file.
* one doc page per individual command listed in src/USER-MISC/README
* examples/USER/misc
----------
.. _PKG-USER-MANIFOLD:
USER-MANIFOLD package
@ -1762,10 +1648,8 @@ Waltham, MA, USA)
* examples/USER/manifold
* http://lammps.sandia.gov/movies.html#manifold
----------
.. _PKG-USER-MEAMC:
USER-MEAMC package
@ -1789,10 +1673,8 @@ Sandia.
* :doc:`pair_style meam/c <pair_meamc>`
* examples/meamc
----------
.. _PKG-USER-MESODPD:
USER-MESODPD package
@ -1822,10 +1704,8 @@ algorithm.
* examples/USER/mesodpd
* http://lammps.sandia.gov/movies.html#mesodpd
----------
.. _PKG-USER-MOFFF:
USER-MOFFF package
@ -1844,8 +1724,6 @@ well as the `MOF+ <MOFplus_>`_ website.
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
**Author:** Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
@ -1859,10 +1737,8 @@ Rochus Schmid (Ruhr-University Bochum).
* :doc:`improper_style inversion/harmonic <improper_inversion_harmonic>`
* examples/USER/mofff
----------
.. _PKG-USER-MOLFILE:
USER-MOLFILE package
@ -1903,10 +1779,8 @@ This package has :ref:`specific installation instructions <user-molfile>` on the
* lib/molfile/README
* :doc:`dump molfile <dump_molfile>`
----------
.. _PKG-USER-NETCDF:
USER-NETCDF package
@ -1931,16 +1805,10 @@ tools:
.. _ovito: http://www.ovito.org
.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
.. _atomeye: http://www.libatoms.org
**Author:** Lars Pastewka (Karlsruhe Institute of Technology).
**Install:**
@ -1954,10 +1822,8 @@ This package has :ref:`specific installation instructions <user-netcdf>` on the
* lib/netcdf/README
* :doc:`dump netcdf <dump_netcdf>`
----------
.. _PKG-USER-OMP:
USER-OMP package
@ -2010,10 +1876,8 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <http://lammps.sandia.gov/bench.html>`_ of web site
----------
.. _PKG-USER-PHONON:
USER-PHONON package
@ -2040,10 +1904,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order"
* :doc:`third_order <third_order>`
* examples/USER/phonon
----------
.. _PKG-USER-PTM:
USER-PTM package
@ -2064,10 +1926,8 @@ Matching methodology.
* src/USER-PTM/LICENSE
* :doc:`compute ptm/atom <compute_ptm_atom>`
----------
.. _PKG-USER-QMMM:
USER-QMMM package
@ -2097,7 +1957,6 @@ changes to LAMMPS itself.
**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy)
**Install:**
This package has :ref:`specific installation instructions <user-qmmm>`
@ -2112,10 +1971,8 @@ on the :doc:`Build extras <Build_extras>` doc page.
* lib/qmmm/example-ec/README
* lib/qmmm/example-mc/README
----------
.. _PKG-USER-QTB:
USER-QTB package
@ -2142,10 +1999,8 @@ simulation.
* :doc:`fix qbmsst <fix_qbmsst>`
* examples/USER/qtb
----------
.. _PKG-USER-QUIP:
USER-QUIP package
@ -2159,8 +2014,6 @@ developed by the Cambridge University group.
.. _quip: https://github.com/libAtoms/QUIP
To use this package you must have the QUIP libAtoms library available
on your system.
@ -2177,10 +2030,8 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d
* :doc:`pair_style quip <pair_quip>`
* examples/USER/quip
----------
.. _PKG-USER-REACTION:
USER-REACTION package
@ -2210,10 +2061,8 @@ molecules, and chiral-sensitive reactions.
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* disarmmd.org
----------
.. _PKG-USER-REAXC:
USER-REAXC package
@ -2237,10 +2086,8 @@ for monitoring molecules as bonds are created and destroyed.
* :doc:`fix reax/c/species <fix_reaxc_species>`
* examples/reax
----------
.. _PKG-USER-SCAFACOS:
USER-SCAFACOS package
@ -2274,10 +2121,8 @@ This package has :ref:`specific installation instructions <user-scafacos>` on th
* :doc:`kspace_modify <kspace_modify>`
* examples/USER/scafacos
----------
.. _PKG-USER-SDPD:
USER-SDPD package
@ -2304,10 +2149,8 @@ Sciences, Iran).
* :doc:`fix rigid/meso <fix_rigid_meso>`
* examples/USER/sdpd
----------
.. _PKG-USER-SMD:
USER-SMD package
@ -2344,10 +2187,8 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
* examples/USER/smd
* http://lammps.sandia.gov/movies.html#smd
----------
.. _PKG-USER-SMTBQ:
USER-SMTBQ package
@ -2369,10 +2210,8 @@ Tetot (LAAS-CNRS, France).
* :doc:`pair_style smtbq <pair_smtbq>`
* examples/USER/smtbq
----------
.. _PKG-USER-SPH:
USER-SPH package
@ -2405,10 +2244,8 @@ Dynamics, Ernst Mach Institute, Germany).
* examples/USER/sph
* http://lammps.sandia.gov/movies.html#sph
----------
.. _PKG-USER-TALLY:
USER-TALLY package
@ -2429,10 +2266,8 @@ stress, etc) about individual interactions.
* :doc:`compute \*/tally <compute_tally>`
* examples/USER/tally
----------
.. _PKG-USER-UEF:
USER-UEF package
@ -2457,10 +2292,8 @@ supporting compute styles and an output option.
* :doc:`dump cfg/uef <dump_cfg_uef>`
* examples/uef
----------
.. _PKG-USER-VTK:
USER-VTK package
@ -2474,12 +2307,8 @@ other visualization packages.
.. _vtk: http://www.vtk.org
.. _paraview: http://www.paraview.org
To use this package you must have VTK library available on your
system.
@ -2496,10 +2325,8 @@ This package has :ref:`specific installation instructions <user-vtk>` on the :do
* lib/vtk/README
* :doc:`dump vtk <dump_vtk>`
----------
.. _PKG-USER-YAFF:
USER-YAFF package

1
doc/src/Python_call.rst
View File

@ -59,7 +59,6 @@ new potential.
To use any of these commands, you only need to build LAMMPS with the
PYTHON package installed:
.. parsed-literal::
make yes-python

16
doc/src/Python_examples.rst
View File

@ -27,10 +27,8 @@ distribution.
| combination of viz\_tool.py and plot.py and gui.py | |
+----------------------------------------------------------------+--------------------------------------------------+
----------
For the viz\_tool.py and vizplotgui\_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
visualization package you have installed.
@ -40,13 +38,10 @@ which is included in the pizza sub-directory. See the `Pizza.py doc pages <pizz
.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
.. parsed-literal::
http://mt.seas.upenn.edu/Archive/Graphics/A
@ -54,12 +49,8 @@ AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
.. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
The latter link is to AtomEye 3 which has the scripting
capability needed by these Python scripts.
@ -68,7 +59,6 @@ open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or
`here <pymolopen_>`_ for more details:
.. parsed-literal::
http://www.pymol.org
@ -76,22 +66,16 @@ from a Python script. See the PyMol WWW pages `here <pymolhome_>`_ or
.. _pymolhome: http://www.pymol.org
.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
The latter link is to the open-source version.
Note that for VMD, you need a fairly current version (1.8.7 works for
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
variables that have to match the VMD installation on your system.
----------
See the python/README file for instructions on how to run them and the
source code for individual scripts for comments about what they do.

1
doc/src/Python_head.rst
View File

@ -4,7 +4,6 @@ Use Python with LAMMPS
These doc pages describe various ways that LAMMPS and Python can be
used together.
.. toctree::
:maxdepth: 1

2
doc/src/Python_install.rst
View File

@ -31,7 +31,6 @@ If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like
this to your ~/.cshrc file, one line for each of the two files:
.. parsed-literal::
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
@ -49,7 +48,6 @@ files are updated with the new version.
If the default settings of "make install-python" are not what you want,
you can invoke install.py from the python directory manually as
.. parsed-literal::
% python install.py -m \<python module\> -l <shared library> -v <version.h file> [-d \<pydir\>]

11
doc/src/Python_library.rst
View File

@ -8,7 +8,6 @@ methods that can be invoked on that object. The sample Python code
below assumes you have first imported the "lammps" module in your
Python script, as follows:
.. code-block:: Python
from lammps import lammps
@ -22,7 +21,6 @@ from a C++ or C or Fortran program, and which are described on the
The python/examples directory has Python scripts which show how Python
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
.. code-block:: Python
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
@ -93,13 +91,10 @@ can run LAMMPS, grab data, change it, and put it back into LAMMPS.
lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags
----------
The lines
.. code-block:: Python
from lammps import lammps
@ -116,7 +111,6 @@ prompt.
If the ptr argument is set like this:
.. code-block:: Python
lmp = lammps(ptr=lmpptr)
@ -133,7 +127,6 @@ instance "lmp" to make calls to that instance of LAMMPS. See the
Note that you can create multiple LAMMPS objects in your Python
script, and coordinate and run multiple simulations, e.g.
.. code-block:: Python
from lammps import lammps
@ -229,7 +222,6 @@ For the scatter methods, the array of coordinates passed to must be a
ctypes vector of ints or doubles, allocated and initialized something
like this:
.. code-block:: Python
from ctypes import \*
@ -247,10 +239,8 @@ like this:
Alternatively, you can just change values in the vector returned by
the gather methods, since they are also ctypes vectors.
----------
As noted above, these Python class methods correspond one-to-one with
the functions in the LAMMPS library interface in src/library.cpp and
library.h. This means you can extend the Python wrapper via the
@ -264,7 +254,6 @@ following steps:
* You should now be able to invoke the new interface function from a
Python script.
----------
.. autoclass:: lammps.lammps

5
doc/src/Python_mpi.rst
View File

@ -18,7 +18,6 @@ LAMMPS instances on subsets of the total MPI ranks.
To install mpi4py (version mpi4py-3.0.3 as of Nov 2019), unpack it
and from its main directory, type
.. parsed-literal::
python setup.py build
@ -28,7 +27,6 @@ Again, the "sudo" is only needed if required to copy mpi4py files into
your Python distribution's site-packages directory. To install with
user privilege into the user local directory type
.. parsed-literal::
python setup.py install --user
@ -36,7 +34,6 @@ user privilege into the user local directory type
If you have successfully installed mpi4py, you should be able to run
Python and type
.. parsed-literal::
from mpi4py import MPI
@ -44,14 +41,12 @@ Python and type
without error. You should also be able to run python in parallel
on a simple test script
.. parsed-literal::
% mpirun -np 4 python test.py
where test.py contains the lines
.. parsed-literal::
from mpi4py import MPI

4
doc/src/Python_shlib.rst
View File

@ -12,7 +12,6 @@ wrap LAMMPS. On Linux this is a library file that ends in ".so", not
From the src directory, type
.. parsed-literal::
make foo mode=shlib
@ -38,7 +37,6 @@ Build LAMMPS as a shared library using CMake
When using CMake the following two options are necessary to generate the LAMMPS
shared library:
.. parsed-literal::
-D BUILD_LIB=on # enable building LAMMPS as a library
@ -52,7 +50,6 @@ library path (e.g. /usr/lib64/) or in the LD\_LIBRARY\_PATH.
If you want to use the shared library with Python the recommended way is to create a virtualenv and use it as
CMAKE\_INSTALL\_PREFIX.
.. parsed-literal::
# create virtualenv
@ -72,7 +69,6 @@ This will also install the Python module into your virtualenv. Since virtualenv
doesn't change your LD\_LIBRARY\_PATH, you still need to add its lib64 folder to
it, which contains the installed liblammps.so.
.. parsed-literal::
export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib64:$LD_LIBRARY_PATH

13
doc/src/Python_test.rst
View File

@ -4,7 +4,6 @@ Test the Python/LAMMPS interface
To test if LAMMPS is callable from Python, launch Python interactively
and type:
.. parsed-literal::
>>> from lammps import lammps
@ -13,7 +12,6 @@ and type:
If you get no errors, you're ready to use LAMMPS from Python. If the
2nd command fails, the most common error to see is
.. parsed-literal::
OSError: Could not load LAMMPS dynamic library
@ -27,7 +25,6 @@ should give you an indication of what went wrong.
You can also test the load directly in Python as follows, without
first importing from the lammps.py file:
.. parsed-literal::
>>> from ctypes import CDLL
@ -44,7 +41,6 @@ Test LAMMPS and Python in serial:
To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:
.. parsed-literal::
>>> from lammps import lammps
@ -53,7 +49,6 @@ interactively from the bench directory:
Or put the same lines in the file test.py and run it as
.. parsed-literal::
% python test.py
@ -62,7 +57,6 @@ Either way, you should see the results of running the in.lj benchmark
on a single processor appear on the screen, the same as if you had
typed something like:
.. parsed-literal::
lmp_g++ -in in.lj
@ -74,7 +68,6 @@ To run LAMMPS in parallel, assuming you have installed the
`PyPar <https://github.com/daleroberts/pypar>`_ package as discussed
above, create a test.py file containing these lines:
.. parsed-literal::
import pypar
@ -88,7 +81,6 @@ To run LAMMPS in parallel, assuming you have installed the
`mpi4py <https://bitbucket.org/mpi4py/mpi4py>`_ package as discussed
above, create a test.py file containing these lines:
.. parsed-literal::
from mpi4py import MPI
@ -102,14 +94,12 @@ above, create a test.py file containing these lines:
You can either script in parallel as:
.. parsed-literal::
% mpirun -np 4 python test.py
and you should see the same output as if you had typed
.. parsed-literal::
% mpirun -np 4 lmp_g++ -in in.lj
@ -134,7 +124,6 @@ Running Python scripts:
Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:
.. parsed-literal::
% python foo.script
@ -144,7 +133,6 @@ one of several ways:
The last command requires that the first line of the script be
something like this:
.. parsed-literal::
#!/usr/local/bin/python
@ -153,7 +141,6 @@ something like this:
where the path points to where you have Python installed, and that you
have made the script file executable:
.. parsed-literal::
% chmod +x foo.script

4
doc/src/Run_basics.rst
View File

@ -5,7 +5,6 @@ LAMMPS is run from the command line, reading commands from a file via
the -in command line flag, or from standard input.
Using the "-in in.file" variant is recommended:
.. code-block:: bash
$ lmp_serial -in in.file
@ -68,7 +67,6 @@ If the LAMMPS command(s) you are using support multi-threading, you
can set the number of threads per MPI task via the environment
variable OMP\_NUM\_THREADS, before you launch LAMMPS:
.. code-block:: bash
$ export OMP_NUM_THREADS=2 # bash
@ -80,10 +78,8 @@ package command. See the :doc:`package <package>` command or
:doc:`Speed <Speed>` doc pages for more details about which accelerator
packages and which commands support multi-threading.
----------
You can experiment with running LAMMPS using any of the input scripts
provided in the examples or bench directory. Input scripts are named
in.\* and sample outputs are named log.\*.P where P is the number of

1
doc/src/Run_head.rst
View File

@ -6,7 +6,6 @@ and :doc:`built an executable <Build>`. The :doc:`Commands <Commands>`
doc page describes how input scripts are structured and the commands
they can contain.
.. toctree::
:maxdepth: 1

49
doc/src/Run_options.rst
View File

@ -25,16 +25,13 @@ letter abbreviation can be used:
For example, the lmp\_mpi executable might be launched as follows:
.. code-block:: bash
$ mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
$ mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
----------
.. _echo:
**-echo style**
@ -46,10 +43,8 @@ can be useful to figure out which line of your script is causing an
input error. The default value is *log*\ . The echo style can also be
set by using the :doc:`echo <echo>` command in the input script itself.
----------
.. _help:
**-help**
@ -61,10 +56,8 @@ want to use was included via the appropriate package at compile time.
LAMMPS will print the info and immediately exit if this switch is
used.
----------
.. _file:
**-in file**
@ -79,10 +72,8 @@ Note that this is a required switch when running LAMMPS in
multi-partition mode, since multiple processors cannot all read from
stdin.
----------
.. _run-kokkos:
**-kokkos on/off keyword/value ...**
@ -114,7 +105,6 @@ settings to use on different platforms is given on the :doc:`Speed kokkos <Speed
* t or threads
* n or numa
.. parsed-literal::
device Nd
@ -127,7 +117,6 @@ have consecutive IDs numbered as 0,1,2,etc. This setting allows you
to launch multiple independent jobs on the node, each with a single
MPI task per node, and assign each job to run on a different GPU.
.. parsed-literal::
gpus Ng Ns
@ -144,7 +133,6 @@ Ng = 1 and Ns is not set.
Depending on which flavor of MPI you are running, LAMMPS will look for
one of these 4 environment variables
.. parsed-literal::
SLURM_LOCALID (various MPI variants compiled with SLURM support)
@ -156,7 +144,6 @@ which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
.. parsed-literal::
threads Nt
@ -169,7 +156,6 @@ the number of physical cores per node, to use your available hardware
optimally. This also sets the number of threads used by the host when
LAMMPS is compiled with CUDA=yes.
.. parsed-literal::
numa Nm
@ -184,10 +170,8 @@ its default value of 1. This is because letting a single process span
multiple NUMA regions induces a significant amount of cross NUMA data
traffic which is slow.
----------
.. _log:
**-log file**
@ -205,10 +189,8 @@ specified file is "none", then no log files are created. Using a
:doc:`log <log>` command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
----------
.. _mpicolor:
**-mpicolor** color
@ -232,10 +214,8 @@ by the :doc:`message <message>` command and the CSlib library LAMMPS
links with from the lib/message directory. See the
:doc:`message <message>` command for more details.
----------
.. _nocite:
**-nocite**
@ -245,10 +225,8 @@ references for specific cite-able features used during a LAMMPS run.
See the `citation page <http://lammps.sandia.gov/cite.html>`_ for more
details.
----------
.. _package:
**-package style args ....**
@ -265,10 +243,8 @@ Along with the "-suffix" command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without
having to edit an input script.
----------
.. _partition:
**-partition 8x2 4 5 ...**
@ -296,10 +272,8 @@ multiple partitions, see the :doc:`Howto multiple <Howto_multiple>` doc
page. World- and universe-style :doc:`variables <variable>` are useful
in this context.
----------
.. _plog:
**-plog file**
@ -314,10 +288,8 @@ replica\_files/log.lammps) If this option is not used the log file for
partition N is log.lammps.N or whatever is specified by the -log
command-line option.
----------
.. _pscreen:
**-pscreen file**
@ -332,17 +304,14 @@ sub-directory (-pscreen replica\_files/screen). If this option is not
used the screen file for partition N is screen.N or whatever is
specified by the -screen command-line option.
----------
.. _reorder:
**-reorder**
This option has 2 forms:
.. parsed-literal::
-reorder nth N
@ -371,21 +340,18 @@ This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the
processors will be reordered from
.. parsed-literal::
0 1 2 3 4 5 6 7 8 9 10 11
to
.. parsed-literal::
0 1 2 4 5 6 8 9 10 3 7 11
so that the processors in each partition will be
.. parsed-literal::
0 1 2 4 5 6 8 9 10
@ -400,7 +366,6 @@ file is as follows. Any number of initial blank or comment lines
(starting with a "#" character) can be present. These should be
followed by P lines of the form:
.. parsed-literal::
I J
@ -424,20 +389,16 @@ itself. See the :doc:`processors out <processors>` command for how
to output info on the final assignment of physical processors to
the LAMMPS simulation domain.
----------
.. _restart2data:
**-restart2data restartfile [remap] datafile keyword value ...**
Convert the restart file into a data file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
.. code-block:: LAMMPS
read_restart restartfile [remap]
@ -461,7 +422,6 @@ should allow the data file to still be produced.
The syntax following restartfile (or remap), namely
.. parsed-literal::
datafile keyword value ...
@ -470,10 +430,8 @@ is identical to the arguments of the :doc:`write_data <write_data>`
command. See its doc page for details. This includes its
optional keyword/value settings.
----------
.. _restart2dump:
**-restart2dump restartfile [remap] group-ID dumpstyle dumpfile arg1 arg2 ...**
@ -482,7 +440,6 @@ Convert the restart file into a dump file and immediately exit. This
is the same operation as if the following 2-line input script were
run:
.. code-block:: LAMMPS
read_restart restartfile [remap]
@ -517,10 +474,8 @@ including ones that affect how parallel dump files are written, e.g.
the *nfile* and *fileper* keywords. See the
:doc:`dump_modify <dump_modify>` doc page for details.
----------
.. _screen:
**-screen file**
@ -538,10 +493,8 @@ multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
----------
.. _suffix:
**-suffix style args**
@ -607,10 +560,8 @@ The :doc:`suffix <suffix>` command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
----------
.. _var:
**-var name value1 value2 ...**

16
doc/src/Run_output.rst
View File

@ -14,7 +14,6 @@ thermodynamic state and a total run time for the simulation. It also
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
.. parsed-literal::
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
@ -47,10 +46,8 @@ simulation. An example set of statistics is shown here:
Neighbor list builds = 26
Dangerous builds = 0
----------
The first section provides a global loop timing summary. The *loop
time* is the total wall-clock time for the simulation to run. The
*Performance* line is provided for convenience to help predict how
@ -60,10 +57,8 @@ line provides the CPU utilization per MPI task; it should be close to
Lower numbers correspond to delays due to file I/O or insufficient
thread utilization.
----------
The *MPI task* section gives the breakdown of the CPU run time (in
seconds) into major categories:
@ -96,7 +91,6 @@ only and thus, because the breakdown for MPI tasks can change from
MPI rank to MPI rank, this breakdown can be very different for
individual ranks. Here is an example output for this section:
.. parsed-literal::
Thread timings breakdown (MPI rank 0):
@ -109,20 +103,16 @@ individual ranks. Here is an example output for this section:
Neigh \| 0.084778 \| 0.086969 \| 0.089161 \| 0.7 \| 12.70
Reduce \| 0.0036485 \| 0.003737 \| 0.0038254 \| 0.1 \| 0.55
----------
The third section above lists the number of owned atoms (Nlocal),
ghost atoms (Nghost), and pair-wise neighbors stored per processor.
The max and min values give the spread of these values across
processors with a 10-bin histogram showing the distribution. The total
number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pair-wise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
@ -135,15 +125,12 @@ non-zero you may wish to reduce the delay factor to insure no force
interactions are missed by atoms moving beyond the neighbor skin
distance before a rebuild takes place.
----------
If an energy minimization was performed via the
:doc:`minimize <minimize>` command, additional information is printed,
e.g.
.. parsed-literal::
Minimization stats:
@ -167,15 +154,12 @@ Multiple force evaluations are typically done at each iteration to
perform a 1d line minimization in the search direction. See the
:doc:`minimize <minimize>` doc page for more details.
----------
If a :doc:`kspace_style <kspace_style>` long-range Coulombics solver
that performs FFTs was used during the run (PPPM, Ewald), then
additional information is printed, e.g.
.. parsed-literal::
FFT time (% of Kspce) = 0.200313 (8.34477)

6
doc/src/Run_windows.rst
View File

@ -14,15 +14,12 @@ Note that the serial executable includes support for multi-threading
parallelization from the styles in the USER-OMP packages. To run with
4 threads, you can type this:
.. parsed-literal::
lmp_serial -in in.lj -pk omp 4 -sf omp
----------
For the MPI executable, which allows you to run LAMMPS under Windows
in parallel, follow these steps.
@ -46,7 +43,6 @@ into the MPICH2 installation directory, then into the sub-directory
Then type something like this:
.. parsed-literal::
mpiexec -localonly 4 lmp_mpi -in in.file
@ -62,7 +58,6 @@ patient before the output shows up.
The parallel executable can also run on a single processor by typing
something like this:
.. parsed-literal::
lmp_mpi -in in.lj
@ -70,7 +65,6 @@ something like this:
Note that the parallel executable also includes OpenMP
multi-threading, which can be combined with MPI using something like:
.. parsed-literal::
mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp

1
doc/src/Speed.rst
View File

@ -19,7 +19,6 @@ page, for several of the standard LAMMPS benchmark problems, as a
function of problem size and number of compute nodes, on different
hardware platforms.
.. toctree::
:maxdepth: 1

3
doc/src/Speed_bench.rst
View File

@ -26,7 +26,6 @@ The 5 standard problems are as follow:
particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
integration
Input files for these 5 problems are provided in the bench directory
of the LAMMPS distribution. Each has 32,000 atoms and runs for 100
timesteps. The size of the problem (number of atoms) can be varied
@ -53,10 +52,8 @@ of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script.
----------
For all the benchmarks, a useful metric is the CPU cost per atom per
timestep. Since performance scales roughly linearly with problem size
and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained

1
doc/src/Speed_compare.rst
View File

@ -77,7 +77,6 @@ section below for examples where this has been done.
to unlock this potential, an Intel compiler is required. The package code
will compile with GNU gcc, but it will not be as efficient.
**Differences between the GPU and KOKKOS packages:**
* The GPU package accelerates only pair force, neighbor list, and (parts

5
doc/src/Speed_gpu.rst
View File

@ -27,7 +27,6 @@ It has the following general features:
NVIDIA support as well as more general OpenCL support, so that the
same functionality is supported on a variety of hardware.
**Required hardware/software:**
To compile and use this package in CUDA mode, you currently need
@ -77,7 +76,6 @@ automatically append "gpu" to styles that support it. Use the "-pk
gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
GPUs/node to use.
.. parsed-literal::
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
@ -108,7 +106,6 @@ and use of multiple MPI tasks/GPU is the same.
Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
"gpu" suffix to individual styles in your input script, e.g.
.. parsed-literal::
pair_style lj/cut/gpu 2.5
@ -172,9 +169,7 @@ results, since they will typically be faster.
This is the maximum memory used at one time on the GPU for data
storage by a single MPI process.
Restrictions
""""""""""""
None.

19
doc/src/Speed_intel.rst
View File

@ -25,7 +25,6 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
rebo, sw, tersoff
* K-Space Styles: pppm, pppm/disp
.. warning::
None of the styles in the USER-INTEL package currently
@ -58,10 +57,8 @@ Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
*src/USER-INTEL/TEST/README* for the raw simulation rates and
instructions to reproduce.
----------
**Accuracy and order of operations:**
In most molecular dynamics software, parallelization parameters
@ -88,7 +85,6 @@ order of operations compared to LAMMPS without acceleration:
Twister generator included in the Intel MKL library (that should be
more robust than the default Masaglia random number generator)
The precision mode (described below) used with the USER-INTEL
package can change the *accuracy* of the calculations. For the
default *mixed* precision option, calculations between pairs or
@ -98,10 +94,8 @@ is performed in double precision to prevent the error from growing
with the number of atoms in the simulation. *Single* precision
mode should not be used without appropriate validation.
----------
**Quick Start for Experienced Users:**
LAMMPS should be built with the USER-INTEL package installed.
@ -120,12 +114,10 @@ not *hardware thread*\ .
* If using *kspace\_style pppm* in the input script, add
"kspace\_modify diff ad" for better performance
For Intel Xeon Phi CPUs:
* Runs should be performed using MCDRAM.
For simulations using *kspace\_style pppm* on Intel CPUs supporting
AVX-512:
@ -136,18 +128,14 @@ AVX-512:
* Do not use thread affinity (set KMP\_AFFINITY=none)
* The "newton off" setting may provide better scalability
For Intel Xeon Phi co-processors (Offload):
* Edit src/MAKE/OPTIONS/Makefile.intel\_co-processor as necessary
* "-pk intel N omp 1" added to command-line where N is the number of
co-processors per node.
----------
**Required hardware/software:**
In order to use offload to co-processors, an Intel Xeon Phi
@ -204,7 +192,6 @@ will report every hardware thread as a separate core allowing one to
determine the number of hardware threads available. On Linux systems,
this information can normally be obtained with:
.. parsed-literal::
cat /proc/cpuinfo
@ -218,7 +205,6 @@ For building with make, several example Makefiles for building with
the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/
directory:
.. parsed-literal::
Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
@ -233,7 +219,6 @@ Phi x200 processors making it easier to cross-compile. For users with
recent installations of Intel Parallel Studio, the process can be as
simple as:
.. parsed-literal::
make yes-user-intel
@ -349,7 +334,6 @@ desired.
Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
.. parsed-literal::
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
@ -362,7 +346,6 @@ can be edited to enable the USER-INTEL package. This requires adding
the :doc:`package intel <package>` command to the top of the input
script. For the second example above, this would be:
.. parsed-literal::
package intel 0 omp 2 mode double
@ -370,7 +353,6 @@ script. For the second example above, this would be:
To enable the USER-INTEL package only for individual styles, you can
add an "intel" suffix to the individual style, e.g.:
.. parsed-literal::
pair_style lj/cut/intel 2.5
@ -527,7 +509,6 @@ MPI task.
Restrictions
""""""""""""
When offloading to a co-processor, :doc:`hybrid <pair_hybrid>` styles
that require skip lists for neighbor builds cannot be offloaded.
Using :doc:`hybrid/overlay <pair_hybrid>` is allowed. Only one intel

15
doc/src/Speed_kokkos.rst
View File

@ -71,7 +71,6 @@ Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
Here is a quick overview of how to use the KOKKOS package
for CPU acceleration, assuming one or more 16-core nodes.
.. parsed-literal::
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading
@ -85,7 +84,6 @@ command. You must use the "-k on" :doc:`command-line switch <Run_options>` to e
additional arguments for hardware settings appropriate to your system.
For OpenMP use:
.. parsed-literal::
-k on t Nt
@ -121,7 +119,6 @@ below.
page for details and default settings. Experimenting with its options
can provide a speed-up for specific calculations. For example:
.. parsed-literal::
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm
@ -154,7 +151,6 @@ they do not migrate during a simulation.
If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:
.. parsed-literal::
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
@ -184,7 +180,6 @@ tasks.
Examples of mpirun commands that follow these rules are shown below.
.. parsed-literal::
Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
@ -210,7 +205,6 @@ threads/task as Nt. The product of these two values should be N, i.e.
details and default settings. Experimenting with its options can provide
a speed-up for specific calculations. For example:
.. parsed-literal::
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm
@ -245,7 +239,6 @@ avoided by using :doc:`-pk kokkos cuda/aware no <package>`. As above for
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
then the number of MPI tasks/node should not exceed N.
.. parsed-literal::
-k on g Ng
@ -253,7 +246,6 @@ then the number of MPI tasks/node should not exceed N.
Here are examples of how to use the KOKKOS package for GPUs, assuming
one or more nodes, each with two GPUs:
.. parsed-literal::
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node
@ -274,7 +266,6 @@ one or more nodes, each with two GPUs:
default settings. Experimenting with its options can provide a speed-up
for specific calculations. For example:
.. parsed-literal::
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
@ -317,7 +308,6 @@ hardware options appropriate to your system, as documented above.
You can use the :doc:`suffix kk <suffix>` command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
.. parsed-literal::
pair_style lj/cut/kk 2.5
@ -333,7 +323,6 @@ used together in a few special cases. In the Makefile, the
KOKKOS\_DEVICES variable must include both "Cuda" and "OpenMP", as is
the case for /src/MAKE/OPTIONS/Makefile.kokkos\_cuda\_mpi
.. parsed-literal::
KOKKOS_DEVICES=Cuda,OpenMP
@ -345,14 +334,12 @@ style in the input script, the Kokkos OpenMP (CPU) version of that
specific style will be used instead. Set the number of OpenMP threads
as "t Nt" and the number of GPUs as "g Ng"
.. parsed-literal::
-k on t Nt g Ng
For example, the command to run with 1 GPU and 8 OpenMP threads is then:
.. parsed-literal::
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk
@ -394,7 +381,6 @@ Generally speaking, the following rules of thumb apply:
* When running on Intel hardware, KOKKOS is not as fast as
the USER-INTEL package, which is optimized for that hardware.
See the `Benchmark page <http://lammps.sandia.gov/bench.html>`_ of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.
@ -441,6 +427,5 @@ GPUs.
Restrictions
""""""""""""
Currently, there are no precision options with the KOKKOS package. All
compilation and computation is performed in double precision.

5
doc/src/Speed_omp.rst
View File

@ -23,7 +23,6 @@ instructions.
These examples assume one or more 16-core nodes.
.. parsed-literal::
env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS
@ -61,7 +60,6 @@ and threads/MPI task is the same.
Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.
.. parsed-literal::
pair_style lj/cut/omp 2.5
@ -140,7 +138,6 @@ circumstances:
with the USER-OMP package, is an alternative way to reduce the number
of MPI tasks assigned to the KSpace calculation.
Additional performance tips are as follows:
* The best parallel efficiency from *omp* styles is typically achieved
@ -154,9 +151,7 @@ Additional performance tips are as follows:
one core and thus is likely to be counterproductive. Instead, binding
MPI tasks to a (multi-core) socket, should solve this issue.
Restrictions
""""""""""""
None.

3
doc/src/Speed_opt.rst
View File

@ -17,7 +17,6 @@ See the :ref:`Build extras <opt>` doc page for instructions.
**Run with the OPT package from the command line:**
.. parsed-literal::
lmp_mpi -sf opt -in in.script # run in serial
@ -31,7 +30,6 @@ automatically append "opt" to styles that support it.
Use the :doc:`suffix opt <suffix>` command, or you can explicitly add an
"opt" suffix to individual styles in your input script, e.g.
.. parsed-literal::
pair_style lj/cut/opt 2.5
@ -49,5 +47,4 @@ Just try out an OPT pair style to see how it performs.
Restrictions
""""""""""""
None.

2
doc/src/Speed_packages.rst
View File

@ -132,7 +132,6 @@ packages. As an example, here is a command that builds with all the
GPU related packages installed (GPU, KOKKOS with Cuda), including
settings to build the needed auxiliary GPU libraries for Kepler GPUs:
.. parsed-literal::
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
@ -178,7 +177,6 @@ are in the individual accelerator sections.
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU.
The individual accelerator package doc pages explain:
* what hardware and software the accelerated package requires

80
doc/src/Tools.rst
View File

@ -18,8 +18,6 @@ visualization for LAMMPS simulations.
.. _pizza: http://pizza.sandia.gov
.. _python: http://www.python.org
Additional tools included in the LAMMPS distribution are described on
this page.
@ -37,10 +35,8 @@ 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.
----------
Pre-processing tools
====================
@ -72,10 +68,8 @@ Miscellaneous tools
| :ref:`vim <vim>` | | | | |
+--------------------------+----------------------+-------------------+--------------------+---------------------------------------+
----------
Tool descriptions
=================
@ -95,10 +89,8 @@ version (and maybe with respect to AMBER as well). Since we don't use
these tools at Sandia, you will need to experiment with them and make
necessary modifications yourself.
----------
.. _binary:
binary2txt tool
@ -107,7 +99,6 @@ binary2txt tool
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
.. parsed-literal::
binary2txt file1 file2 ...
@ -116,10 +107,8 @@ which creates file1.txt, file2.txt, etc. This tool must be compiled
on a platform that can read the binary file created by a LAMMPS run,
since binary files are not compatible across all platforms.
----------
.. _charmm:
ch2lmp tool
@ -146,10 +135,8 @@ Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
Tigran Abramyan, (Clemson University) and
Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
----------
.. _chain:
chain tool
@ -162,7 +149,6 @@ chains and solvent atoms can strongly overlap, so LAMMPS needs to run
the system initially with a "soft" pair potential to un-overlap it.
The syntax for running the tool is
.. parsed-literal::
chain < def.chain > data.file
@ -171,10 +157,8 @@ See the def.chain or def.chain.ab files in the tools directory for
examples of definition files. This tool was used to create the system
for the :doc:`chain benchmark <Speed_bench>`.
----------
.. _colvars:
colvars tools
@ -192,7 +176,6 @@ abf\_integrate:
MC-based integration of multidimensional free energy gradient
Version 20110511
.. parsed-literal::
Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0\|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
@ -201,10 +184,8 @@ The LAMMPS interface to the colvars collective variable library, as
well as these tools, were created by Axel Kohlmeyer (akohlmey at
gmail.com) at ICTP, Italy.
----------
.. _createatoms:
createatoms tool
@ -219,10 +200,8 @@ See the included Manual.pdf for details.
The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
----------
.. _doxygen:
doxygen tool
@ -236,10 +215,8 @@ See the included README file for details.
The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
----------
.. _drude:
drude tool
@ -254,10 +231,8 @@ See the header of the polarizer.py file for details.
The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
----------
.. _eamdb:
eam database tool
@ -274,10 +249,8 @@ and is based on his paper:
X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
144113 (2004).
----------
.. _eamgn:
eam generate tool
@ -291,10 +264,8 @@ produce are in the potentials directory, and can be used with the
The source files and potentials were provided by Gerolf Ziegenhain
(gerolf at ziegenhain.com).
----------
.. _eff:
eff tool
@ -307,10 +278,8 @@ electron force field (eFF).
These tools were provided by Andres Jaramillo-Botero at CalTech
(ajaramil at wag.caltech.edu).
----------
.. _emacs:
emacs tool
@ -323,10 +292,8 @@ with various highlighting options set up.
These tools were provided by Aidan Thompson at Sandia
(athomps at sandia.gov).
----------
.. _fep:
fep tool
@ -341,10 +308,8 @@ Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
See README file in the tools/fep directory.
----------
.. _ipi:
i-pi tool
@ -363,10 +328,8 @@ See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
:doc:`fix ipi <fix_ipi>` doc page for further details on running PIMD
calculations with LAMMPS.
----------
.. _ipp:
ipp tool
@ -382,10 +345,8 @@ sandia.gov.
See two examples in the tools/ipp directory. One of them is for the
tools/createatoms tool's input file.
----------
.. _kate:
kate tool
@ -398,10 +359,8 @@ scripts. See the README.txt file for details.
The file was provided by Alessandro Luigi Sellerio
(alessandro.sellerio at ieni.cnr.it).
----------
.. _arc:
lmp2arc tool
@ -419,10 +378,8 @@ This tool was written by John Carpenter (Cray), Michael Peachey
This tool was updated for the current LAMMPS C++ version by Jeff
Greathouse at Sandia (jagreat at sandia.gov).
----------
.. _cfg:
lmp2cfg tool
@ -435,10 +392,8 @@ the README file for more information.
This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
----------
.. _matlab:
matlab tool
@ -458,12 +413,8 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
.. _matlabhome: http://www.mathworks.com
----------
.. _micelle:
micelle2d tool
@ -476,7 +427,6 @@ atoms can strongly overlap, so LAMMPS needs to run the system
initially with a "soft" pair potential to un-overlap it. The syntax
for running the tool is
.. parsed-literal::
micelle2d < def.micelle2d > data.file
@ -485,10 +435,8 @@ See the def.micelle2d file in the tools directory for an example of a
definition file. This tool was used to create the system for the
:doc:`micelle example <Examples>`.
----------
.. _moltemplate:
moltemplate tool
@ -505,10 +453,8 @@ supports it. It has its own WWW page at
`http://moltemplate.org <http://moltemplate.org>`_.
The latest sources can be found `on its GitHub page <https://github.com/jewettaij/moltemplate/releases>`_
----------
.. _msi:
msi2lmp tool
@ -527,10 +473,8 @@ development, so there are no changes except for the occasional bug fix.
See the README file in the tools/msi2lmp folder for more information.
----------
.. _phonon:
phonon tool
@ -547,10 +491,8 @@ for example problems that can be post-processed with this tool.
This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
University.
----------
.. _polybond:
polybond tool
@ -566,10 +508,8 @@ See the Manual.pdf for details and example scripts.
This tool was written by Zachary Kraus at Georgia Tech.
----------
.. _pymol:
pymol\_asphere tool
@ -581,22 +521,16 @@ particles into an input file for the `PyMol visualization package <pymolhome_>`_
.. _pymolhome: http://www.pymol.org
.. _pymolopen: http://sourceforge.net/scm/?type=svn&group\_id=4546
Specifically, the tool triangulates the ellipsoids so they can be
viewed as true ellipsoidal particles within PyMol. See the README and
examples directory within pymol\_asphere for more information.
This tool was written by Mike Brown at Sandia.
----------
.. _pythontools:
python tool
@ -614,10 +548,8 @@ that perform common LAMMPS post-processing tasks, such as:
These are simple scripts built on `Pizza.py <pizza_>`_ modules. See the
README for more info on Pizza.py and how to use these scripts.
----------
.. _replica:
replica tool
@ -634,10 +566,8 @@ the README.md file for further details. Try out the peptide example provided.
This tool was written by (and is maintained by) Tanmoy Sanyal,
while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
----------
.. _reax\_tool:
reax tool
@ -650,10 +580,8 @@ the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.
----------
.. _smd:
smd tool
@ -671,10 +599,8 @@ This tool was written by the USER-SMD package author, Georg
Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
----------
.. _spin:
spin tool
@ -690,10 +616,8 @@ This tool was written by the SPIN package author, Julien
Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
Ivanov, at University of Iceland (ali5 at hi.is).
----------
.. _singularity\_tool:
singularity tool
@ -704,10 +628,8 @@ that can be used to build container images for building and testing
LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
container software. Contributions for additional variants are welcome.
----------
.. _vim:
vim tool
@ -720,10 +642,8 @@ file for details.
These files were provided by Gerolf Ziegenhain (gerolf at
ziegenhain.com)
----------
.. _xmgrace:
xmgrace tool

12
doc/src/angle_charmm.rst
View File

@ -15,7 +15,6 @@ angle_style charmm/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style charmm
@ -23,7 +22,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style charmm
@ -38,7 +36,6 @@ The *charmm* angle style uses the potential
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
with an additional Urey\_Bradley term based on the distance :math:`r` between
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`,
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
@ -60,10 +57,8 @@ or :doc:`read_restart <read_restart>` commands:
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -82,14 +77,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
@ -101,13 +93,9 @@ Related commands
**Default:** none
----------
.. _angle-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

15
doc/src/angle_class2.rst
View File

@ -15,7 +15,6 @@ angle_style class2/p6 command
Syntax
""""""
.. code-block:: LAMMPS
angle_style class2
@ -23,7 +22,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style class2
@ -43,7 +41,6 @@ The *class2* angle style uses the potential
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
the equilibrium bond lengths.
@ -94,10 +91,8 @@ the angle type.
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -116,17 +111,14 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
.. math::
E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
* :math:`\theta_0` (degrees)
@ -138,14 +130,11 @@ In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
The bond-bond and bond-angle terms remain unchanged.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the CLASS2
package. For the *class2/p6* style LAMMPS needs to be built with the
USER-MOFFF package. See the :doc:`Build package <Build_package>` doc
@ -158,12 +147,8 @@ Related commands
**Default:** none
----------
.. _angle-Sun:
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).

9
doc/src/angle_coeff.rst
View File

@ -6,7 +6,6 @@ angle_coeff command
Syntax
""""""
.. code-block:: LAMMPS
angle_coeff N args
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_coeff 1 300.0 107.0
@ -45,7 +43,6 @@ Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previ
for the same angle type. For example, these commands set the coeffs
for all angle types, then overwrite the coeffs for just angle type 2:
.. code-block:: LAMMPS
angle_coeff * 200.0 107.0 1.2
@ -58,7 +55,6 @@ coefficients for all N types must be listed in the file. For example,
under the "Angle Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
.. parsed-literal::
1 300.0 107.0
@ -68,10 +64,8 @@ rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its
doc page for details.
----------
The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc
@ -81,14 +75,11 @@ On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
:doc:`angle_coeff <angle_coeff>` command.
----------
Restrictions
""""""""""""
This command must come after the simulation box is defined by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.

8
doc/src/angle_cosine.rst
View File

@ -12,7 +12,6 @@ angle_style cosine/kk command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine
@ -20,7 +19,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine
@ -35,7 +33,6 @@ The *cosine* angle style uses the potential
E = K [1 + \cos(\theta)]
where :math:`K` is defined for each angle type.
The following coefficients must be defined for each angle type via the
@ -45,10 +42,8 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy)
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -67,14 +62,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.

5
doc/src/angle_cosine_buck6d.rst
View File

@ -6,7 +6,6 @@ angle_style cosine/buck6d command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/buck6d
@ -14,7 +13,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/buck6d
@ -52,14 +50,11 @@ with the :doc:`pair_style buck6d <pair_buck6d_coul_gauss>` styles and needs
the :doc:`special_bonds <special_bonds>` 1-3 interactions to be weighted
0.0 to prevent double counting.
----------
Restrictions
""""""""""""
*cosine/buck6d* can only be used in combination with the
:doc:`pair_style buck6d <pair_buck6d_coul_gauss>` style and with a
:doc:`special_bonds <special_bonds>` 0.0 weighting of 1-3 interactions.

8
doc/src/angle_cosine_delta.rst
View File

@ -9,7 +9,6 @@ angle_style cosine/delta/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/delta
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/delta
@ -32,7 +30,6 @@ The *cosine/delta* angle style uses the potential
E = K [1 - \cos(\theta - \theta_0)]
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
@ -47,10 +44,8 @@ or :doc:`read_restart <read_restart>` commands:
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -69,14 +64,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.

12
doc/src/angle_cosine_periodic.rst
View File

@ -9,7 +9,6 @@ angle_style cosine/periodic/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/periodic
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/periodic
@ -36,7 +34,6 @@ center:
E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
@ -55,10 +52,8 @@ constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum f
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear
geometry.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -77,14 +72,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.
@ -96,13 +88,9 @@ Related commands
**Default:** none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

8
doc/src/angle_cosine_shift.rst
View File

@ -9,7 +9,6 @@ angle_style cosine/shift/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/shift
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/shift
@ -32,7 +30,6 @@ The *cosine/shift* angle style uses the potential
E = -\frac{U_{\text{min}}}{2} \left[ 1 + \cos(\theta-\theta_0) \right]
where :math:`\theta_0` is the equilibrium angle. The potential is bounded
between :math:`-U_{\text{min}}` and zero. In the neighborhood of the minimum
:math:`E = - U_{\text{min}} + U_{\text{min}}/4(\theta - \theta_0)^2` hence
@ -46,10 +43,8 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`U_{\text{min}}` (energy)
* :math:`\theta` (angle)
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -68,14 +63,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
USER-MISC package.

7
doc/src/angle_cosine_shift_exp.rst
View File

@ -9,7 +9,6 @@ angle_style cosine/shift/exp/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/shift/exp
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/shift/exp
@ -56,10 +54,8 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\theta` (angle)
* :math:`A` (real number)
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -78,14 +74,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.

8
doc/src/angle_cosine_squared.rst
View File

@ -9,7 +9,6 @@ angle_style cosine/squared/omp command
Syntax
""""""
.. code-block:: LAMMPS
angle_style cosine/squared
@ -17,7 +16,6 @@ Syntax
Examples
""""""""
.. code-block:: LAMMPS
angle_style cosine/squared
@ -32,7 +30,6 @@ The *cosine/squared* angle style uses the potential
E = K [\cos(\theta) - \cos(\theta_0)]^2
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
@ -47,10 +44,8 @@ or :doc:`read_restart <read_restart>` commands:
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
@ -69,14 +64,11 @@ by including their suffix, or you can use the :doc:`-suffix command-line switch
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc page
for more info.

Some files were not shown because too many files have changed in this diff Show More