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Build LAMMPS
************
LAMMPS can be built as an executable or library from source code via
either traditional makefiles (which may require manual editing)
for use with GNU make or gmake, or a build environment generated by CMake
(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an
alternative you can download a package with pre-built executables
as described on the :doc:`Install <Install>` doc page.
.. toctree::
:maxdepth: 1
Build_cmake
Build_make
Build_link
Build_basics
Build_settings
Build_package
Build_extras
Build_windows
Build_development
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Build LAMMPS :h2
LAMMPS can be built as an executable or library from source code via
either traditional makefiles (which may require manual editing)
for use with GNU make or gmake, or a build environment generated by CMake
(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an
alternative you can download a package with pre-built executables
as described on the "Install"_Install.html doc page.
<!-- RST
.. toctree::
:maxdepth: 1
Build_cmake
Build_make
Build_link
Build_basics
Build_settings
Build_package
Build_extras
Build_windows
Build_development
END_RST -->
<!-- HTML_ONLY -->
"Build LAMMPS with CMake"_Build_cmake.html
"Build LAMMPS with make"_Build_make.html
"Link LAMMPS as a library to another code"_Build_link.html
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
"Packages with extra build options"_Build_extras.html
"Notes for building LAMMPS on Windows"_Build_windows.html
"Development build options (CMake only)"_Build_development.html :all(b)
If you have problems building LAMMPS, it is often due to software
issues on your local machine. If you can, find a local expert to
help. If you're still stuck, send an email to the "LAMMPS mail
list"_http://lammps.sandia.gov/mail.html.

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Basic build options
===================
The following topics are covered on this page, for building both with
CMake and make:
* :ref:`Serial vs parallel build <serial>`
* :ref:`Choice of compiler and compile/link options <compile>`
* :ref:`Build LAMMPS as an executable or a library <exe>`
* :ref:`Build the LAMMPS documentation <doc>`
* :ref:`Install LAMMPS after a build <install>`
----------
.. _serial:
Serial vs parallel build
-------------------------------------
LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
library. Or it can built to run on a single processor (serial)
without MPI. It can also be built with support for OpenMP threading
(see more discussion below).
**CMake variables**\ :
.. parsed-literal::
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no (default)
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
The executable created by CMake (after running make) is lmp\_name. If
the LAMMPS\_MACHINE variable is not specified, the executable is just
lmp. Using BUILD\_MPI=no will produce a serial executable.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal::
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
For a parallel build, if MPI is installed on your system in the usual
place (e.g. under /usr/local), you do not need to specify the 3
variables MPI\_INC, MPI\_PATH, MPI\_LIB. The MPI wrapper on the compiler
(e.g. mpicxx, mpiCC) knows where to find the needed include and
library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
are found, and the name of the library files (MPI\_LIB).
For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
src/STUBS. You also need to build the STUBS library for your platform
before making LAMMPS itself. A "make serial" build does this for.
Otherwise, type "make mpi-stubs" from the src directory, or "make"
from the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
**CMake and make info**\ :
If you are installing MPI yourself, we recommend MPICH2 from Argonne
National Laboratory or OpenMPI. MPICH can be downloaded from the
`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_. Other MPI packages should also work.
If you are running on a large parallel machine, your system admins or
the vendor should have already installed a version of MPI, which is
likely to be faster than a self-installed MPICH or OpenMPI, so find
out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by
the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
details. The USER-INTEL package also provides OpenMP support (it is
compatible with USER-OMP) and adds vectorization support when compiled
with the Intel compilers on top of that. Also, the KOKKOS package can
be compiled for using OpenMP threading.
However, there are a few commands in LAMMPS that have native OpenMP
support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
USER-DPD packages. In addition some packages support OpenMP threading
indirectly through the libraries they interface to: e.g. LATTE and
USER-COLVARS. See the :doc:`Packages details <Packages_details>` doc
page for more info on these packages and the doc pages for their
respective commands for OpenMP threading info.
For CMake, if you use BUILD\_OMP=yes, you can use these packages and
turn on their native OpenMP support and turn on their native OpenMP
support at run time, by setting the OMP\_NUM\_THREADS environment
variable before you launch LAMMPS.
For building via conventional make, the CCFLAGS and LINKFLAGS
variables in Makefile.machine need to include the compiler flag that
enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
compilers it is -qopenmp. If you are using a different compiler,
please refer to its documentation.
.. _default-none-issues:
**OpenMP Compiler compatibility info**\ :
Some compilers do not fully support the 'default(none)' directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 directives used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all 'default(none)' directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with 'default(shared)'
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
---------------------------------------------------------
The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than
open-source compilers like GNU. On boxes with Intel CPUs, we suggest
trying the `Intel C++ compiler <intel_>`_.
.. _intel: https://software.intel.com/en-us/intel-compilers
On parallel clusters or supercomputers which use "modules" for their
compile/link environments, you can often access different compilers by
simply loading the appropriate module before building LAMMPS.
**CMake variables**\ :
.. parsed-literal::
-D CMAKE_CXX_COMPILER=name # name of C++ compiler
-D CMAKE_C_COMPILER=name # name of C compiler
-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler
-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
.. parsed-literal::
Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
.. note::
When the cmake command completes, it prints info to the screen
as to which compilers it is using, and what flags will be used in the
compilation. Note that if the top-level compiler is mpicxx, it is
simply a wrapper on a real compiler. The underlying compiler info is
what will be listed in the CMake output. You should check to insure
you are using the compiler and optimization flags are the ones you
want.
**Makefile.machine settings**\ :
Parallel build (see src/MAKE/Makefile.mpi):
.. parsed-literal::
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
Serial build (see src/MAKE/Makefile.serial):
.. parsed-literal::
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. You should always use mpicxx or mpiCC for
a parallel build, since these compiler wrappers will include
a variety of settings appropriate for your MPI installation.
.. note::
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
optimization flags that are either required or recommended for optimal
performance. You need to include these in the CCFLAGS and LINKFLAGS
settings above. For details, see the individual package doc pages
listed on the :doc:`Speed packages <Speed_packages>` doc page. Or
examine these files in the src/MAKE/OPTIONS directory. They
correspond to each of the 5 accelerator packages and their hardware
variants:
.. parsed-literal::
Makefile.opt # OPT package
Makefile.omp # USER-OMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-INTEL package for KNLs
Makefile.gpu # GPU package
Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)
Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP)
----------
.. _exe:
Build LAMMPS as an executable or a library
----------------------------------------------------
LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the :doc:`Howto couple <Howto_couple>` doc
page for more info on coupling LAMMPS to other codes. See the
:doc:`Python <Python_head>` doc page for more info on wrapping and
running LAMMPS from Python via its library interface.
**CMake variables**\ :
.. parsed-literal::
-D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default)
-D BUILD_SHARED_LIBS=value # yes or no (default)
-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
Setting BUILD\_EXE=no will not produce an executable. Setting
BUILD\_LIB=yes will produce a static library named liblammps.a.
Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
libraries will be named liblammps\_name.a or liblammps\_name.so instead.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make machine # build LAMMPS executable lmp_machine
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
The two library builds also create generic soft links, named
liblammps.a and liblammps.so, which point to the liblammps\_machine
files.
**CMake and make info**\ :
Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
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, distributed by
Argonne National Lab, as a shared library in the default
/usr/local/lib location:
.. _mpich: http://www-unix.mcs.anl.gov/mpi
.. parsed-literal::
./configure --enable-shared
make
make install
You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
----------
.. _doc:
Build the LAMMPS documentation
----------------------------------------
**CMake variable**\ :
.. parsed-literal::
-D BUILD_DOC=value # yes or no (default)
This will create the HTML doc pages within the CMake build directory.
The reason to do this is if you want to "install" LAMMPS on a system
after the CMake build via "make install", and include the doc pages in
the install.
**Traditional make**\ :
.. parsed-literal::
cd lammps/doc
make html # html doc pages
make pdf # single Manual.pdf file
This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
.. note::
You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
`download page <http://lammps.sandia.gov/download.html>`_.
----------
.. _tools:
Build LAMMPS tools
------------------------------
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make.
**CMake variable**\ :
.. parsed-literal::
-D BUILD_TOOLS=value # yes or no (default)
The generated binaries will also become part of the LAMMPS installation (see below)
**Traditional make**\ :
.. parsed-literal::
cd lammps/tools
make all # build all binaries of tools
make binary2txt # build only binary2txt tool
make chain # build only chain tool
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
----------
.. _install:
Install LAMMPS after a build
------------------------------------------
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
**CMake variable**\ :
.. parsed-literal::
cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
make # perform make after CMake command
make install # perform the installation into prefix
**Traditional make**\ :
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Basic build options :h3
The following topics are covered on this page, for building both with
CMake and make:
"Serial vs parallel build"_#serial
"Choice of compiler and compile/link options"_#compile
"Build LAMMPS as an executable or a library"_#exe
"Build the LAMMPS documentation"_#doc
"Install LAMMPS after a build"_#install :ul
:line
Serial vs parallel build :h4,link(serial)
LAMMPS can be built to run in parallel using the ubiquitous "MPI
(message-passing
interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface
library. Or it can built to run on a single processor (serial)
without MPI. It can also be built with support for OpenMP threading
(see more discussion below).
[CMake variables]:
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no (default)
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value :pre
The executable created by CMake (after running make) is lmp_name. If
the LAMMPS_MACHINE variable is not specified, the executable is just
lmp. Using BUILD_MPI=no will produce a serial executable.
[Traditional make]:
cd lammps/src
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre
Serial build (see src/MAKE/Makefile.serial):
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs :pre
For a parallel build, if MPI is installed on your system in the usual
place (e.g. under /usr/local), you do not need to specify the 3
variables MPI_INC, MPI_PATH, MPI_LIB. The MPI wrapper on the compiler
(e.g. mpicxx, mpiCC) knows where to find the needed include and
library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
are found, and the name of the library files (MPI_LIB).
For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
src/STUBS. You also need to build the STUBS library for your platform
before making LAMMPS itself. A "make serial" build does this for.
Otherwise, type "make mpi-stubs" from the src directory, or "make"
from the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform.
The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
that calls gettimeofday() . If your system doesn't support
gettimeofday() , you'll need to insert code to call another timer.
Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
[CMake and make info]:
If you are installing MPI yourself, we recommend MPICH2 from Argonne
National Laboratory or OpenMPI. MPICH can be downloaded from the
"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.
OpenMPI can be downloaded from the "OpenMPI
site"_http://www.open-mpi.org. Other MPI packages should also work.
If you are running on a large parallel machine, your system admins or
the vendor should have already installed a version of MPI, which is
likely to be faster than a self-installed MPICH or OpenMPI, so find
out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by
the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for
details. The USER-INTEL package also provides OpenMP support (it is
compatible with USER-OMP) and adds vectorization support when compiled
with the Intel compilers on top of that. Also, the KOKKOS package can
be compiled for using OpenMP threading.
However, there are a few commands in LAMMPS that have native OpenMP
support. These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
USER-DPD packages. In addition some packages support OpenMP threading
indirectly through the libraries they interface to: e.g. LATTE and
USER-COLVARS. See the "Packages details"_Packages_details.html doc
page for more info on these packages and the doc pages for their
respective commands for OpenMP threading info.
For CMake, if you use BUILD_OMP=yes, you can use these packages and
turn on their native OpenMP support and turn on their native OpenMP
support at run time, by setting the OMP_NUM_THREADS environment
variable before you launch LAMMPS.
For building via conventional make, the CCFLAGS and LINKFLAGS
variables in Makefile.machine need to include the compiler flag that
enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
compilers it is -qopenmp. If you are using a different compiler,
please refer to its documentation.
[OpenMP Compiler compatibility info]: :link(default-none-issues)
Some compilers do not fully support the 'default(none)' directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 directives used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all 'default(none)' directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with 'default(shared)'
while dropping all 'shared()' directives. The script
'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
this conversion.
:line
Choice of compiler and compile/link options :h4,link(compile)
The choice of compiler and compiler flags can be important for
performance. Vendor compilers can produce faster code than
open-source compilers like GNU. On boxes with Intel CPUs, we suggest
trying the "Intel C++ compiler"_intel.
:link(intel,https://software.intel.com/en-us/intel-compilers)
On parallel clusters or supercomputers which use "modules" for their
compile/link environments, you can often access different compilers by
simply loading the appropriate module before building LAMMPS.
[CMake variables]:
-D CMAKE_CXX_COMPILER=name # name of C++ compiler
-D CMAKE_C_COMPILER=name # name of C compiler
-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre
-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler :pre
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any "accelerator
packages"_Speed_packages.html you have included in the build.
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
in C or Fortran are built with a compiler consistent with the one used
for all the C++ files:
Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre
NOTE: When the cmake command completes, it prints info to the screen
as to which compilers it is using, and what flags will be used in the
compilation. Note that if the top-level compiler is mpicxx, it is
simply a wrapper on a real compiler. The underlying compiler info is
what will be listed in the CMake output. You should check to insure
you are using the compiler and optimization flags are the ones you
want.
[Makefile.machine settings]:
Parallel build (see src/MAKE/Makefile.mpi):
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O :pre
Serial build (see src/MAKE/Makefile.serial):
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O :pre
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. You should always use mpicxx or mpiCC for
a parallel build, since these compiler wrappers will include
a variety of settings appropriate for your MPI installation.
NOTE: If you build LAMMPS with any "accelerator
packages"_Speed_packages.html included, they have specific
optimization flags that are either required or recommended for optimal
performance. You need to include these in the CCFLAGS and LINKFLAGS
settings above. For details, see the individual package doc pages
listed on the "Speed packages"_Speed_packages.html doc page. Or
examine these files in the src/MAKE/OPTIONS directory. They
correspond to each of the 5 accelerator packages and their hardware
variants:
Makefile.opt # OPT package
Makefile.omp # USER-OMP package
Makefile.intel_cpu # USER-INTEL package for CPUs
Makefile.intel_coprocessor # USER-INTEL package for KNLs
Makefile.gpu # GPU package
Makefile.kokkos_cuda_mpi # KOKKOS package for GPUs
Makefile.kokkos_omp # KOKKOS package for CPUs (OpenMP)
Makefile.kokkos_phi # KOKKOS package for KNLs (OpenMP) :pre
:line
Build LAMMPS as an executable or a library :h4,link(exe)
LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the "Howto couple"_Howto_couple.html doc
page for more info on coupling LAMMPS to other codes. See the
"Python"_Python_head.html doc page for more info on wrapping and
running LAMMPS from Python via its library interface.
[CMake variables]:
-D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default)
-D BUILD_SHARED_LIBS=value # yes or no (default)
-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value :pre
Setting BUILD_EXE=no will not produce an executable. Setting
BUILD_LIB=yes will produce a static library named liblammps.a.
Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
libraries will be named liblammps_name.a or liblammps_name.so instead.
[Traditional make]:
cd lammps/src
make machine # build LAMMPS executable lmp_machine
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so :pre
The two library builds also create generic soft links, named
liblammps.a and liblammps.so, which point to the liblammps_machine
files.
[CMake and make info]:
Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
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, distributed by
Argonne National Lab, as a shared library in the default
/usr/local/lib location:
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
./configure --enable-shared
make
make install :pre
You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
:line
Build the LAMMPS documentation :h4,link(doc)
[CMake variable]:
-D BUILD_DOC=value # yes or no (default) :pre
This will create the HTML doc pages within the CMake build directory.
The reason to do this is if you want to "install" LAMMPS on a system
after the CMake build via "make install", and include the doc pages in
the install.
[Traditional make]:
cd lammps/doc
make html # html doc pages
make pdf # single Manual.pdf file :pre
This will create a lammps/doc/html dir with the HTML doc pages so that
you can browse them locally on your system. Type "make" from the
lammps/doc dir to see other options.
NOTE: You can also download a tarball of the documentation for the
current LAMMPS version (HTML and PDF files), from the website
"download page"_http://lammps.sandia.gov/download.html.
:line
Build LAMMPS tools :h4,link(tools)
Some tools described in "Auxiliary tools"_Tools.html can be built directly
using CMake or Make.
[CMake variable]:
-D BUILD_TOOLS=value # yes or no (default) :pre
The generated binaries will also become part of the LAMMPS installation (see below)
[Traditional make]:
cd lammps/tools
make all # build all binaries of tools
make binary2txt # build only binary2txt tool
make chain # build only chain tool
make micelle2d # build only micelle2d tool
make thermo_extract # build only thermo_extract tool
:pre
:line
Install LAMMPS after a build :h4,link(install)
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
[CMake variable]:
cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake
make # perform make after CMake command
make install # perform the installation into prefix :pre
[Traditional make]:
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.

179
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View File

@ -1,24 +1,17 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Build LAMMPS with CMake :h3
Build LAMMPS with CMake
=======================
This page is a short summary of how to use CMake to build LAMMPS.
Details on CMake variables that enable specific LAMMPS build options
are given on the pages linked to from the "Build"_Build.html doc page.
are given on the pages linked to from the :doc:`Build <Build>` doc page.
Richard Berger (Temple U) has also written a "more comprehensive
guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start.
:line
----------
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,
@ -26,10 +19,13 @@ 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:
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
cmake \[options ...\] ../cmake # configuration with (command-line) cmake
make # compilation :pre
.. parsed-literal::
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
cmake [options ...] ../cmake # configuration with (command-line) cmake
make # compilation
The cmake command will detect available features, enable selected
packages and options, and will generate the build environment. By default
@ -55,15 +51,20 @@ even more.
After compilation, you may optionally install the LAMMPS executable into
your system with:
make install # optional, copy LAMMPS executable & library elsewhere :pre
.. parsed-literal::
make install # optional, copy LAMMPS executable & library elsewhere
This will install the lammps executable and library (if requested), some
tools (if configured) and additional files like library API headers,
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
tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
to ${HOME}/.local
----------
:line
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
@ -74,7 +75,7 @@ output. See more details on each below.
You can specify a variety of options with any of the 3 versions, which
affect how the build is performed and what is included in the LAMMPS
executable. Links to pages explaining all the options are listed on
the "Build"_Build.html doc page.
the :doc:`Build <Build>` doc page.
You must perform the CMake build system generation and compilation in
a new directory you create. It can be anywhere on your local machine.
@ -85,13 +86,14 @@ separate directory you create. All the auxiliary files created by one
build process (executable, object files, log files, etc) are stored in
this directory or sub-directories within it that CMake creates.
NOTE: To perform a CMake build, no packages can be installed or a
build been previously attempted in the LAMMPS src directory by using
"make" commands to "perform a conventional LAMMPS
build"_Build_make.html. CMake detects if this is the case and
generates an error, telling you to type "make no-all purge" in the src
directory to un-install all packages. The purge removes all the *.h
files auto-generated by make.
.. note::
To perform a CMake build, no packages can be installed or a
build been previously attempted in the LAMMPS src directory by using
"make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`. CMake detects if this is the case and
generates an error, telling you to type "make no-all purge" in the src
directory to un-install all packages. The purge removes all the \*.h
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
@ -106,12 +108,17 @@ 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.
:line
[Command-line version of CMake]:
----------
cmake \[options ...\] /path/to/lammps/cmake # build from any dir
cmake \[options ...\] ../cmake # build from lammps/build :pre
**Command-line version of CMake**\ :
.. parsed-literal::
cmake [options ...] /path/to/lammps/cmake # build from any dir
cmake [options ...] ../cmake # build from lammps/build
The cmake command takes one required argument, which is the LAMMPS
cmake directory which contains the CMakeLists.txt file.
@ -119,17 +126,20 @@ 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:
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-G output # style of output CMake generates
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring :pre
.. parsed-literal::
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-G output # style of output CMake generates
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring
All the LAMMPS-specific -D variables that a LAMMPS build supports are
described on the pages linked to from the "Build"_Build.html doc page.
described on the pages linked to from the :doc:`Build <Build>` doc page.
All of these variable names are upper-case and their values are
lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of
lower-case, e.g. -D LAMMPS\_SIZES=smallbig. For boolean values, any of
these forms can be used: yes/no, on/off, 1/0.
On Unix/Linux machines, CMake generates a Makefile by default to
@ -138,12 +148,14 @@ generated via the -G switch, e.g. Visual Studio on a Windows machine,
Xcode on MacOS, or KDevelop on Linux. Type "cmake --help" to see the
"Generator" styles of output your system supports.
NOTE: When CMake runs, it prints configuration info to the screen.
You should review this to verify all the features you requested were
enabled, including packages. You can also see what compilers and
compile options will be used for the build. Any errors in CMake
variable syntax will also be flagged, e.g. mis-typed variable names or
variable values.
.. note::
When CMake runs, it prints configuration info to the screen.
You should review this to verify all the features you requested were
enabled, including packages. You can also see what compilers and
compile options will be used for the build. Any errors in CMake
variable syntax will also be flagged, e.g. mis-typed variable names or
variable values.
CMake creates a CMakeCache.txt file when it runs. This stores all the
settings, so that when running CMake again you can use the current
@ -158,55 +170,76 @@ 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.
:line
[Curses version (terminal-style menu) of CMake]:
----------
ccmake ../cmake :pre
**Curses version (terminal-style menu) of CMake**\ :
.. parsed-literal::
ccmake ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to type [c], for the second you
have to type [g]. You may need to type [c] multiple times, and may be
separately. For the first you have to type **c**\ , for the second you
have to type **g**\ . You may need to type **c** multiple times, and may be
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
in between. Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
more information.
:line
[GUI version of CMake]:
----------
cmake-gui ../cmake :pre
**GUI version of CMake**\ :
.. parsed-literal::
cmake-gui ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to click on the [Configure] button,
for the second you have to click on the [Generate] button. You may
need to click on [Configure] multiple times, and may be required to
separately. For the first you have to click on the **Configure** button,
for the second you have to click on the **Generate** button. You may
need to click on **Configure** multiple times, and may be required to
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
Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
for more information.
:line
[Installing CMake]
----------
**Installing CMake**
Check if your machine already has CMake installed:
which cmake # do you have it?
which cmake3 # version 3 may have this name
cmake --version # what specific version you have :pre
.. parsed-literal::
which cmake # do you have it?
which cmake3 # version 3 may have this name
cmake --version # what specific version you have
On clusters or supercomputers which use environment modules to manage
software packages, do this:
module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name :pre
.. parsed-literal::
module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name
Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
"https://cmake.org/download/"_https://cmake.org/download/.
`https://cmake.org/download/ <https://cmake.org/download/>`_.
Instructions on how to install it on various platforms can be found
"on this page"_https://cmake.org/install/.
`on this page <https://cmake.org/install/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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@ -0,0 +1,120 @@
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
------------------------------------------
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.
.. parsed-literal::
-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:
.. parsed-literal::
make VERBOSE=1
----------
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
-------------------------------------------------------------------------
Compilers such as GCC and Clang support generating binaries which use different
sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
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.
.. parsed-literal::
-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
---------------------------------------
We do extensive regression testing of the LAMMPS code base on a continuous
basis. Some of the logic to do this has been added to the CMake build so
developers can run the tests directly on their workstation.
.. note::
this is incomplete and only represents a small subset of tests that we run
.. parsed-literal::
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
.. parsed-literal::
make test
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the run
faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
.. parsed-literal::
-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:
.. parsed-literal::
make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
.. parsed-literal::
pip install git+https://github.com/gcovr/gcovr.git
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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@ -1,86 +0,0 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Development build options (CMake only) :h3
The CMake build of LAMMPS has a few extra options which are useful during
development, testing or debugging.
:line
Verify compilation flags :h4,link(compilation)
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.
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes :pre
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
make VERBOSE=1 :pre
:line
Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
Compilers such as GCC and Clang support generating binaries which use different
sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
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.
-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
:pre
:line
Code Coverage and Testing :h4,link(testing)
We do extensive regression testing of the LAMMPS code base on a continuous
basis. Some of the logic to do this has been added to the CMake build so
developers can run the tests directly on their workstation.
NOTE: this is incomplete and only represents a small subset of tests that we run
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
:pre
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
make test
:pre
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the run
faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes :pre
This will also add the following targets to generate coverage reports after running the LAMMPS executable:
make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
:pre
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
pip install git+https://github.com/gcovr/gcovr.git :pre
:pre

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@ -1,30 +1,23 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Link LAMMPS as a library to another code :h3
Link LAMMPS as a library to another code
========================================
LAMMPS can be used as a library by another application, including
Python scripts. The files src/library.cpp and library.h define the
C-style API for using LAMMPS as a library. See the "Howto
library"_Howto_library.html doc page for a description of the
C-style API for using LAMMPS as a library. See the :doc:`Howto library <Howto_library>` doc page for a description of the
interface and how to extend it for your needs.
The "Build basics"_Build_basics.html doc page explains how to build
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in one of
these 2 files:
liblammps.so # shared library
liblammps.a # static library
:line
[Link with LAMMPS as a static library]:
----------
**Link with LAMMPS as a static library**\ :
The calling application can link to LAMMPS as a static library with a
link command like this:
@ -34,52 +27,65 @@ g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
The -L argument is the path to where the liblammps.a file is. The
-llammps argument is shorthand for the file liblammps.a.
:line
[Link with LAMMPS as a shared library]:
----------
**Link with LAMMPS as a shared library**\ :
If you wish to link to liblammps.so, the operating system finds shared
libraries to load at run-time using the environment variable
LD_LIBRARY_PATH. To enable this you can do one of two things:
LD\_LIBRARY\_PATH. To enable this you can do one of two things:
(1) Copy the liblammps.so file to a location the system can find it,
such as /usr/local/lib. I.e. a directory already listed in your
LD_LIBRARY_PATH variable. You can type
LD\_LIBRARY\_PATH variable. You can type
printenv LD_LIBRARY_PATH :pre
.. parsed-literal::
printenv LD_LIBRARY_PATH
to see what directories are in that list.
(2) Add the LAMMPS src directory (or the directory you perform CMake
build in) to your LD_LIBRARY_PATH, so that the current version of the
build in) to your LD\_LIBRARY\_PATH, so that the current version of the
shared library is always available to programs that use it.
For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
:line
.. parsed-literal::
[Calling the LAMMPS library]:
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
namespace; you can safely use any of its classes and methods from
within the calling code, as needed.
When used from a C or Fortran program, the library has a simple
C-style interface, provided in src/library.cpp and src/library.h.
See the "Python library"_Python_library.html doc page for a
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the "Howto couple"_Howto_couple.html doc page.
the :doc:`Howto couple <Howto_couple>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

77
doc/src/Build_make.txt → doc/src/Build_make.rst
View File

@ -1,13 +1,5 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Build LAMMPS with make :h3
Build LAMMPS with make
======================
Building LAMMPS with traditional makefiles requires that you have a
Makefile."machine" file appropriate for your system in the src/MAKE,
@ -16,20 +8,22 @@ below). It can include various options for customizing your LAMMPS
build with a number of global compilation options and features.
To include LAMMPS packages (i.e. optional commands and styles) you
must install them first, as discussed on the "Build
package"_Build_package.html doc page. If the packages require
must install them first, as discussed on the :doc:`Build package <Build_package>` doc page. If the packages require
provided or external libraries, you must build those libraries before
building LAMMPS. Building "LAMMPS with CMake"_Build_cmake.html can
building LAMMPS. Building :doc:`LAMMPS with CMake <Build_cmake>` can
automate all of this for many types of machines, especially
workstations, desktops and laptops, so we suggest you try it first.
These commands perform a default LAMMPS build, producing the LAMMPS
executable lmp_serial or lmp_mpi in lammps/src:
executable lmp\_serial or lmp\_mpi in lammps/src:
cd lammps/src
make serial # build a serial LAMMPS executable
make mpi # build a parallel LAMMPS executable with MPI
make # see a variety of make options :pre
.. parsed-literal::
cd lammps/src
make serial # build a serial LAMMPS executable
make mpi # build a parallel LAMMPS executable with MPI
make # see a variety of make options
This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
@ -46,20 +40,27 @@ executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
re-compiled.
NOTE: When you build LAMMPS for the first time, a long list of *.d
files will be printed out rapidly. This is not an error; it is the
Makefile doing its normal creation of dependencies.
.. note::
When you build LAMMPS for the first time, a long list of \*.d
files will be printed out rapidly. This is not an error; it is the
Makefile doing its normal creation of dependencies.
----------
:line
The lammps/src/MAKE tree contains all the Makefile.machine files
included in the LAMMPS distribution. Typing "make machine" uses
Makefile.machine. Thus the "make serial" or "make mpi" lines above
use Makefile.serial and Makefile.mpi. Others are in these dirs:
OPTIONS # Makefiles which enable specific options
MACHINES # Makefiles for specific machines
MINE # customized Makefiles you create (you may need to create this folder) :pre
.. parsed-literal::
OPTIONS # Makefiles which enable specific options
MACHINES # Makefiles for specific machines
MINE # customized Makefiles you create (you may need to create this folder)
Typing "make" lists all the available Makefile.machine files. A file
with the same name can appear in multiple folders (not a good idea).
@ -74,12 +75,20 @@ customized machine Makefile are contributed by users. Since both
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make intel_cpu # build with the USER-INTEL package optimized for CPUs
make knl # build with the USER-INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs
make omp # build with the USER-OMP package optimized for OpenMP
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs :pre
.. parsed-literal::
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make intel_cpu # build with the USER-INTEL package optimized for CPUs
make knl # build with the USER-INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs
make omp # build with the USER-OMP package optimized for OpenMP
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

265
doc/src/Build_package.rst Normal file
View File

@ -0,0 +1,265 @@
Include packages in build
=========================
In LAMMPS, a package is a group of files that enable a specific set of
features. For example, force fields for molecular systems or
rigid-body constraints are in packages. In the src directory, each
package is a sub-directory with the package name in capital letters.
An overview of packages is given on the :doc:`Packages <Packages>` doc
page. Brief overviews of each package are on the :doc:`Packages details <Packages_details>` doc page.
When building LAMMPS, you can choose to include or exclude each
package. In general there is no need to include a package if you
never plan to use its features.
If you get a run-time error that a LAMMPS command or style is
"Unknown", it is often because the command is contained in a package,
and your build did not include that package. Running LAMMPS with the
:doc:`-h command-line switch <Run_options>` will print all the included
packages and commands for that executable.
For the majority of packages, if you follow the single step below to
include it, you can then build LAMMPS exactly the same as you would
without any packages installed. A few packages may require additional
steps, as explained on the :doc:`Build extras <Build_extras>` doc page.
These links take you to the extra instructions for those select
packages:
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
The mechanism for including packages is simple but different for CMake
versus make.
**CMake variables**\ :
.. parsed-literal::
-D PKG_NAME=value # yes or no (default)
Examples:
.. parsed-literal::
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes
All standard and user packages are included the same way. Note that
USER packages have a hyphen between USER and the rest of the package
name, not an underscore.
See the shortcut section below for how to install many packages at
once with CMake.
.. note::
If you toggle back and forth between building with CMake vs
make, no packages in the src directory can be installed when you
invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
**Traditional make**\ :
.. parsed-literal::
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # un-install a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
.. parsed-literal::
make no-rigid
make yes-user-intel
All standard and user packages are included the same way.
See the shortcut section below for how to install many packages at
once with make.
.. note::
You must always re-build LAMMPS (via make) after installing or
un-installing a package, for the action to take effect.
.. note::
You cannot install or un-install packages and build LAMMPS in a
single make command with multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody.
**CMake and make info**\ :
Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived
from files in other packages. LAMMPS checks for this and does the
right thing. Individual files are only included if their dependencies
are already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
When you download a LAMMPS tarball or download LAMMPS source files
from the Git or SVN repositories, no packages are pre-installed in the
src directory.
.. note::
Prior to Aug 2018, if you downloaded a tarball, 3 packages
(KSPACE, MANYBODY, MOLECULE) were pre-installed in the 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,
CMake allows initializing the variable cache using script files. These
are regular CMake files which can manipulate and set variables, and
can also contain control flow constructs.
LAMMPS includes several of these files to define configuration
"presets", similar to the options that exist for the Make based
system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs.
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/all\_on.cmake [OPTIONS] ../cmake | enable all packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake | enable just a few core packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake | enable most common packages |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake | disable packages that do require extra libraries or tools |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake | change settings to use the Clang compilers by default |
+-------------------------------------------------------------+-----------------------------------------------------------+
| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake | enable all packages compatible with MinGW compilers |
+-------------------------------------------------------------+-----------------------------------------------------------+
.. note::
Running cmake this way manipulates the variable cache in your
current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running
cmake with new flags.
**Example:**
.. parsed-literal::
# build LAMMPS with most commonly used packages, but then remove
# those requiring additional library or tools, but still enable
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on .
# to reset the package selection from above to the default of no packages
# 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
and their installation when building LAMMPS via traditional make.
Just type "make" in lammps/src to see a one-line summary.
These commands install/un-install sets of packages:
+-----------------------------------+-----------------------------------------------------+
| make yes-all | install all packages |
+-----------------------------------+-----------------------------------------------------+
| make no-all | un-install all packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-standard or make yes-std | install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make no-standard or make no-std | un-install standard packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-user | install user packages |
+-----------------------------------+-----------------------------------------------------+
| make no-user | un-install user packages |
+-----------------------------------+-----------------------------------------------------+
| make yes-lib | install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-lib | un-install packages that require extra libraries |
+-----------------------------------+-----------------------------------------------------+
| make yes-ext | install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
| make no-ext | un-install packages that require external libraries |
+-----------------------------------+-----------------------------------------------------+
which install/un-install various sets of packages. Typing "make
package" will list all the these commands.
.. note::
Installing or un-installing a package works by simply copying
files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are included or excluded when LAMMPS is built.
The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally
need to use these commands unless you are editing LAMMPS files or are
:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
site.
Type "make package-status" or "make ps" to show which packages are
currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
Type "make package-installed" or "make pi" to show which packages are
currently installed, without listing the status of packages that are
not installed.
Type "make package-update" or "make pu" to overwrite src files with
files from the package sub-directories if the package is installed.
It should be used after a :doc:`patch has been applied <Install_patch>`,
since patches only update the files in the package sub-directory, but
not the src files.
Type "make package-overwrite" to overwrite files in the package
sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

240
doc/src/Build_package.txt
View File

@ -1,240 +0,0 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Include packages in build :h3
In LAMMPS, a package is a group of files that enable a specific set of
features. For example, force fields for molecular systems or
rigid-body constraints are in packages. In the src directory, each
package is a sub-directory with the package name in capital letters.
An overview of packages is given on the "Packages"_Packages.html doc
page. Brief overviews of each package are on the "Packages
details"_Packages_details.html doc page.
When building LAMMPS, you can choose to include or exclude each
package. In general there is no need to include a package if you
never plan to use its features.
If you get a run-time error that a LAMMPS command or style is
"Unknown", it is often because the command is contained in a package,
and your build did not include that package. Running LAMMPS with the
"-h command-line switch"_Run_options.html will print all the included
packages and commands for that executable.
For the majority of packages, if you follow the single step below to
include it, you can then build LAMMPS exactly the same as you would
without any packages installed. A few packages may require additional
steps, as explained on the "Build extras"_Build_extras.html doc page.
These links take you to the extra instructions for those select
packages:
"COMPRESS"_Build_extras.html#compress,
"GPU"_Build_extras.html#gpu,
"KIM"_Build_extras.html#kim,
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MESSAGE"_Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
"PYTHON"_Build_extras.html#python,
"VORONOI"_Build_extras.html#voronoi,
"USER-ADIOS"_Build_extras.html#user-adios,
"USER-ATC"_Build_extras.html#user-atc,
"USER-AWPMD"_Build_extras.html#user-awpmd,
"USER-COLVARS"_Build_extras.html#user-colvars,
"USER-H5MD"_Build_extras.html#user-h5md,
"USER-INTEL"_Build_extras.html#user-intel,
"USER-MOLFILE"_Build_extras.html#user-molfile,
"USER-NETCDF"_Build_extras.html#user-netcdf,
"USER-PLUMED"_Build_extras.html#user-plumed,
"USER-OMP"_Build_extras.html#user-omp,
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
"USER-SCAFACOS"_Build_extras.html#user-scafacos,
"USER-SMD"_Build_extras.html#user-smd,
"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
The mechanism for including packages is simple but different for CMake
versus make.
[CMake variables]:
-D PKG_NAME=value # yes or no (default) :pre
Examples:
-D PKG_MANYBODY=yes
-D PKG_USER-INTEL=yes :pre
All standard and user packages are included the same way. Note that
USER packages have a hyphen between USER and the rest of the package
name, not an underscore.
See the shortcut section below for how to install many packages at
once with CMake.
NOTE: If you toggle back and forth between building with CMake vs
make, no packages in the src directory can be installed when you
invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
[Traditional make]:
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # un-install a package with name
make mpi # build LAMMPS with whatever packages are now installed :pre
Examples:
make no-rigid
make yes-user-intel :pre
All standard and user packages are included the same way.
See the shortcut section below for how to install many packages at
once with make.
NOTE: You must always re-build LAMMPS (via make) after installing or
un-installing a package, for the action to take effect.
NOTE: You cannot install or un-install packages and build LAMMPS in a
single make command with multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody.
[CMake and make info]:
Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived
from files in other packages. LAMMPS checks for this and does the
right thing. Individual files are only included if their dependencies
are already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
When you download a LAMMPS tarball or download LAMMPS source files
from the Git or SVN repositories, no packages are pre-installed in the
src directory.
NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages
(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
That is no longer the case, so that CMake will build as-is without the
need to un-install those packages.
:line
[CMake shortcuts for installing many packages]:
Instead of specifying all the CMake options via the command-line,
CMake allows initializing the variable cache using script files. These
are regular CMake files which can manipulate and set variables, and
can also contain control flow constructs.
LAMMPS includes several of these files to define configuration
"presets", similar to the options that exist for the Make based
system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs.
cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake |
enable all packages |
cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
disable all packages |
cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
enable just a few core packages |
cmake -C ../cmake/presets/most.cmake \[OPTIONS\] ../cmake |
enable most common packages |
cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake |
disable packages that do require extra libraries or tools |
cmake -C ../cmake/presets/clang.cmake \[OPTIONS\] ../cmake |
change settings to use the Clang compilers by default |
cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake |
enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l)
NOTE: Running cmake this way manipulates the variable cache in your
current build directory. You can combine multiple presets and options
in a single cmake run, or change settings incrementally by running
cmake with new flags.
[Example:]
# build LAMMPS with most commonly used packages, but then remove
# those requiring additional library or tools, but still enable
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on . :pre
# to reset the package selection from above to the default of no packages
# but leaving all other settings untouched. You can run:
cmake -C ../cmake/presets/no_all.cmake . :pre
:line
[Make shortcuts for installing many packages]:
The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.
Just type "make" in lammps/src to see a one-line summary.
These commands install/un-install sets of packages:
make yes-all | install all packages
make no-all | un-install all packages
make yes-standard or make yes-std | install standard packages
make no-standard or make no-std| un-install standard packages
make yes-user | install user packages
make no-user | un-install user packages
make yes-lib | install packages that require extra libraries
make no-lib | un-install packages that require extra libraries
make yes-ext | install packages that require external libraries
make no-ext | un-install packages that require external libraries :tb(s=|,a=l)
which install/un-install various sets of packages. Typing "make
package" will list all the these commands.
NOTE: Installing or un-installing a package works by simply copying
files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are included or excluded when LAMMPS is built.
The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally
need to use these commands unless you are editing LAMMPS files or are
"installing a patch"_Install_patch.html downloaded from the LAMMPS web
site.
Type "make package-status" or "make ps" to show which packages are
currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
Type "make package-installed" or "make pi" to show which packages are
currently installed, without listing the status of packages that are
not installed.
Type "make package-update" or "make pu" to overwrite src files with
files from the package sub-directories if the package is installed.
It should be used after a "patch has been applied"_Install_patch.html,
since patches only update the files in the package sub-directory, but
not the src files.
Type "make package-overwrite" to overwrite files in the package
sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.

495
doc/src/Build_settings.rst Normal file
View File

@ -0,0 +1,495 @@
Optional build settings
=======================
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
| :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
| :ref:`Size of LAMMPS data types <size>`
| :ref:`Read or write compressed files <gzip>`
| :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
| :ref:`Memory allocation alignment <align>`
| :ref:`Workaround for long long integers <longlong>`
| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
|
----------
.. _cxx11:
C++11 standard compliance test
------------------------------------------
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to switch. To determine the impact of requiring C++11,
we have added a simple compliance test to the source code, that will cause
the compilation to abort, if C++11 compliance is not available or enabled.
To bypass this check, you need to change a setting in the makefile or
when calling CMake.
**CMake variable**\ :
.. parsed-literal::
-D DISABLE_CXX11_REQUIREMENT=yes
You can set additional C++ compiler flags (beyond those selected by CMake)
through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
.. parsed-literal::
-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
**Makefile.machine setting**\ to bypass the C++11 test and compile in C++98 mode:
.. parsed-literal::
LMP_INC = -DLAMMPS_CXX98
**Makefile.machine setting**\ to enable the C++11 with older (but not too old) GNU c++ (e.g. on CentOS 7):
.. parsed-literal::
CCFLAGS = -g -O3 -std=c++11
----------
.. _fft:
FFT library
---------------------
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system.
**CMake variables**\ :
.. parsed-literal::
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
.. note::
The values for the FFT variable must be in upper-case. This is
an exception to the rule that all CMake variables can be specified
with lower-case values.
Usually these settings are all that is needed. If FFTW3 is selected,
then CMake will try to detect, if threaded FFTW libraries are available
and enable them by default. This setting is independent of whether
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:
.. parsed-literal::
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
-D FFTW3_LIBRARIES=path # path to FFTW3 libraries
-D FFT_FFTW_THREADS=on # enable using threaded FFTW3 libraries
-D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library
-D MKL_LIBRARIES=path
**Makefile.machine settings**\ :
.. parsed-literal::
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT\_PACK\_ARRAY if not specified
.. parsed-literal::
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier
As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
make can find the FFT header and library files. You must specify
FFT\_LIB with the appropriate FFT libraries to include in the link.
**CMake and make info**\ :
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
of the FFTs and the number of processors used, the other libraries listed
here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run when using the
:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
doc page gives more details. A more detailed (and time consuming)
report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT\_SINGLE
setting trades off a little accuracy for reduced memory use and
parallel communication costs for transposing 3d FFT data.
When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
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.
.. parsed-literal::
make clean
./configure --enable-single; make; make install
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
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
------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
# default is LAMMPS\_SMALLBIG if not specified
**CMake and make info**\ :
The default "smallbig" setting allows for simulations with:
* total atom count = 2\^63 atoms (about 9e18)
* total timesteps = 2\^63 (about 9e18)
* atom IDs = 2\^31 (about 2 billion)
* image flags = roll over at 512
The "bigbig" setting increases the latter two limits. It allows for:
* total atom count = 2\^63 atoms (about 9e18)
* total timesteps = 2\^63 (about 9e18)
* atom IDs = 2\^63 (about 9e18)
* image flags = roll over at about 1 million (2\^20)
The "smallsmall" setting is only needed if your machine does not
support 8-byte integers. It allows for:
* total atom count = 2\^31 atoms (about 2 billion)
* total timesteps = 2\^31 (about 2 billion)
* atom IDs = 2\^31 (about 2 billion)
* image flags = roll over at 512 (2\^9)
Atom IDs are not required for atomic systems which do not store bond
topology information, though IDs are enabled by default. The
:doc:`atom_modify id no <atom_modify>` command will turn them off. Atom
IDs are required for molecular systems with bond topology (bonds,
angles, dihedrals, etc). Thus if you model a molecular system with
more than 2 billion atoms, you need the "bigbig" setting.
Image flags store 3 values per atom which count the number of times an
atom has moved through the periodic box in each dimension. See the
:doc:`dump <dump>` doc page for a discussion. If an atom moves through
the periodic box more than this limit, the value will "roll over",
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.
Note that the USER-ATC package and the USER-INTEL package are currently
not compatible with the "bigbig" setting. Also, there are limitations
when using the library interface. Some functions with known issues
have been replaced by dummy calls printing a corresponding error rather
than crashing randomly or corrupting data.
Also note that the GPU package requires its lib/gpu library to be
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
--------------------------------------------------
The :doc:`dump image <dump_image>` command has options to output JPEG or
PNG image files. Likewise the :doc:`dump movie <dump_image>` command
outputs movie files in MPEG format. Using these options requires the
following settings:
**CMake variables**\ :
.. parsed-literal::
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
.. parsed-literal::
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
**Makefile.machine settings**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
find the graphics header and library files. You must specify JPG\_LIB
with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
i.e. a dir in your PATH environment variable.
**CMake and make info**\ :
Using ffmpeg to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
.. note::
On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using ffmpeg to hang or
crash.
----------
.. _gzip:
Read or write compressed files
-----------------------------------------
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ :
.. parsed-literal::
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_GZIP
**CMake and make info**\ :
This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be
found by LAMMPS during a run.
.. note::
On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which is
what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
----------
.. _align:
Memory allocation alignment
---------------------------------------
This setting enables the use of the posix\_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make
vector instructions on CPUs more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries.
On most current systems, the malloc() implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
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
------------------------------------------------
If your system or MPI version does not recognize "long long" data
types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on
those systems:
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
----------
.. _exceptions:
Exception handling when using LAMMPS as a library
------------------------------------------------------------------
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python.
**CMake variable**\ :
.. parsed-literal::
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
.. parsed-literal::
LMP_INC = -DLAMMPS_EXCEPTIONS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

367
doc/src/Build_settings.txt
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@ -1,367 +0,0 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Optional build settings :h3
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
"Size of LAMMPS data types"_#size
"Read or write compressed files"_#gzip
"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command
"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command
"Memory allocation alignment"_#align
"Workaround for long long integers"_#longlong
"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
:line
C++11 standard compliance test :h4,link(cxx11)
The LAMMPS developers plan to transition to make the C++11 standard the
minimum requirement for compiling LAMMPS. Currently this only applies to
some packages like KOKKOS while the rest aims to be compatible with the C++98
standard. Most currently used compilers are compatible with C++11; some need
to set extra flags to switch. To determine the impact of requiring C++11,
we have added a simple compliance test to the source code, that will cause
the compilation to abort, if C++11 compliance is not available or enabled.
To bypass this check, you need to change a setting in the makefile or
when calling CMake.
[CMake variable]:
-D DISABLE_CXX11_REQUIREMENT=yes
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_CXX98
:line
FFT library :h4,link(fft)
When the KSPACE package is included in a LAMMPS build, the
"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system.
[CMake variables]:
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy :pre
NOTE: The values for the FFT variable must be in upper-case. This is
an exception to the rule that all CMake variables can be specified
with lower-case values.
Usually these settings are all that is needed. If CMake cannot find
the FFT library, you can set these variables:
-D FFTW3_INCLUDE_DIRS=path # path to FFTW3 include files
-D FFTW3_LIBRARIES=path # path to FFTW3 libraries
-D MKL_INCLUDE_DIRS=path # ditto for Intel MKL library
-D MKL_LIBRARIES=path :pre
[Makefile.machine settings]:
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
# default is FFT_PACK_ARRAY if not specified
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre
As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if
make can find the FFT header and library files. You must specify
FFT_LIB with the appropriate FFT libraries to include in the link.
[CMake and make info]:
The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the
size of the FFTs and the number of processors used, the other
libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run using the "kspace_style
pppm"_kspace_style.html command. The "Run output"_Run_output.html
doc page gives more details.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from "www.fftw.org"_http://www.fftw.org. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ./configure; make;
make install. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type "./configure --help" to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see FFT_LIB setting above).
Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT_SINGLE
setting trades off a little accuracy for reduced memory use and
parallel communication costs for transposing 3d FFT data.
When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW
library a second time with support for single-precision.
For FFTW3, do the following, which should produce the additional
library libfftw3f.a
make clean
./configure --enable-single; make; make install :pre
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
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.
:line
Size of LAMMPS data types :h4,link(size)
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
[CMake variable]:
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall :pre
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
# default is LAMMPS_SMALLBIG if not specified
[CMake and make info]:
The default "smallbig" setting allows for simulations with:
total atom count = 2^63 atoms (about 9e18)
total timesteps = 2^63 (about 9e18)
atom IDs = 2^31 (about 2 billion)
image flags = roll over at 512 :ul
The "bigbig" setting increases the latter two limits. It allows for:
total atom count = 2^63 atoms (about 9e18)
total timesteps = 2^63 (about 9e18)
atom IDs = 2^63 (about 9e18)
image flags = roll over at about 1 million (2^20) :ul
The "smallsmall" setting is only needed if your machine does not
support 8-byte integers. It allows for:
total atom count = 2^31 atoms (about 2 billion)
total timesteps = 2^31 (about 2 billion)
atom IDs = 2^31 (about 2 billion)
image flags = roll over at 512 (2^9) :ul
Atom IDs are not required for atomic systems which do not store bond
topology information, though IDs are enabled by default. The
"atom_modify id no"_atom_modify.html command will turn them off. Atom
IDs are required for molecular systems with bond topology (bonds,
angles, dihedrals, etc). Thus if you model a molecular system with
more than 2 billion atoms, you need the "bigbig" setting.
Image flags store 3 values per atom which count the number of times an
atom has moved through the periodic box in each dimension. See the
"dump"_dump.html doc page for a discussion. If an atom moves through
the periodic box more than this limit, the value will "roll over",
e.g. from 511 to -512, which can cause diagnostics like the
mean-squared displacement, as calculated by the "compute
msd"_compute_msd.html command, to be faulty.
Note that the USER-ATC package and the USER-INTEL package are currently
not compatible with the "bigbig" setting. Also, there are limitations
when using the library interface. Some functions with known issues
have been replaced by dummy calls printing a corresponding error rather
than crashing randomly or corrupting data.
Also note that the GPU package requires its lib/gpu library to be
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.
:line
Output of JPG, PNG, and movie files :h4,link(graphics)
The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command
outputs movie files in MPEG format. Using these options requires the
following settings:
[CMake variables]:
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no :pre
Usually these settings are all that is needed. If CMake cannot find
the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file
-D PNG_INCLUDE_DIR=path # path to png.h header file
-D PNG_LIBRARIES=path # path to libpng.a (.so) file
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre
[Makefile.machine settings]:
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG :pre
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names :pre
As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can
find the graphics header and library files. You must specify JPG_LIB
with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
i.e. a dir in your PATH environment variable.
[CMake and make info]:
Using ffmpeg to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
NOTE: On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using ffmpeg to hang or
crash.
:line
Read or write compressed files :h4,link(gzip)
If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html.
[CMake variables]:
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it :pre
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_GZIP :pre
[CMake and make info]:
This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be
found by LAMMPS during a run.
NOTE: On some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which is
what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
:line
Memory allocation alignment :h4,link(align)
This setting enables the use of the posix_memalign() call instead of
malloc() when LAMMPS allocates large chunks or memory. This can make
vector instructions on CPUs more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries.
On most current systems, the malloc() implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries.
[CMake variable]:
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) :pre
Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign()
and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 :pre
Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated
with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot]
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.
:line
Workaround for long long integers :h4,link(longlong)
If your system or MPI version does not recognize "long long" data
types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on
those systems:
[CMake variable]:
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default) :pre
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
:line
Exception handling when using LAMMPS as a library :h4,link(exceptions)
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled LAMMPS errors do not kill the caller.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python.
[CMake variable]:
-D LAMMPS_EXCEPTIONS=value # yes or no (default) :pre
[Makefile.machine setting]:
LMP_INC = -DLAMMPS_EXCEPTIONS :pre

53
doc/src/Build_windows.txt → doc/src/Build_windows.rst
View File

@ -1,22 +1,19 @@
"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
Notes for building LAMMPS on Windows
====================================
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
* :ref:`General remarks <generic>`
* :ref:`Running Linux on Windows <linux>`
* :ref:`Using GNU GCC ported to Windows <gnu>`
* :ref:`Using a cross-compiler <cross>`
:line
Notes for building LAMMPS on Windows :h3
----------
"General remarks"_#generic
"Running Linux on Windows"_#linux
"Using GNU GCC ported to Windows"_#gnu
"Using a cross-compiler"_#cross :ul
:line
.. _generic:
General remarks :h4,link(generic)
General remarks
-----------------------------
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today runs on Linux as well.
@ -26,8 +23,10 @@ providing assistance in resolving portability issues. This particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences with some low-level functionality.
.. _linux:
Running Linux on Windows :h4,link(linux)
Running Linux on Windows
------------------------------------
So before trying to build LAMMPS on Windows, please consider if using
the pre-compiled Windows binary packages are sufficient for your needs
@ -39,10 +38,12 @@ or - if have a recently updated Windows 10 installation - consider using
the Windows subsystem for Linux, which allows to run a bash shell from
Ubuntu and from there on, you can pretty much use that shell like you
are running on an Ubuntu Linux machine (e.g. installing software via
apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
.. _gnu:
Using GNU GCC ported to Windows :h4,link(gnu)
Using GNU GCC ported to Windows
-----------------------------------------
One option for compiling LAMMPS on Windows natively, that has been known
to work in the past is to install a bash shell, unix shell utilities,
@ -54,8 +55,8 @@ and the corresponding new code. A machine makefile for using cygwin for
the old build system is provided. Using CMake for this mode of compilation
is untested and not likely to work.
When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define
in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
flags in LIB makefile variable. Try adding -static-libgcc or -static or
both to the linker flags when your resulting LAMMPS Windows executable
complains about missing .dll files. The CMake configuration should set
@ -67,8 +68,10 @@ requiring changes to the LAMMPS source code, or figure out corrections
yourself, please report them on the lammps-users mailing list, or file
them as an issue or pull request on the LAMMPS GitHub project.
.. _cross:
Using a cross-compiler :h4,link(cross)
Using a cross-compiler
----------------------------------
If you need to provide custom LAMMPS binaries for Windows, but do not
need to do the compilation on Windows, please consider using a Linux
@ -81,8 +84,7 @@ using the mingw32-cmake and mingw64-cmake wrappers that are bundled
with the cross-compiler environment on Fedora machines. A CMake preset
selecting all packages compatible with this cross-compilation build
is provided. You likely need to disable the GPU package unless you
download and install the contents of the pre-compiled "OpenCL ICD loader
library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz
download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
into your MinGW64 cross-compiler environment. The cross-compilation
currently will only produce non-MPI serial binaries.
@ -93,10 +95,17 @@ of these pre-compiled LAMMPS packages for Windows. We will try to resolve
issues to the best of our abilities if we become aware of them. However
this is subject to time constraints and focus on HPC platforms.
.. _native:
Native Visual C++ support :h4,link(native)
Native Visual C++ support
--------------------------------------
Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio
style build environment, but the LAMMPS code itself is not fully ported
to support Visual C++. Volunteers to take on this task are welcome.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

29
doc/src/Commands.rst Normal file
View File

@ -0,0 +1,29 @@
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
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
:maxdepth: 1
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
.. toctree::
:maxdepth: 1
Commands_removed

60
doc/src/Commands.txt
View File

@ -1,60 +0,0 @@
"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html#comm)
:line
Commands :h2
These pages describe how a LAMMPS input script is formatted and the
commands in it are used to define a LAMMPS simulation.
<!-- RST
.. toctree::
:maxdepth: 1
Commands_input
Commands_parse
Commands_structure
Commands_category
.. toctree::
:maxdepth: 1
Commands_all
Commands_fix
Commands_compute
Commands_pair
Commands_bond
Commands_kspace
.. toctree::
:maxdepth: 1
Commands_removed
END_RST -->
<!-- HTML_ONLY -->
"LAMMPS input scripts"_Commands_input.html
"Parsing rules for input scripts"_Commands_parse.html
"Input script structure"_Commands_structure.html
"Commands by category"_Commands_category.html :all(b)
"General commands"_Commands_all.html
"Fix commands"_Commands_fix.html
"Compute commands"_Commands_compute.html
"Pair commands"_Commands_pair.html
"Bond, angle, dihedral, improper commands"_Commands_bond.html
"KSpace solvers"_Commands_kspace.html :all(b)
"Removed commands and packages"_Commands_removed.html :all(b)
<!-- END_HTML_ONLY -->

139
doc/src/Commands_all.rst Normal file
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@ -0,0 +1,139 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
General commands
================
An alphabetic list of all general LAMMPS commands.
.. table_from_list::
:columns: 6
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
* :doc:`bond_coeff <bond_coeff>`
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`
* :doc:`comm_style <comm_style>`
* :doc:`compute <compute>`
* :doc:`compute_modify <compute_modify>`
* :doc:`create_atoms <create_atoms>`
* :doc:`create_bonds <create_bonds>`
* :doc:`create_box <create_box>`
* :doc:`delete_atoms <delete_atoms>`
* :doc:`delete_bonds <delete_bonds>`
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump atom/adios <dump_adios>`
* :doc:`dump custom/adios <dump_adios>`
* :doc:`dump image <dump_image>`
* :doc:`dump movie <dump_image>`
* :doc:`dump netcdf <dump_netcdf>`
* :doc:`dump netcdf/mpiio <dump_netcdf>`
* :doc:`dump vtk <dump_vtk>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`group <group>`
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`if <if>`
* :doc:`improper_coeff <improper_coeff>`
* :doc:`improper_style <improper_style>`
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`
* :doc:`min_style <min_style>`
* :doc:`min_style spin <min_spin>`
* :doc:`molecule <molecule>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`
* :doc:`neb/spin <neb_spin>`
* :doc:`neigh_modify <neigh_modify>`
* :doc:`neighbor <neighbor>`
* :doc:`newton <newton>`
* :doc:`next <next>`
* :doc:`package <package>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`
* :doc:`print <print>`
* :doc:`processors <processors>`
* :doc:`python <python>`
* :doc:`quit <quit>`
* :doc:`read_data <read_data>`
* :doc:`read_dump <read_dump>`
* :doc:`read_restart <read_restart>`
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
* :doc:`run_style <run_style>`
* :doc:`server <server>`
* :doc:`set <set>`
* :doc:`shell <shell>`
* :doc:`special_bonds <special_bonds>`
* :doc:`suffix <suffix>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
* :doc:`temper/grem <temper_grem>`
* :doc:`temper/npt <temper_npt>`
* :doc:`thermo <thermo>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`third_order <third_order>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`
* :doc:`undump <undump>`
* :doc:`unfix <unfix>`
* :doc:`units <units>`
* :doc:`variable <variable>`
* :doc:`velocity <velocity>`
* :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`

138
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@ -1,138 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
General commands :h3
An alphabetic list of all general LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"bond_write"_bond_write.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump adios"_dump_adios.html,
"dump image"_dump_image.html,
"dump movie"_dump_image.html,
"dump netcdf"_dump_netcdf.html,
"dump netcdf/mpiio"_dump_netcdf.html,
"dump vtk"_dump_vtk.html,
"dump_modify"_dump_modify.html,
"dynamical_matrix"_dynamical_matrix.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"group2ndx"_group2ndx.html,
"hyper"_hyper.html,
"if"_if.html,
"info"_info.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kim_init"_kim_commands.html,
"kim_interactions"_kim_commands.html,
"kim_query"_kim_commands.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"min_style spin"_min_spin.html,
"molecule"_molecule.html,
"ndx2group"_group2ndx.html,
"neb"_neb.html,
"neb/spin"_neb_spin.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"python"_python.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_ids"_reset_ids.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"temper/grem"_temper_grem.html,
"temper/npt"_temper_npt.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timer"_timer.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_coeff"_write_coeff.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)

160
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@ -0,0 +1,160 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
.. _bond:
Bond_style potentials
=====================
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles 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
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
* :doc:`oxdna/fene <bond_oxdna>`
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`table (o) <bond_table>`
.. _angle:
Angle_style potentials
======================
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles 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
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
* :doc:`cosine (ko) <angle_cosine>`
* :doc:`cosine/buck6d <angle_cosine_buck6d>`
* :doc:`cosine/delta (o) <angle_cosine_delta>`
* :doc:`cosine/periodic (o) <angle_cosine_periodic>`
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
Dihedral_style potentials
=========================
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
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
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
*
*
*
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`
* :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
* :doc:`nharmonic (o) <dihedral_nharmonic>`
* :doc:`opls (iko) <dihedral_opls>`
* :doc:`quadratic (o) <dihedral_quadratic>`
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
.. _improper:
Improper_style potentials
=========================
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
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
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
*
*
*
*
*
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`
* :doc:`distance <improper_distance>`
* :doc:`distharm <improper_distharm>`
* :doc:`fourier (o) <improper_fourier>`
* :doc:`harmonic (iko) <improper_harmonic>`
* :doc:`inversion/harmonic <improper_inversion_harmonic>`
* :doc:`ring (o) <improper_ring>`
* :doc:`sqdistharm <improper_sqdistharm>`
* :doc:`umbrella (o) <improper_umbrella>`

148
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@ -1,148 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html#bond,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Bond, angle, dihedral, and improper commands :h3
:line
Bond_style potentials :h3,link(bond)
All LAMMPS "bond_style"_bond_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_bond_none.html,
"zero"_bond_zero.html,
"hybrid"_bond_hybrid.html,
,
,
,
,
,
"class2 (ko)"_bond_class2.html,
"fene (iko)"_bond_fene.html,
"fene/expand (o)"_bond_fene_expand.html,
"gromos (o)"_bond_gromos.html,
"harmonic (iko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
"mm3"_bond_mm3.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"oxdna/fene"_bond_oxdna.html,
"oxdna2/fene"_bond_oxdna.html,
"quartic (o)"_bond_quartic.html,
"table (o)"_bond_table.html :tb(c=4,ea=c)
:line
Angle_style potentials :h3,link(angle)
All LAMMPS "angle_style"_angle_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_angle_none.html,
"zero"_angle_zero.html,
"hybrid"_angle_hybrid.html,
,
,
,
,
,
"charmm (iko)"_angle_charmm.html,
"class2 (ko)"_angle_class2.html,
"class2/p6"_angle_class2.html,
"cosine (ko)"_angle_cosine.html,
"cosine/buck6d"_angle_cosine_buck6d.html,
"cosine/delta (o)"_angle_cosine_delta.html,
"cosine/periodic (o)"_angle_cosine_periodic.html,
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"cosine/squared (o)"_angle_cosine_squared.html,
"cross"_angle_cross.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
"mm3"_angle_mm3.html,
"quartic (o)"_angle_quartic.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h3,link(dihedral)
All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_dihedral_none.html,
"zero"_dihedral_zero.html,
"hybrid"_dihedral_hybrid.html,
,
,
,
,
,
"charmm (iko)"_dihedral_charmm.html,
"charmmfsw"_dihedral_charmm.html,
"class2 (ko)"_dihedral_class2.html,
"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
"fourier (io)"_dihedral_fourier.html,
"harmonic (iko)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical"_dihedral_spherical.html,
"table (o)"_dihedral_table.html,
"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line
Improper_style potentials :h3,link(improper)
All LAMMPS "improper_style"_improper_style.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_improper_none.html,
"zero"_improper_zero.html,
"hybrid"_improper_hybrid.html,
,
,
,
,
,
"class2 (ko)"_improper_class2.html,
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
"distharm"_improper_distharm.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"inversion/harmonic"_improper_inversion_harmonic.html,
"ring (o)"_improper_ring.html,
"sqdistharm"_improper_sqdistharm.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

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Commands by category
====================
This page lists most of the LAMMPS commands, grouped by category. The
:doc:`General commands <Commands_all>` doc page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:
* :doc:`newton <newton>`,
* :doc:`package <package>`,
* :doc:`processors <processors>`,
* :doc:`suffix <suffix>`,
* :doc:`units <units>`
Setup simulation box:
* :doc:`boundary <boundary>`,
* :doc:`box <box>`,
* :doc:`change_box <change_box>`,
* :doc:`create_box <create_box>`,
* :doc:`dimension <dimension>`,
* :doc:`lattice <lattice>`,
* :doc:`region <region>`
Setup atoms:
* :doc:`atom_modify <atom_modify>`,
* :doc:`atom_style <atom_style>`,
* :doc:`balance <balance>`,
* :doc:`create_atoms <create_atoms>`,
* :doc:`create_bonds <create_bonds>`,
* :doc:`delete_atoms <delete_atoms>`,
* :doc:`delete_bonds <delete_bonds>`,
* :doc:`displace_atoms <displace_atoms>`,
* :doc:`group <group>`,
* :doc:`mass <mass>`,
* :doc:`molecule <molecule>`,
* :doc:`read_data <read_data>`,
* :doc:`read_dump <read_dump>`,
* :doc:`read_restart <read_restart>`,
* :doc:`replicate <replicate>`,
* :doc:`set <set>`,
* :doc:`velocity <velocity>`
Force fields:
* :doc:`angle_coeff <angle_coeff>`,
* :doc:`angle_style <angle_style>`,
* :doc:`bond_coeff <bond_coeff>`,
* :doc:`bond_style <bond_style>`,
* :doc:`bond_write <bond_write>`,
* :doc:`dielectric <dielectric>`,
* :doc:`dihedral_coeff <dihedral_coeff>`,
* :doc:`dihedral_style <dihedral_style>`,
* :doc:`improper_coeff <improper_coeff>`,
* :doc:`improper_style <improper_style>`,
* :doc:`kspace_modify <kspace_modify>`,
* :doc:`kspace_style <kspace_style>`,
* :doc:`pair_coeff <pair_coeff>`,
* :doc:`pair_modify <pair_modify>`,
* :doc:`pair_style <pair_style>`,
* :doc:`pair_write <pair_write>`,
* :doc:`special_bonds <special_bonds>`
Settings:
* :doc:`comm_modify <comm_modify>`,
* :doc:`comm_style <comm_style>`,
* :doc:`info <info>`,
* :doc:`min_modify <min_modify>`,
* :doc:`min_style <min_style>`,
* :doc:`neigh_modify <neigh_modify>`,
* :doc:`neighbor <neighbor>`,
* :doc:`partition <partition>`,
* :doc:`reset_timestep <reset_timestep>`,
* :doc:`run_style <run_style>`,
* :doc:`timer <timer>`,
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes):
* :doc:`compute <compute>`,
* :doc:`compute_modify <compute_modify>`,
* :doc:`fix <fix>`,
* :doc:`fix_modify <fix_modify>`,
* :doc:`uncompute <uncompute>`,
* :doc:`unfix <unfix>`
Output:
* :doc:`dump image <dump_image>`,
* :doc:`dump movie <dump_image>`,
* :doc:`dump <dump>`,
* :doc:`dump_modify <dump_modify>`,
* :doc:`restart <restart>`,
* :doc:`thermo <thermo>`,
* :doc:`thermo_modify <thermo_modify>`,
* :doc:`thermo_style <thermo_style>`,
* :doc:`undump <undump>`,
* :doc:`write_coeff <write_coeff>`,
* :doc:`write_data <write_data>`,
* :doc:`write_dump <write_dump>`,
* :doc:`write_restart <write_restart>`
Actions:
* :doc:`minimize <minimize>`,
* :doc:`neb <neb>`,
* :doc:`neb_spin <neb_spin>`,
* :doc:`prd <prd>`,
* :doc:`rerun <rerun>`,
* :doc:`run <run>`,
* :doc:`tad <tad>`,
* :doc:`temper <temper>`
Input script control:
* :doc:`clear <clear>`,
* :doc:`echo <echo>`,
* :doc:`if <if>`,
* :doc:`include <include>`,
* :doc:`jump <jump>`,
* :doc:`label <label>`,
* :doc:`log <log>`,
* :doc:`next <next>`,
* :doc:`print <print>`,
* :doc:`python <python>`,
* :doc:`quit <quit>`,
* :doc:`shell <shell>`,
* :doc:`variable <variable>`

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"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Commands by category :h3
This page lists most of the LAMMPS commands, grouped by category. The
"General commands"_Commands_all.html doc page lists all general commands
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:
"newton"_newton.html,
"package"_package.html,
"processors"_processors.html,
"suffix"_suffix.html,
"units"_units.html :ul
Setup simulation box:
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"create_box"_create_box.html,
"dimension"_dimension.html,
"lattice"_lattice.html,
"region"_region.html :ul
Setup atoms:
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"create_atoms"_create_atoms.html,
"create_bonds"_create_bonds.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html,
"group"_group.html,
"mass"_mass.html,
"molecule"_molecule.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"replicate"_replicate.html,
"set"_set.html,
"velocity"_velocity.html :ul
Force fields:
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"bond_write"_bond_write.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"special_bonds"_special_bonds.html :ul
Settings:
"comm_modify"_comm_modify.html,
"comm_style"_comm_style.html,
"info"_info.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"partition"_partition.html,
"reset_timestep"_reset_timestep.html,
"run_style"_run_style.html,
"timer"_timer.html,
"timestep"_timestep.html :ul
Operations within timestepping (fixes) and diagnostics (computes):
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"uncompute"_uncompute.html,
"unfix"_unfix.html :ul
Output:
"dump image"_dump_image.html,
"dump movie"_dump_image.html,
"dump"_dump.html,
"dump_modify"_dump_modify.html,
"restart"_restart.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"undump"_undump.html,
"write_coeff"_write_coeff.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :ul
Actions:
"minimize"_minimize.html,
"neb"_neb.html,
"neb_spin"_neb_spin.html,
"prd"_prd.html,
"rerun"_rerun.html,
"run"_run.html,
"tad"_tad.html,
"temper"_temper.html :ul
Input script control:
"clear"_clear.html,
"echo"_echo.html,
"if"_if.html,
"include"_include.html,
"jump"_jump.html,
"label"_label.html,
"log"_log.html,
"next"_next.html,
"print"_print.html,
"python"_python.html,
"quit"_quit.html,
"shell"_shell.html,
"variable"_variable.html :ul

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.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Compute commands
================
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles 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: 6
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`
* :doc:`aggregate/atom <compute_cluster_atom>`
* :doc:`angle <compute_angle>`
* :doc:`angle/local <compute_angle_local>`
* :doc:`angmom/chunk <compute_angmom_chunk>`
* :doc:`basal/atom <compute_basal_atom>`
* :doc:`body/local <compute_body_local>`
* :doc:`bond <compute_bond>`
* :doc:`bond/local <compute_bond_local>`
* :doc:`centro/atom <compute_centro_atom>`
* :doc:`centroid/stress/atom <compute_stress_atom>`
* :doc:`chunk/atom <compute_chunk_atom>`
* :doc:`chunk/spread/atom <compute_chunk_spread_atom>`
* :doc:`cluster/atom <compute_cluster_atom>`
* :doc:`cna/atom <compute_cna_atom>`
* :doc:`cnp/atom <compute_cnp_atom>`
* :doc:`com <compute_com>`
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom <compute_coord_atom>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
* :doc:`dilatation/atom <compute_dilatation_atom>`
* :doc:`dipole/chunk <compute_dipole_chunk>`
* :doc:`displace/atom <compute_displace_atom>`
* :doc:`dpd <compute_dpd>`
* :doc:`dpd/atom <compute_dpd_atom>`
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
* :doc:`entropy/atom <compute_entropy_atom>`
* :doc:`erotate/asphere <compute_erotate_asphere>`
* :doc:`erotate/rigid <compute_erotate_rigid>`
* :doc:`erotate/sphere <compute_erotate_sphere>`
* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
* :doc:`event/displace <compute_event_displace>`
* :doc:`fep <compute_fep>`
* :doc:`force/tally <compute_tally>`
* :doc:`fragment/atom <compute_cluster_atom>`
* :doc:`global/atom <compute_global_atom>`
* :doc:`group/group <compute_group_group>`
* :doc:`gyration <compute_gyration>`
* :doc:`gyration/chunk <compute_gyration_chunk>`
* :doc:`gyration/shape <compute_gyration_shape>`
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`
* :doc:`improper/local <compute_improper_local>`
* :doc:`inertia/chunk <compute_inertia_chunk>`
* :doc:`ke <compute_ke>`
* :doc:`ke/atom <compute_ke_atom>`
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`
* :doc:`msd/nongauss <compute_msd_nongauss>`
* :doc:`omega/chunk <compute_omega_chunk>`
* :doc:`orientorder/atom <compute_orientorder_atom>`
* :doc:`pair <compute_pair>`
* :doc:`pair/local <compute_pair_local>`
* :doc:`pe <compute_pe>`
* :doc:`pe/atom <compute_pe_atom>`
* :doc:`pe/mol/tally <compute_tally>`
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/cylinder <compute_pressure_cylinder>`
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
* :doc:`property/local <compute_property_local>`
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`rdf <compute_rdf>`
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slice <compute_slice>`
* :doc:`smd/contact/radius <compute_smd_contact_radius>`
* :doc:`smd/damage <compute_smd_damage>`
* :doc:`smd/hourglass/error <compute_smd_hourglass_error>`
* :doc:`smd/internal/energy <compute_smd_internal_energy>`
* :doc:`smd/plastic/strain <compute_smd_plastic_strain>`
* :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>`
* :doc:`smd/rho <compute_smd_rho>`
* :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`
* :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`
* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>`
* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`
* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`
* :doc:`smd/vol <compute_smd_vol>`
* :doc:`snap <compute_sna_atom>`
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/mop <compute_stress_mop>`
* :doc:`stress/mop/profile <compute_stress_mop>`
* :doc:`stress/tally <compute_tally>`
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
* :doc:`temp (k) <compute_temp>`
* :doc:`temp/asphere <compute_temp_asphere>`
* :doc:`temp/body <compute_temp_body>`
* :doc:`temp/chunk <compute_temp_chunk>`
* :doc:`temp/com <compute_temp_com>`
* :doc:`temp/cs <compute_temp_cs>`
* :doc:`temp/deform <compute_temp_deform>`
* :doc:`temp/deform/eff <compute_temp_deform_eff>`
* :doc:`temp/drude <compute_temp_drude>`
* :doc:`temp/eff <compute_temp_eff>`
* :doc:`temp/partial <compute_temp_partial>`
* :doc:`temp/profile <compute_temp_profile>`
* :doc:`temp/ramp <compute_temp_ramp>`
* :doc:`temp/region <compute_temp_region>`
* :doc:`temp/region/eff <compute_temp_region_eff>`
* :doc:`temp/rotate <compute_temp_rotate>`
* :doc:`temp/sphere <compute_temp_sphere>`
* :doc:`temp/uef <compute_temp_uef>`
* :doc:`ti <compute_ti>`
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`

163
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@ -1,163 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Compute commands :h3
An alphabetic list of all LAMMPS "compute"_compute.html commands.
Some styles have accelerated versions. This is indicated by
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
"ackland/atom"_compute_ackland_atom.html,
"adf"_compute_adf.html,
"aggregate/atom"_compute_cluster_atom.html,
"angle"_compute_angle.html,
"angle/local"_compute_angle_local.html,
"angmom/chunk"_compute_angmom_chunk.html,
"basal/atom"_compute_basal_atom.html,
"body/local"_compute_body_local.html,
"bond"_compute_bond.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"chunk/atom"_compute_chunk_atom.html,
"chunk/spread/atom"_compute_chunk_spread_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"cnp/atom"_compute_cnp_atom.html,
"com"_compute_com.html,
"com/chunk"_compute_com_chunk.html,
"contact/atom"_compute_contact_atom.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral"_compute_dihedral.html,
"dihedral/local"_compute_dihedral_local.html,
"dilatation/atom"_compute_dilatation_atom.html,
"dipole/chunk"_compute_dipole_chunk.html,
"displace/atom"_compute_displace_atom.html,
"dpd"_compute_dpd.html,
"dpd/atom"_compute_dpd_atom.html,
"edpd/temp/atom"_compute_edpd_temp_atom.html,
"entropy/atom"_compute_entropy_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/rigid"_compute_erotate_rigid.html,
"erotate/sphere"_compute_erotate_sphere.html,
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
"event/displace"_compute_event_displace.html,
"fep"_compute_fep.html,
"force/tally"_compute_tally.html,
"fragment/atom"_compute_cluster_atom.html,
"global/atom"_compute_global_atom.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/chunk"_compute_gyration_chunk.html,
"gyration/shape"_compute_gyration_shape.html,
"heat/flux"_compute_heat_flux.html,
"heat/flux/tally"_compute_tally.html,
"hexorder/atom"_compute_hexorder_atom.html,
"improper"_compute_improper.html,
"improper/local"_compute_improper_local.html,
"inertia/chunk"_compute_inertia_chunk.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"ke/eff"_compute_ke_eff.html,
"ke/rigid"_compute_ke_rigid.html,
"meso/e/atom"_compute_meso_e_atom.html,
"meso/rho/atom"_compute_meso_rho_atom.html,
"meso/t/atom"_compute_meso_t_atom.html,
"momentum"_compute_momentum.html,
"msd"_compute_msd.html,
"msd/chunk"_compute_msd_chunk.html,
"msd/nongauss"_compute_msd_nongauss.html,
"omega/chunk"_compute_omega_chunk.html,
"orientorder/atom"_compute_orientorder_atom.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pe/mol/tally"_compute_tally.html,
"pe/tally"_compute_tally.html,
"plasticity/atom"_compute_plasticity_atom.html,
"pressure"_compute_pressure.html,
"pressure/cylinder"_compute_pressure_cylinder.html,
"pressure/uef"_compute_pressure_uef.html,
"property/atom"_compute_property_atom.html,
"property/chunk"_compute_property_chunk.html,
"property/local"_compute_property_local.html,
"ptm/atom"_compute_ptm_atom.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/chunk"_compute_reduce_chunk.html,
"reduce/region"_compute_reduce.html,
"rigid/local"_compute_rigid_local.html,
"saed"_compute_saed.html,
"slice"_compute_slice.html,
"smd/contact/radius"_compute_smd_contact_radius.html,
"smd/damage"_compute_smd_damage.html,
"smd/hourglass/error"_compute_smd_hourglass_error.html,
"smd/internal/energy"_compute_smd_internal_energy.html,
"smd/plastic/strain"_compute_smd_plastic_strain.html,
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
"smd/rho"_compute_smd_rho.html,
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
"smd/vol"_compute_smd_vol.html,
"sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,
"spin"_compute_spin.html,
"stress/atom"_compute_stress_atom.html,
"stress/mop"_compute_stress_mop.html,
"stress/mop/profile"_compute_stress_mop.html,
"stress/tally"_compute_tally.html,
"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
"temp (k)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/body"_compute_temp_body.html,
"temp/chunk"_compute_temp_chunk.html,
"temp/com"_compute_temp_com.html,
"temp/cs"_compute_temp_cs.html,
"temp/deform"_compute_temp_deform.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/drude"_compute_temp_drude.html,
"temp/eff"_compute_temp_eff.html,
"temp/partial"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html,
"temp/sphere"_compute_temp_sphere.html,
"temp/uef"_compute_temp_uef.html,
"ti"_compute_ti.html,
"torque/chunk"_compute_torque_chunk.html,
"vacf"_compute_vacf.html,
"vcm/chunk"_compute_vcm_chunk.html,
"voronoi/atom"_compute_voronoi_atom.html,
"xrd"_compute_xrd.html :tb(c=6,ea=c)

242
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.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Fix commands
============
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
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: 6
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
* :doc:`ave/atom <fix_ave_atom>`
* :doc:`ave/chunk <fix_ave_chunk>`
* :doc:`ave/correlate <fix_ave_correlate>`
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`
* :doc:`client/md <fix_client_md>`
* :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>`
* :doc:`controller <fix_controller>`
* :doc:`deform (k) <fix_deform>`
* :doc:`deposit <fix_deposit>`
* :doc:`dpd/energy (k) <fix_dpd_energy>`
* :doc:`drag <fix_drag>`
* :doc:`drude <fix_drude>`
* :doc:`drude/transform/direct <fix_drude_transform>`
* :doc:`drude/transform/inverse <fix_drude_transform>`
* :doc:`dt/reset <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`
* :doc:`eos/cv <fix_eos_cv>`
* :doc:`eos/table <fix_eos_table>`
* :doc:`eos/table/rx (k) <fix_eos_table_rx>`
* :doc:`evaporate <fix_evaporate>`
* :doc:`external <fix_external>`
* :doc:`ffl <fix_ffl>`
* :doc:`filter/corotate <fix_filter_corotate>`
* :doc:`flow/gauss <fix_flow_gauss>`
* :doc:`freeze (k) <fix_freeze>`
* :doc:`gcmc <fix_gcmc>`
* :doc:`gld <fix_gld>`
* :doc:`gle <fix_gle>`
* :doc:`gravity (ko) <fix_gravity>`
* :doc:`grem <fix_grem>`
* :doc:`halt <fix_halt>`
* :doc:`heat <fix_heat>`
* :doc:`hyper/global <fix_hyper_global>`
* :doc:`hyper/local <fix_hyper_local>`
* :doc:`imd <fix_imd>`
* :doc:`indent <fix_indent>`
* :doc:`ipi <fix_ipi>`
* :doc:`langevin (k) <fix_langevin>`
* :doc:`langevin/drude <fix_langevin_drude>`
* :doc:`langevin/eff <fix_langevin_eff>`
* :doc:`langevin/spin <fix_langevin_spin>`
* :doc:`latte <fix_latte>`
* :doc:`lb/fluid <fix_lb_fluid>`
* :doc:`lb/momentum <fix_lb_momentum>`
* :doc:`lb/pc <fix_lb_pc>`
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`meso <fix_meso>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`meso/stationary <fix_meso_stationary>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
* :doc:`msst <fix_msst>`
* :doc:`mvv/dpd <fix_mvv_dpd>`
* :doc:`mvv/edpd <fix_mvv_dpd>`
* :doc:`mvv/tdpd <fix_mvv_dpd>`
* :doc:`neb <fix_neb>`
* :doc:`neb/spin <fix_neb_spin>`
* :doc:`nph (ko) <fix_nh>`
* :doc:`nph/asphere (o) <fix_nph_asphere>`
* :doc:`nph/body <fix_nph_body>`
* :doc:`nph/eff <fix_nh_eff>`
* :doc:`nph/sphere (o) <fix_nph_sphere>`
* :doc:`nphug <fix_nphug>`
* :doc:`npt (iko) <fix_nh>`
* :doc:`npt/asphere (o) <fix_npt_asphere>`
* :doc:`npt/body <fix_npt_body>`
* :doc:`npt/cauchy <fix_npt_cauchy>`
* :doc:`npt/eff <fix_nh_eff>`
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`nve (iko) <fix_nve>`
* :doc:`nve/asphere (i) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
* :doc:`nve/awpmd <fix_nve_awpmd>`
* :doc:`nve/body <fix_nve_body>`
* :doc:`nve/dot <fix_nve_dot>`
* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
* :doc:`nve/eff <fix_nve_eff>`
* :doc:`nve/limit <fix_nve_limit>`
* :doc:`nve/line <fix_nve_line>`
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`nve/noforce <fix_nve_noforce>`
* :doc:`nve/sphere (ko) <fix_nve_sphere>`
* :doc:`nve/spin <fix_nve_spin>`
* :doc:`nve/tri <fix_nve_tri>`
* :doc:`nvk <fix_nvk>`
* :doc:`nvt (iko) <fix_nh>`
* :doc:`nvt/asphere (o) <fix_nvt_asphere>`
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`
* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* :doc:`nvt/sllod (io) <fix_nvt_sllod>`
* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
* :doc:`nvt/sphere (o) <fix_nvt_sphere>`
* :doc:`nvt/uef <fix_nh_uef>`
* :doc:`oneway <fix_oneway>`
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`
* :doc:`pour <fix_pour>`
* :doc:`precession/spin <fix_precession_spin>`
* :doc:`press/berendsen <fix_press_berendsen>`
* :doc:`print <fix_print>`
* :doc:`propel/self <fix_propel_self>`
* :doc:`property/atom (k) <fix_property_atom>`
* :doc:`python/invoke <fix_python_invoke>`
* :doc:`python/move <fix_python_move>`
* :doc:`qbmsst <fix_qbmsst>`
* :doc:`qeq/comb (o) <fix_qeq_comb>`
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`rattle <fix_shake>`
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
* :doc:`reax/c/species (k) <fix_reaxc_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`
* :doc:`rigid/nph (o) <fix_rigid>`
* :doc:`rigid/nph/small <fix_rigid>`
* :doc:`rigid/npt (o) <fix_rigid>`
* :doc:`rigid/npt/small <fix_rigid>`
* :doc:`rigid/nve (o) <fix_rigid>`
* :doc:`rigid/nve/small <fix_rigid>`
* :doc:`rigid/nvt (o) <fix_rigid>`
* :doc:`rigid/nvt/small <fix_rigid>`
* :doc:`rigid/small (o) <fix_rigid>`
* :doc:`rx (k) <fix_rx>`
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`shake <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`
* :doc:`spring/self <fix_spring_self>`
* :doc:`srd <fix_srd>`
* :doc:`store/force <fix_store_force>`
* :doc:`store/state <fix_store_state>`
* :doc:`tdpd/source <fix_dpd_source>`
* :doc:`temp/berendsen <fix_temp_berendsen>`
* :doc:`temp/csld <fix_temp_csvr>`
* :doc:`temp/csvr <fix_temp_csvr>`
* :doc:`temp/rescale <fix_temp_rescale>`
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
* :doc:`tfmc <fix_tfmc>`
* :doc:`thermal/conductivity <fix_thermal_conductivity>`
* :doc:`ti/spring <fix_ti_spring>`
* :doc:`tmd <fix_tmd>`
* :doc:`ttm <fix_ttm>`
* :doc:`ttm/mod <fix_ttm>`
* :doc:`tune/kspace <fix_tune_kspace>`
* :doc:`vector <fix_vector>`
* :doc:`viscosity <fix_viscosity>`
* :doc:`viscous <fix_viscous>`
* :doc:`wall/body/polygon <fix_wall_body_polygon>`
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
* :doc:`wall/colloid <fix_wall>`
* :doc:`wall/ees <fix_wall_ees>`
* :doc:`wall/gran <fix_wall_gran>`
* :doc:`wall/gran/region <fix_wall_gran_region>`
* :doc:`wall/harmonic <fix_wall>`
* :doc:`wall/lj1043 <fix_wall>`
* :doc:`wall/lj126 <fix_wall>`
* :doc:`wall/lj93 (k) <fix_wall>`
* :doc:`wall/morse <fix_wall>`
* :doc:`wall/piston <fix_wall_piston>`
* :doc:`wall/reflect (k) <fix_wall_reflect>`
* :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`

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@ -1,240 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Fix commands :h3
An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles
have accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"adapt"_fix_adapt.html,
"adapt/fep"_fix_adapt_fep.html,
"addforce"_fix_addforce.html,
"addtorque"_fix_addtorque.html,
"append/atoms"_fix_append_atoms.html,
"atc"_fix_atc.html,
"atom/swap"_fix_atom_swap.html,
"ave/atom"_fix_ave_atom.html,
"ave/chunk"_fix_ave_chunk.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
"ave/histo"_fix_ave_histo.html,
"ave/histo/weight"_fix_ave_histo.html,
"ave/time"_fix_ave_time.html,
"aveforce"_fix_aveforce.html,
"balance"_fix_balance.html,
"bocs"_fix_bocs.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/react"_fix_bond_react.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"client/md"_fix_client_md.html,
"cmap"_fix_cmap.html,
"colvars"_fix_colvars.html,
"controller"_fix_controller.html,
"deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html,
"dpd/energy (k)"_fix_dpd_energy.html,
"drag"_fix_drag.html,
"drude"_fix_drude.html,
"drude/transform/direct"_fix_drude_transform.html,
"drude/transform/inverse"_fix_drude_transform.html,
"dt/reset"_fix_dt_reset.html,
"edpd/source"_fix_dpd_source.html,
"efield"_fix_efield.html,
"ehex"_fix_ehex.html,
"electron/stopping"_fix_electron_stopping.html,
"enforce2d (k)"_fix_enforce2d.html,
"eos/cv"_fix_eos_cv.html,
"eos/table"_fix_eos_table.html,
"eos/table/rx (k)"_fix_eos_table_rx.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"ffl"_fix_ffl.html,
"filter/corotate"_fix_filter_corotate.html,
"flow/gauss"_fix_flow_gauss.html,
"freeze (k)"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gle"_fix_gle.html,
"gravity (ko)"_fix_gravity.html,
"grem"_fix_grem.html,
"halt"_fix_halt.html,
"heat"_fix_heat.html,
"hyper/global"_fix_hyper_global.html,
"hyper/local"_fix_hyper_local.html,
"imd"_fix_imd.html,
"indent"_fix_indent.html,
"ipi"_fix_ipi.html,
"langevin (k)"_fix_langevin.html,
"langevin/drude"_fix_langevin_drude.html,
"langevin/eff"_fix_langevin_eff.html,
"langevin/spin"_fix_langevin_spin.html,
"latte"_fix_latte.html,
"lb/fluid"_fix_lb_fluid.html,
"lb/momentum"_fix_lb_momentum.html,
"lb/pc"_fix_lb_pc.html,
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
"lb/viscous"_fix_lb_viscous.html,
"lineforce"_fix_lineforce.html,
"manifoldforce"_fix_manifoldforce.html,
"meso"_fix_meso.html,
"meso/move"_fix_meso_move.html,
"meso/stationary"_fix_meso_stationary.html,
"momentum (k)"_fix_momentum.html,
"move"_fix_move.html,
"mscg"_fix_mscg.html,
"msst"_fix_msst.html,
"mvv/dpd"_fix_mvv_dpd.html,
"mvv/edpd"_fix_mvv_dpd.html,
"mvv/tdpd"_fix_mvv_dpd.html,
"neb"_fix_neb.html,
"neb_spin"_fix_neb_spin.html,
"nph (ko)"_fix_nh.html,
"nph/asphere (o)"_fix_nph_asphere.html,
"nph/body"_fix_nph_body.html,
"nph/eff"_fix_nh_eff.html,
"nph/sphere (o)"_fix_nph_sphere.html,
"nphug (o)"_fix_nphug.html,
"npt (iko)"_fix_nh.html,
"npt/asphere (o)"_fix_npt_asphere.html,
"npt/body"_fix_npt_body.html,
"npt/eff"_fix_nh_eff.html,
"npt/sphere (o)"_fix_npt_sphere.html,
"npt/uef"_fix_nh_uef.html,
"nve (iko)"_fix_nve.html,
"nve/asphere (i)"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/awpmd"_fix_nve_awpmd.html,
"nve/body"_fix_nve_body.html,
"nve/dot"_fix_nve_dot.html,
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"nve/eff"_fix_nve_eff.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere (ko)"_fix_nve_sphere.html,
"nve/spin"_fix_nve_spin.html,
"nve/tri"_fix_nve_tri.html,
"nvk"_fix_nvk.html,
"nvt (iko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
"nvt/body"_fix_nvt_body.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
"nvt/sllod (io)"_fix_nvt_sllod.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"nvt/sphere (o)"_fix_nvt_sphere.html,
"nvt/uef"_fix_nh_uef.html,
"oneway"_fix_oneway.html,
"orient/bcc"_fix_orient.html,
"orient/fcc"_fix_orient.html,
"phonon"_fix_phonon.html,
"pimd"_fix_pimd.html,
"planeforce"_fix_planeforce.html,
"plumed"_fix_plumed.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"precession/spin"_fix_precession_spin.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom (k)"_fix_property_atom.html,
"python/invoke"_fix_python_invoke.html,
"python/move"_fix_python_move.html,
"qbmsst"_fix_qbmsst.html,
"qeq/comb (o)"_fix_qeq_comb.html,
"qeq/dynamic"_fix_qeq.html,
"qeq/fire"_fix_qeq.html,
"qeq/point"_fix_qeq.html,
"qeq/reax (ko)"_fix_qeq_reax.html,
"qeq/shielded"_fix_qeq.html,
"qeq/slater"_fix_qeq.html,
"qmmm"_fix_qmmm.html,
"qtb"_fix_qtb.html,
"rattle"_fix_shake.html,
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
"reax/c/species (k)"_fix_reaxc_species.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rhok"_fix_rhok.html,
"rigid (o)"_fix_rigid.html,
"rigid/meso"_fix_rigid_meso.html,
"rigid/nph (o)"_fix_rigid.html,
"rigid/nph/small"_fix_rigid.html,
"rigid/npt (o)"_fix_rigid.html,
"rigid/npt/small"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nve/small"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
"rigid/nvt/small"_fix_rigid.html,
"rigid/small (o)"_fix_rigid.html,
"rx (k)"_fix_rx.html,
"saed/vtk"_fix_saed_vtk.html,
"setforce (k)"_fix_setforce.html,
"shake"_fix_shake.html,
"shardlow (k)"_fix_shardlow.html,
"smd"_fix_smd.html,
"smd/adjust_dt"_fix_smd_adjust_dt.html,
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
"smd/setvel"_fix_smd_setvel.html,
"smd/wall_surface"_fix_smd_wall_surface.html,
"spring"_fix_spring.html,
"spring/chunk"_fix_spring_chunk.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"tdpd/source"_fix_dpd_source.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/csld"_fix_temp_csvr.html,
"temp/csvr"_fix_temp_csvr.html,
"temp/rescale"_fix_temp_rescale.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"tfmc"_fix_tfmc.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"ti/spring"_fix_ti_spring.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"ttm/mod"_fix_ttm.html,
"tune/kspace"_fix_tune_kspace.html,
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/body/polygon"_fix_wall_body_polygon.html,
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/ees"_fix_wall_ees.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93 (k)"_fix_wall.html,
"wall/morse"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect (k)"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/region/ees"_fix_wall_ees.html,
"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

39
doc/src/Commands_input.txt → doc/src/Commands_input.rst
View File

@ -1,13 +1,5 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
LAMMPS input scripts :h3
LAMMPS input scripts
====================
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
@ -24,15 +16,21 @@ 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:
timestep 0.5
run 100
run 100 :pre
.. code-block:: LAMMPS
timestep 0.5
run 100
run 100
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
.. code-block:: LAMMPS
run 100
timestep 0.5
run 100
In the first case, the specified timestep (0.5 fs) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
@ -47,14 +45,13 @@ belong to the group.
(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
"read_data"_read_data.html command initializes the system by setting
:doc:`read_data <read_data>` command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
values are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read\_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. The "Errors"_Errors.html doc page gives
WARNING message is printed. The :doc:`Errors <Errors>` doc page gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.

39
doc/src/Commands_kspace.rst Normal file
View File

@ -0,0 +1,39 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
KSpace solvers
==============
All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles 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
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`
* :doc:`ewald/dipole <kspace_style>`
* :doc:`ewald/dipole/spin <kspace_style>`
* :doc:`msm (o) <kspace_style>`
* :doc:`msm/cg (o) <kspace_style>`
* :doc:`pppm (giko) <kspace_style>`
* :doc:`pppm/cg (o) <kspace_style>`
* :doc:`pppm/dipole <kspace_style>`
* :doc:`pppm/dipole/spin <kspace_style>`
* :doc:`pppm/disp (io) <kspace_style>`
* :doc:`pppm/disp/tip4p (o) <kspace_style>`
* :doc:`pppm/stagger <kspace_style>`
* :doc:`pppm/tip4p (o) <kspace_style>`
* :doc:`scafacos <kspace_style>`

37
doc/src/Commands_kspace.txt
View File

@ -1,37 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands.html)
:line
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
KSpace solvers :h3
All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"ewald (o)"_kspace_style.html,
"ewald/disp"_kspace_style.html,
"msm (o)"_kspace_style.html,
"msm/cg (o)"_kspace_style.html,
"pppm (gok)"_kspace_style.html,
"pppm/cg (o)"_kspace_style.html,
"pppm/disp (i)"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/stagger"_kspace_style.html,
"pppm/tip4p (o)"_kspace_style.html,
"scafacos"_kspace_style.html :tb(c=4,ea=c)

259
doc/src/Commands_pair.rst Normal file
View File

@ -0,0 +1,259 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Pair_style potentials
======================
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles 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
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
*
*
*
*
* :doc:`adp (o) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
* :doc:`body/nparticle <pair_body_nparticle>`
* :doc:`body/rounded/polygon <pair_body_rounded_polygon>`
* :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`
* :doc:`bop <pair_bop>`
* :doc:`born (go) <pair_born>`
* :doc:`born/coul/dsf <pair_born>`
* :doc:`born/coul/dsf/cs <pair_cs>`
* :doc:`born/coul/long (go) <pair_born>`
* :doc:`born/coul/long/cs (g) <pair_cs>`
* :doc:`born/coul/msm (o) <pair_born>`
* :doc:`born/coul/wolf (go) <pair_born>`
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
* :doc:`brownian (o) <pair_brownian>`
* :doc:`brownian/poly (o) <pair_brownian>`
* :doc:`buck (giko) <pair_buck>`
* :doc:`buck/coul/cut (giko) <pair_buck>`
* :doc:`buck/coul/long (giko) <pair_buck>`
* :doc:`buck/coul/long/cs <pair_cs>`
* :doc:`buck/coul/msm (o) <pair_buck>`
* :doc:`buck/long/coul/long (o) <pair_buck_long>`
* :doc:`buck/mdf <pair_mdf>`
* :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`
* :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`
* :doc:`colloid (go) <pair_colloid>`
* :doc:`comb (o) <pair_comb>`
* :doc:`comb3 <pair_comb>`
* :doc:`cosine/squared <pair_cosine_squared>`
* :doc:`coul/cut (gko) <pair_coul>`
* :doc:`coul/cut/soft (o) <pair_fep_soft>`
* :doc:`coul/debye (gko) <pair_coul>`
* :doc:`coul/diel (o) <pair_coul_diel>`
* :doc:`coul/dsf (gko) <pair_coul>`
* :doc:`coul/long (gko) <pair_coul>`
* :doc:`coul/long/cs (g) <pair_cs>`
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (gio) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (go) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
* :doc:`e3b <pair_e3b>`
* :doc:`drip <pair_drip>`
* :doc:`eam (gikot) <pair_eam>`
* :doc:`eam/alloy (gikot) <pair_eam>`
* :doc:`eam/cd (o) <pair_eam>`
* :doc:`eam/cd/old (o) <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_meso>`
* :doc:`eff/cut <pair_eff>`
* :doc:`eim (o) <pair_eim>`
* :doc:`exp6/rx (k) <pair_exp6_rx>`
* :doc:`extep <pair_extep>`
* :doc:`gauss (go) <pair_gauss>`
* :doc:`gauss/cut (o) <pair_gauss>`
* :doc:`gayberne (gio) <pair_gayberne>`
* :doc:`gran/hertz/history (o) <pair_gran>`
* :doc:`gran/hooke (o) <pair_gran>`
* :doc:`gran/hooke/history (ko) <pair_gran>`
* :doc:`granular <pair_granular>`
* :doc:`gw <pair_gw>`
* :doc:`gw/zbl <pair_gw>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kim <pair_kim>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`list <pair_list>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
* :doc:`lj/class2/coul/long (gko) <pair_class2>`
* :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
* :doc:`lj/class2/soft <pair_fep_soft>`
* :doc:`lj/cubic (go) <pair_lj_cubic>`
* :doc:`lj/cut (gikot) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/msm (go) <pair_lj>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj>`
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/thole/long (o) <pair_thole>`
* :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
* :doc:`lj/cut/tip4p/long (got) <pair_lj>`
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`lj/expand (gko) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
* :doc:`lj/gromacs (gko) <pair_gromacs>`
* :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
* :doc:`lj/long/coul/long (iot) <pair_lj_long>`
* :doc:`lj/long/dipole/long <pair_dipole>`
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`lj96/cut (go) <pair_lj96>`
* :doc:`local/density <pair_local_density>`
* :doc:`lubricate (o) <pair_lubricate>`
* :doc:`lubricate/poly (o) <pair_lubricate>`
* :doc:`lubricateU <pair_lubricateU>`
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_meso>`
* :doc:`mdpd/rhosum <pair_meso>`
* :doc:`meam/c <pair_meamc>`
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`
* :doc:`morse/soft <pair_fep_soft>`
* :doc:`multi/lucy <pair_multi_lucy>`
* :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`
* :doc:`oxdna/coaxstk <pair_oxdna>`
* :doc:`oxdna/excv <pair_oxdna>`
* :doc:`oxdna/hbond <pair_oxdna>`
* :doc:`oxdna/stk <pair_oxdna>`
* :doc:`oxdna/xstk <pair_oxdna>`
* :doc:`oxdna2/coaxstk <pair_oxdna2>`
* :doc:`oxdna2/dh <pair_oxdna2>`
* :doc:`oxdna2/excv <pair_oxdna2>`
* :doc:`oxdna2/hbond <pair_oxdna2>`
* :doc:`oxdna2/stk <pair_oxdna2>`
* :doc:`oxdna2/xstk <pair_oxdna2>`
* :doc:`oxrna2/excv <pair_oxrna2>`
* :doc:`oxrna2/hbond <pair_oxrna2>`
* :doc:`oxrna2/dh <pair_oxrna2>`
* :doc:`oxrna2/stk <pair_oxrna2>`
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
* :doc:`peri/ves <pair_peri>`
* :doc:`polymorphic <pair_polymorphic>`
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smd/hertz <pair_smd_hertz>`
* :doc:`smd/tlsph <pair_smd_tlsph>`
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (k) <pair_snap>`
* :doc:`snap (k) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj <pair_sph_lj>`
* :doc:`sph/rhosum <pair_sph_rhosum>`
* :doc:`sph/taitwater <pair_sph_taitwater>`
* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
* :doc:`spin/dipole/cut <pair_spin_dipole>`
* :doc:`spin/dipole/long <pair_spin_dipole>`
* :doc:`spin/dmi <pair_spin_dmi>`
* :doc:`spin/exchange <pair_spin_exchange>`
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`table (gko) <pair_table>`
* :doc:`table/rx (k) <pair_table_rx>`
* :doc:`tdpd <pair_meso>`
* :doc:`tersoff (giko) <pair_tersoff>`
* :doc:`tersoff/mod (gko) <pair_tersoff_mod>`
* :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`
* :doc:`tersoff/table (o) <pair_tersoff>`
* :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
* :doc:`thole <pair_thole>`
* :doc:`tip4p/cut (o) <pair_coul>`
* :doc:`tip4p/long (o) <pair_coul>`
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

253
doc/src/Commands_pair.txt
View File

@ -1,253 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
"General commands"_Commands_all.html,
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
Pair_style potentials :h3
All LAMMPS "pair_style"_pair_style.html commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
"hybrid (k)"_pair_hybrid.html,
"hybrid/overlay (k)"_pair_hybrid.html,
,
,
,
,
"adp (o)"_pair_adp.html,
"agni (o)"_pair_agni.html,
"airebo (io)"_pair_airebo.html,
"airebo/morse (io)"_pair_airebo.html,
"atm"_pair_atm.html,
"awpmd/cut"_pair_awpmd.html,
"beck (go)"_pair_beck.html,
"body/nparticle"_pair_body_nparticle.html,
"body/rounded/polygon"_pair_body_rounded_polygon.html,
"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,
"born/coul/dsf/cs"_pair_cs.html,
"born/coul/long (go)"_pair_born.html,
"born/coul/long/cs (g)"_pair_cs.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"born/coul/wolf/cs (g)"_pair_cs.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (giko)"_pair_buck.html,
"buck/coul/cut (giko)"_pair_buck.html,
"buck/coul/long (giko)"_pair_buck.html,
"buck/coul/long/cs"_pair_cs.html,
"buck/coul/msm (o)"_pair_buck.html,
"buck/long/coul/long (o)"_pair_buck_long.html,
"buck/mdf"_pair_mdf.html,
"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
"colloid (go)"_pair_colloid.html,
"comb (o)"_pair_comb.html,
"comb3"_pair_comb.html,
"cosine/squared"_pair_cosine_squared.html,
"coul/cut (gko)"_pair_coul.html,
"coul/cut/soft (o)"_pair_fep_soft.html,
"coul/debye (gko)"_pair_coul.html,
"coul/diel (o)"_pair_coul_diel.html,
"coul/dsf (gko)"_pair_coul.html,
"coul/long (gko)"_pair_coul.html,
"coul/long/cs (g)"_pair_cs.html,
"coul/long/soft (o)"_pair_fep_soft.html,
"coul/msm (o)"_pair_coul.html,
"coul/shield"_pair_coul_shield.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"coul/wolf/cs"_pair_cs.html,
"dpd (gio)"_pair_dpd.html,
"dpd/fdt"_pair_dpd_fdt.html,
"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
"dpd/tstat (go)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"e3b"_pair_e3b.html,
"drip"_pair_drip.html,
"eam (gikot)"_pair_eam.html,
"eam/alloy (gikot)"_pair_eam.html,
"eam/cd (o)"_pair_eam.html,
"eam/cd/old (o)"_pair_eam.html,
"eam/fs (gikot)"_pair_eam.html,
"edip (o)"_pair_edip.html,
"edip/multi"_pair_edip.html,
"edpd"_pair_meso.html,
"eff/cut"_pair_eff.html,
"eim (o)"_pair_eim.html,
"exp6/rx (k)"_pair_exp6_rx.html,
"extep"_pair_extep.html,
"gauss (go)"_pair_gauss.html,
"gauss/cut (o)"_pair_gauss.html,
"gayberne (gio)"_pair_gayberne.html,
"gran/hertz/history (o)"_pair_gran.html,
"gran/hooke (o)"_pair_gran.html,
"gran/hooke/history (ko)"_pair_gran.html,
"granular"_pair_granular.html,
"gw"_pair_gw.html,
"gw/zbl"_pair_gw.html,
"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
"kim"_pair_kim.html,
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lcbop"_pair_lcbop.html,
"lebedeva/z"_pair_lebedeva_z.html,
"lennard/mdf"_pair_mdf.html,
"line/lj"_pair_line_lj.html,
"list"_pair_list.html,
"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
"lj/charmm/coul/long (gikot)"_pair_charmm.html,
"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
"lj/charmm/coul/msm (o)"_pair_charmm.html,
"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
"lj/charmmfsw/coul/long"_pair_charmm.html,
"lj/class2 (gko)"_pair_class2.html,
"lj/class2/coul/cut (ko)"_pair_class2.html,
"lj/class2/coul/cut/soft"_pair_fep_soft.html,
"lj/class2/coul/long (gko)"_pair_class2.html,
"lj/class2/coul/long/soft"_pair_fep_soft.html,
"lj/class2/soft"_pair_fep_soft.html,
"lj/cubic (go)"_pair_lj_cubic.html,
"lj/cut (gikot)"_pair_lj.html,
"lj/cut/coul/cut (gko)"_pair_lj.html,
"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
"lj/cut/coul/debye (gko)"_pair_lj.html,
"lj/cut/coul/dsf (gko)"_pair_lj.html,
"lj/cut/coul/long (gikot)"_pair_lj.html,
"lj/cut/coul/long/cs"_pair_cs.html,
"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
"lj/cut/coul/msm (go)"_pair_lj.html,
"lj/cut/coul/wolf (o)"_pair_lj.html,
"lj/cut/dipole/cut (go)"_pair_dipole.html,
"lj/cut/dipole/long (g)"_pair_dipole.html,
"lj/cut/dipole/sf (go)"_pair_dipole.html,
"lj/cut/soft (o)"_pair_fep_soft.html,
"lj/cut/thole/long (o)"_pair_thole.html,
"lj/cut/tip4p/cut (o)"_pair_lj.html,
"lj/cut/tip4p/long (ot)"_pair_lj.html,
"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
"lj/expand (gko)"_pair_lj_expand.html,
"lj/expand/coul/long (g)"_pair_lj_expand.html,
"lj/gromacs (gko)"_pair_gromacs.html,
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
"lj/long/coul/long (iot)"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long (o)"_pair_lj_long.html,
"lj/mdf"_pair_mdf.html,
"lj/sdk (gko)"_pair_sdk.html,
"lj/sdk/coul/long (go)"_pair_sdk.html,
"lj/sdk/coul/msm (o)"_pair_sdk.html,
"lj/sf/dipole/sf (go)"_pair_dipole.html,
"lj/smooth (o)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
"lj96/cut (go)"_pair_lj96.html,
"local/density"_pair_local_density.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"mdpd"_pair_meso.html,
"mdpd/rhosum"_pair_meso.html,
"meam/c"_pair_meamc.html,
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
"mie/cut (g)"_pair_mie.html,
"momb"_pair_momb.html,
"morse (gkot)"_pair_morse.html,
"morse/smooth/linear (o)"_pair_morse.html,
"morse/soft"_pair_fep_soft.html,
"multi/lucy"_pair_multi_lucy.html,
"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut (o)"_pair_nm.html,
"nm/cut/coul/cut (o)"_pair_nm.html,
"nm/cut/coul/long (o)"_pair_nm.html,
"oxdna/coaxstk"_pair_oxdna.html,
"oxdna/excv"_pair_oxdna.html,
"oxdna/hbond"_pair_oxdna.html,
"oxdna/stk"_pair_oxdna.html,
"oxdna/xstk"_pair_oxdna.html,
"oxdna2/coaxstk"_pair_oxdna2.html,
"oxdna2/dh"_pair_oxdna2.html,
"oxdna2/excv"_pair_oxdna2.html,
"oxdna2/hbond"_pair_oxdna2.html,
"oxdna2/stk"_pair_oxdna2.html,
"oxdna2/xstk"_pair_oxdna2.html,
"peri/eps"_pair_peri.html,
"peri/lps (o)"_pair_peri.html,
"peri/pmb (o)"_pair_peri.html,
"peri/ves"_pair_peri.html,
"polymorphic"_pair_polymorphic.html,
"python"_pair_python.html,
"quip"_pair_quip.html,
"reax/c (ko)"_pair_reaxc.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
"smd/hertz"_pair_smd_hertz.html,
"smd/tlsph"_pair_smd_tlsph.html,
"smd/tri_surface"_pair_smd_triangulated_surface.html,
"smd/ulsph"_pair_smd_ulsph.html,
"smtbq"_pair_smtbq.html,
"snap (k)"_pair_snap.html,
"snap (k)"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
"sph/lj"_pair_sph_lj.html,
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"spin/dipole/cut"_pair_spin_dipole.html,
"spin/dipole/long"_pair_spin_dipole.html,
"spin/dmi"_pair_spin_dmi.html,
"spin/exchange"_pair_spin_exchange.html,
"spin/magelec"_pair_spin_magelec.html,
"spin/neel"_pair_spin_neel.html,
"srp"_pair_srp.html,
"sw (giko)"_pair_sw.html,
"table (gko)"_pair_table.html,
"table/rx (k)"_pair_table_rx.html,
"tdpd"_pair_meso.html,
"tersoff (giko)"_pair_tersoff.html,
"tersoff/mod (gko)"_pair_tersoff_mod.html,
"tersoff/mod/c (o)"_pair_tersoff_mod.html,
"tersoff/table (o)"_pair_tersoff.html,
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
"thole"_pair_thole.html,
"tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html,
"tip4p/long/soft (o)"_pair_fep_soft.html,
"tri/lj"_pair_tri_lj.html,
"ufm (got)"_pair_ufm.html,
"vashishta (gko)"_pair_vashishta.html,
"vashishta/table (o)"_pair_vashishta.html,
"yukawa (gko)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

94
doc/src/Commands_parse.txt → doc/src/Commands_parse.rst
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@ -1,13 +1,5 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Parsing rules for input scripts :h3
Parsing rules for input scripts
===============================
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
@ -30,6 +22,10 @@ comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
.. code-block:: LAMMPS
# this is a comment
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
@ -37,11 +33,11 @@ variables that are replaced with a text string. See an exception in
If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
"x".
How the variable is converted to a text string depends on what style
of variable it is; see the "variable"_variable.html doc page for details.
of variable it is; see the :doc:`variable <variable>` doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
@ -50,17 +46,23 @@ will be evaluated and its numeric result returned as a string.
As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an "equal-style variable"_variable.html. This is a way
evaluated as an :doc:`equal-style variable <variable>`. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete :pre
.. code-block:: LAMMPS
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
can be replaced by
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
.. code-block:: LAMMPS
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
so that you do not have to define (or discard) a temporary variable X.
@ -73,21 +75,27 @@ specified a high-precision "%.20g" is used as the default.
This can be useful for formatting print output to a desired precision:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
.. code-block:: LAMMPS
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
variable a equal 2
variable b2 equal 4
print "B2 = $\{b$a\}" :pre
.. code-block:: LAMMPS
variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
"equal-style variable"_variable.html.
you could use $(v\_x-1.0), since the latter is valid syntax for an
:doc:`equal-style variable <variable>`.
See the "variable"_variable.html command for more details of how
See the :doc:`variable <variable>` command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
@ -108,29 +116,33 @@ multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are not
needed. For example:
print "Volume = $v"
print 'Volume = $v'
if "$\{steps\} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
""" :pre
.. code-block:: LAMMPS
print "Volume = $v"
print 'Volume = $v'
if "${steps} > 1000" then quit
variable a string "red green blue &
purple orange cyan"
print """
System volume = $v
System temperature = $t
"""
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
See the "dump modify format"_dump_modify.html, "print"_print.html,
"if"_if.html, and "python"_python.html commands for examples.
See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
:doc:`if <if>`, and :doc:`python <python>` commands for examples.
A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).
NOTE: If the argument is itself a command that requires a quoted
argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
.. note::
If the argument is itself a command that requires a quoted
argument (e.g. using a :doc:`print <print>` command as part of an
:doc:`if <if>` or :doc:`run every <run>` command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.

57
doc/src/Commands_removed.txt → doc/src/Commands_removed.rst
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@ -1,13 +1,5 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands.html)
:line
Removed commands and packages :h3
Removed commands and packages
=============================
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
@ -15,52 +7,61 @@ LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
Fix ave/spatial and fix ave/spatial/sphere :h4
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the "compute chunk/atom"_compute_chunk_atom.html command
and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
MEAM package :h4
MEAM package
------------
The MEAM package has been removed since it was superseded by the
"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. The code in
the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
which removes several restrictions (e.g. there can be multiple instances
in hybrid pair styles) and allows for some optimizations leading
to better performance. The new pair style "meam/c"_pair_meamc.html has
to better performance. The new pair style :doc:`meam/c <pair_meamc>` has
the exact same syntax as the old "meam" pair style and thus pair style
"meam"_pair_meamc.html is an alias to the new style and backward
:doc:`meam <pair_meamc>` is an alias to the new style and backward
compatibility of old inputs is preserved.
REAX package :h4
REAX package
------------
The REAX package has been removed since it was superseded by the
"USER-REAXC package"_Package_details.html#PKG-USER-REAXC. The USER-REAXC
:ref:`USER-REAXC package <PKG-USER-REAXC>`. The USER-REAXC
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via USER-OMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
USER-CUDA package :h4
USER-CUDA package
-----------------
The USER-CUDA package had been removed, since it had been unmaintained
for a long time and had known bugs and problems. Significant parts of
the design were transferred to the
"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
:ref:`KOKKOS package <PKG-KOKKOS>`, which has similar
performance characteristics on Nvidia GPUs. Both, the KOKKOS
and the "GPU package"_Package_details.html#PKG-GPU are maintained
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
restart2data tool :h4
restart2data tool
-----------------
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands "read_restart"_read_restart.html and
"write_data"_write_data.html can be used to the same effect. For added
convenience this conversion can also be triggered by "command line
flags"_Run_options.html
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

86
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@ -0,0 +1,86 @@
Input script structure
======================
This page describes the structure of a typical LAMMPS input script.
The examples directory in the LAMMPS distribution contains many sample
input scripts; it is discussed on the :doc:`Examples <Examples>` doc
page.
A LAMMPS input script typically has 4 parts:
1. Initialization
2. Atom definition
3. Settings
4. Run a simulation
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are :doc:`units <units>`,
:doc:`dimension <dimension>`, :doc:`newton <newton>`,
:doc:`processors <processors>`, :doc:`boundary <boundary>`,
:doc:`atom_style <atom_style>`, :doc:`atom_modify <atom_modify>`.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`,
:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
:doc:`improper_style <improper_style>`.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: :doc:`lattice <lattice>`,
:doc:`region <region>`, :doc:`create_box <create_box>`,
:doc:`create_atoms <create_atoms>`. The entire set of atoms can be
duplicated to make a larger simulation using the
:doc:`replicate <replicate>` command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
:doc:`bond_coeff <bond_coeff>`, :doc:`angle_coeff <angle_coeff>`,
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`improper_coeff <improper_coeff>`,
:doc:`kspace_style <kspace_style>`, :doc:`dielectric <dielectric>`,
:doc:`special_bonds <special_bonds>`.
Various simulation parameters are set by these commands:
:doc:`neighbor <neighbor>`, :doc:`neigh_modify <neigh_modify>`,
:doc:`group <group>`, :doc:`timestep <timestep>`,
:doc:`reset_timestep <reset_timestep>`, :doc:`run_style <run_style>`,
:doc:`min_style <min_style>`, :doc:`min_modify <min_modify>`.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The :doc:`fix <fix>` command comes in many flavors.
Various computations can be specified for execution during a
simulation using the :doc:`compute <compute>`,
:doc:`compute_modify <compute_modify>`, and :doc:`variable <variable>`
commands.
Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
and :doc:`restart <restart>` commands.
(4) Run a simulation
A molecular dynamics simulation is run using the :doc:`run <run>`
command. Energy minimization (molecular statics) is performed using
the :doc:`minimize <minimize>` command. A parallel tempering
(replica-exchange) simulation can be run using the
:doc:`temper <temper>` command.

95
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@ -1,95 +0,0 @@
"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Input script structure :h3
This page describes the structure of a typical LAMMPS input script.
The examples directory in the LAMMPS distribution contains many sample
input scripts; it is discussed on the "Examples"_Examples.html doc
page.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
E & = & E_a + E_{bb} + E_{ba} \\
E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
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)
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K [1 + \cos(\theta)]
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
$$
\end{document}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: t
%%% End:

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\documentclass[12pt]{article}
\begin{document}
$$
E = K [1 - \cos(\theta - \theta_0)]
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
$$
\end{document}

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\documentstyle[12pt]{article}
\begin{document}
$$
E=-U_{min}
\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
\quad\mbox{with}\quad
U(\theta,\theta_0)
=-0.5 \left(1+\cos(\theta-\theta_0) \right)
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K [\cos(\theta) - \cos(\theta_0)]^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
-\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
\vec{F_j} & = & -\vec{F_i} \\
\end{eqnarray*}
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
\cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (\cos\gamma - \cos\gamma_0)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
\vec{r_{ij}} \times \vec{\mu_j}
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K [ 1.0 + c \cos ( n \theta) ]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (\theta - \theta_0)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2
\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^6 \right] + \epsilon
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K (r^2 - r_0^2)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - r_0)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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