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Merge branch 'master' of https://github.com/lammps/lammps into lammps-master

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Jacob Gissinger
2021-04-27 14:46:33 -04:00
parent e21c63192a 3455172f7d
commit 1e294111e7
4905 changed files with 257534 additions and 191333 deletions
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27
doc/src/Build_basics.rst
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@ -1,7 +1,7 @@
Basic build options
===================
The following topics are covered on this page, for building both with
The following topics are covered on this page, for building with both
CMake and make:
* :ref:`Serial vs parallel build <serial>`
@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
.. note::
The file ``src/STUBS/mpi.c`` provides a CPU timer function
The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
called ``MPI_Wtime()`` that calls ``gettimeofday()``. If your
operating system does not support ``gettimeofday()``, you will
need to insert code to call another timer. Note that the
@ -234,14 +234,21 @@ LAMMPS.
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 Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
# Building with PGI/Nvidia Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
For compiling with the Clang/LLVM compilers a CMake preset is
provided that can be loaded with
`-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the compiler
toolchain to the Intel compilers.
toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
will switch to the LLVM based oneAPI Intel compilers,
and `-C ../cmake/presets/pgi.cmake`
will switch the compiler to the PGI compilers.
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By
@ -523,6 +530,20 @@ you want to copy files to is protected.
make # perform make after CMake command
make install # perform the installation into prefix
During the installation process CMake will by default remove any runtime
path settings for loading shared libraries. Because of this you may
have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
environment variable, if you are installing LAMMPS into a non-system
location and/or are linking to libraries in a non-system location that
depend on such runtime path settings.
As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
to ``on`` and then the runtime paths for any linked shared libraries
and the library installation folder for the LAMMPS library will be
embedded and thus the requirement to set environment variables is avoided.
The ``off`` setting is usually preferred for packaged binaries or when
setting up environment modules, the ``on`` setting is more convenient
for installing software into a non-system or personal folder.
.. tab:: Traditional make
There is no "install" option in the ``src/Makefile`` for LAMMPS.

190
doc/src/Build_extras.rst
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@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`MESSAGE <message>`
* :ref:`MLIAP <mliap>`
* :ref:`MSCG <mscg>`
* :ref:`OPT <opt>`
* :ref:`POEMS <poems>`
@ -51,6 +52,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PACE <user-pace>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
@ -119,21 +121,21 @@ CMake build
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_50
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
@ -160,19 +162,32 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
.. code:: bash
# AMDGPU target
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# CUDA target (not recommended, use GPU_ARCH=cuda)
@ -218,11 +233,20 @@ Makefile if desired:
* ``CUDA_PRECISION`` = precision (double, mixed, single)
* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
The file Makefile.linux_multi is set up to include support for multiple
The file Makefile.cuda is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
To enable GPU binning via CUDA performance primitives set the Makefile variable
``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``. This should **not** be used with
most modern GPUs.
To support the CUDA multiprocessor server you can set the define
``-DCUDA_PROXY``. Please note that in this case you must **not** use
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
to empty.
If the library build is successful, 3 files should be created:
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS
@ -249,18 +273,18 @@ To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS.
If you would like to use the :doc:`kim_query <kim_commands>`
If you would like to use the :doc:`kim query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
If you would like to use the :doc:`kim_property <kim_commands>`
If you would like to use the :doc:`kim property <kim_commands>`
command, you need to build LAMMPS with the PYTHON package installed
and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
for more details on this. After successfully building LAMMPS with Python, you
also need to install the kim-property Python package, which can be easily done using
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
information is available at:
also need to install the ``kim-property`` Python package, which can be easily
done using *pip* as ``pip install kim-property``, or from the *conda-forge*
channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
In addition to installing the KIM API, it is also necessary to install the
@ -282,6 +306,7 @@ minutes to hours) to build. Of course you only need to do that once.)
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests, value = no (default) or yes
If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
will be downloaded and built inside the CMake build directory. If
@ -290,11 +315,16 @@ minutes to hours) to build. Of course you only need to do that once.)
``PKG_CONFIG_PATH`` environment variable so that libkim-api can be
found, or run the command ``source kim-api-activate``.
Extra unit tests can only be available if they are explicitly requested
(``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
more details on this.
.. tab:: Traditional make
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src dir, using a command like
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
the specified args.
@ -314,7 +344,7 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: make
LMP_INC = -DLMP_NO_SSL_CHECK
LMP_INC = -DLMP_NO_SSL_CHECK
Debugging OpenKIM web queries in LAMMPS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -338,6 +368,39 @@ specify your own CA cert path by setting the environment variable
``CURL_CA_BUNDLE`` to the path of your choice. A call to the KIM web
query would get this value from the environment variable.
.. _kim_extra_unittests:
KIM Extra unit tests (CMake only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
During development, testing, or debugging, if
:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
Enabling the extra unit tests have some requirements,
* It requires to have internet access.
* It requires to have libcurl installed with the matching development headers
and the curl-config tool.
* It requires to build LAMMPS with the PYTHON package installed and linked to
Python 3.6 or later. See the :ref:`PYTHON package build info <python>` for
more details on this.
* It requires to have ``kim-property`` Python package installed, which can be
easily done using *pip* as ``pip install kim-property``, or from the
*conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
to learn how to install the specific KIM models.
----------
.. _kokkos:
@ -482,11 +545,14 @@ They must be specified in uppercase.
* - VEGA906
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- GPU
- AMD GPU GFX908
* - INTEL_GEN
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.2 of the Kokkos library.
This list was last updated for version 3.3 of the Kokkos library.
.. tabs::
@ -732,6 +798,54 @@ be installed on your system.
----------
.. _mliap:
MLIAP package
---------------------------
Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
package. There will be an error message if this requirement is not satisfied.
Using the *mliappy* model also requires enabling Python support, which
in turn requires the :ref:`PYTHON <PKG-PYTHON>`
package **and** requires you have the `cython <https://cython.org>`_ software
installed and with it a working ``cythonize`` command. This feature requires
compiling LAMMPS with Python version 3.6 or later.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D MLIAP_ENABLE_PYTHON=value # enable mliappy model (default is autodetect)
Without this setting, CMake will check whether it can find a
suitable Python version and the ``cythonize`` command and choose
the default accordingly. During the build procedure the provided
.pyx file(s) will be automatically translated to C++ code and compiled.
Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
as that can lead to compilation errors if Python support is not enabled.
If you did by accident, please remove the generated .cpp and .h files.
.. tab:: Traditional make
The build uses the ``lib/python/Makefile.mliap_python`` file in the
compile/link process to add a rule to update the files generated by
the ``cythonize`` command in case the corresponding .pyx file(s) were
modified. You may need to modify ``lib/python/Makefile.lammps``
if the LAMMPS build fails.
To manually enforce building MLIAP with Python support enabled,
you can add
``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
You may have to manually run the ``cythonize`` command on .pyx file(s)
in the ``src`` folder, if this is not automatically done during
installing the MLIAP package. Please do **not** run ``cythonize``
in the ``src/MLIAP`` folder, as that can lead to compilation errors
if Python support is not enabled.
If you did by accident, please remove the generated .cpp and .h files.
----------
.. _mscg:
MSCG package
@ -1134,6 +1248,46 @@ be built for the most part with all major versions of the C++ language.
----------
.. _user-pace:
USER-PACE package
-----------------------------
This package requires a library that can be downloaded and built
in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
.. tabs::
.. tab:: CMake build
By default the library will be downloaded from the git repository
and built automatically when the USER-PACE package is enabled with
``-D PKG_USER-PACE=yes``. The location for the sources may be
customized by setting the variable ``PACELIB_URL`` when
configuring with CMake (e.g. to use a local archive on machines
without internet access). Since CMake checks the validity of the
archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
if you provide a different library version than what is downloaded
automatically.
.. tab:: Traditional make
You can download and build the USER-PACE library
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.
.. code-block:: bash
$ make lib-pace # print help message
$ make lib-pace args="-b" # download and build the default version in lib/pace
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
----------
.. _user-plumed:
USER-PLUMED package

16
doc/src/Build_link.rst
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@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
.. note::
Care should be taken to use the same MPI library for the calling code
and the LAMMPS library. The ``library.h`` file includes ``mpi.h``
and uses definitions from it so those need to be available and
consistent. When LAMMPS is compiled with the included STUBS MPI
library, then its ``mpi.h`` file needs to be included. While it is
technically possible to use a full MPI library in the calling code
and link to a serial LAMMPS library compiled with MPI STUBS, it is
recommended to use the *same* MPI library for both, and then use
``MPI_Comm_split()`` in the calling code to pass a suitable
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
and the LAMMPS library unless LAMMPS is to be compiled without (real)
MPI support using the include STUBS MPI library.
Link with LAMMPS as a static library
------------------------------------
@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
-llammps_serial -lpoems -lmpi_stubs
@ -174,7 +166,7 @@ the POEMS package installed becomes:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
Locating liblammps.so at runtime

11
doc/src/Build_manual.rst
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@ -74,7 +74,11 @@ For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
that virtual environment via the ``pip`` tool. For rendering embedded
LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
engine needs to be downloaded.
engine needs to be downloaded. If you need to pass additional options
to the pip commands to work (e.g. to use a web proxy or to point to
additional SSL certificates) you can set them via the ``PIP_OPTIONS``
environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
at beginning of the makefile.
The actual translation is then done via ``make`` commands in the doc
folder. The following ``make`` commands are available:
@ -108,7 +112,10 @@ installation of the HTML manual pages into the "install" step when
installing LAMMPS after the CMake build via ``cmake --build . --target
install``. The documentation build is included in the default build
target, but can also be requested independently with
``cmake --build . --target doc``.
``cmake --build . --target doc``. If you need to pass additional options
to the pip commands to work (e.g. to use a web proxy or to point to
additional SSL certificates) you can set them via the ``PIP_OPTIONS``
environment variable.
.. code-block:: bash

23
doc/src/Build_package.rst
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@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` 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>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :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-PACE <user-pace>` | :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.
@ -160,6 +160,7 @@ one of them as a starting point and customize it to your needs.
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross compilers

7
doc/src/Commands_all.rst
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@ -60,11 +60,7 @@ An alphabetic list of all general LAMMPS commands.
* :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_property <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kim <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
@ -90,6 +86,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`plugin <plugin>`
* :doc:`prd <prd>`
* :doc:`print <print>`
* :doc:`processors <processors>`

2
doc/src/Commands_bond.rst
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@ -126,7 +126,7 @@ OPT.
* :doc:`quadratic (o) <dihedral_quadratic>`
* :doc:`spherical <dihedral_spherical>`
* :doc:`table (o) <dihedral_table>`
* :doc:`table/cut <dihedral_table_cut>`
* :doc:`table/cut <dihedral_table>`
.. _improper:

11
doc/src/Commands_fix.rst
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@ -46,6 +46,7 @@ OPT.
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`client/md <fix_client_md>`
* :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>`
@ -114,7 +115,7 @@ OPT.
* :doc:`nph/eff <fix_nh_eff>`
* :doc:`nph/sphere (o) <fix_nph_sphere>`
* :doc:`nphug <fix_nphug>`
* :doc:`npt (iko) <fix_nh>`
* :doc:`npt (giko) <fix_nh>`
* :doc:`npt/asphere (o) <fix_npt_asphere>`
* :doc:`npt/body <fix_npt_body>`
* :doc:`npt/cauchy <fix_npt_cauchy>`
@ -122,8 +123,8 @@ OPT.
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`numdiff <fix_numdiff>`
* :doc:`nve (iko) <fix_nve>`
* :doc:`nve/asphere (i) <fix_nve_asphere>`
* :doc:`nve (giko) <fix_nve>`
* :doc:`nve/asphere (gi) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
* :doc:`nve/awpmd <fix_nve_awpmd>`
* :doc:`nve/body <fix_nve_body>`
@ -138,7 +139,7 @@ OPT.
* :doc:`nve/spin <fix_nve_spin>`
* :doc:`nve/tri <fix_nve_tri>`
* :doc:`nvk <fix_nvk>`
* :doc:`nvt (iko) <fix_nh>`
* :doc:`nvt (giko) <fix_nh>`
* :doc:`nvt/asphere (o) <fix_nvt_asphere>`
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`
@ -221,6 +222,8 @@ OPT.
* :doc:`temp/rescale <fix_temp_rescale>`
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
* :doc:`tfmc <fix_tfmc>`
* :doc:`tgnpt/drude <fix_tgnh_drude>`
* :doc:`tgnvt/drude <fix_tgnh_drude>`
* :doc:`thermal/conductivity <fix_thermal_conductivity>`
* :doc:`ti/spring <fix_ti_spring>`
* :doc:`tmd <fix_tmd>`

11
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@ -26,6 +26,7 @@ OPT.
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
*
@ -33,7 +34,6 @@ OPT.
*
*
*
*
* :doc:`adp (o) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
@ -69,6 +69,7 @@ OPT.
* :doc:`comb3 <pair_comb>`
* :doc:`cosine/squared <pair_cosine_squared>`
* :doc:`coul/cut (gko) <pair_coul>`
* :doc:`coul/cut/global (o) <pair_coul>`
* :doc:`coul/cut/soft (o) <pair_fep_soft>`
* :doc:`coul/debye (gko) <pair_coul>`
* :doc:`coul/diel (o) <pair_coul_diel>`
@ -96,6 +97,7 @@ OPT.
* :doc:`eam/cd <pair_eam>`
* :doc:`eam/cd/old <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`eam/he <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_mesodpd>`
@ -121,7 +123,7 @@ OPT.
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm (giko) <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>`
@ -162,6 +164,7 @@ OPT.
* :doc:`lj/long/dipole/long <pair_dipole>`
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
@ -185,7 +188,7 @@ OPT.
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mliap <pair_mliap>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`
@ -213,6 +216,7 @@ OPT.
* :doc:`oxrna2/stk <pair_oxrna2>`
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace <pair_pace>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -262,6 +266,7 @@ OPT.
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

23
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@ -162,3 +162,26 @@ LAMMPS:
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.
.. admonition:: ASCII versus UTF-8
:class: note
LAMMPS expects and processes 7-bit ASCII format text internally.
Many modern environments use UTF-8 encoding, which is a superset
of the 7-bit ASCII character table and thus mostly compatible.
However, there are several non-ASCII characters that can look
very similar to their ASCII equivalents or are invisible (so they
look like a blank), but are encoded differently. Web browsers,
PDF viewers, document editors are known to sometimes replace one
with the other for a better looking output. However, that can
lead to problems, for instance, when using cut-n-paste of input
file examples from web pages, or when using a document editor
(not a dedicated plain text editor) for writing LAMMPS inputs.
LAMMPS will try to detect this and substitute the non-ASCII
characters with their ASCII equivalents where known. There also
is going to be a warning printed, if this occurs. It is
recommended to avoid such characters altogether in LAMMPS input,
data and potential files. The replacement tables are likely
incomplete and dependent on users reporting problems processing
correctly looking input containing UTF-8 encoded non-ASCII
characters.

2
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@ -13,6 +13,8 @@ of time and requests from the LAMMPS user community.
Developer_org
Developer_flow
Developer_write
Developer_notes
Developer_plugins
Developer_unittest
Classes
Developer_utils

227
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@ -0,0 +1,227 @@
Notes for developers and code maintainers
-----------------------------------------
This section documents how some of the code functionality within
LAMMPS works at a conceptual level. Comments on code in source files
typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs. The topics
on this page are intended to document code functionality at a higher level.
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Fixes can calculate contributions to the instantaneous energy and/or
virial of the system, both in a global and peratom sense. Fixes that
perform thermostatting or barostatting can calculate the cumulative
energy they add to or subtract from the system, which is accessed by
the *ecouple* and *econserve* thermodynamic keywords. This subsection
explains how both work and what flags to set in a new fix to enable
this functionality.
Let's start with thermostatting and barostatting fixes. Examples are
the :doc:`fix langevin <fix_langevin>` and :doc:`fix npt <fix_nh>`
commands. Here is what the fix needs to do:
* Set the variable *ecouple_flag* = 1 in the constructor. Also set
*scalar_flag* = 1, *extscalar* = 1, and *global_freq* to a timestep
increment which matches how often the fix is invoked.
* Implement a compute_scalar() method that returns the cumulative
energy added or subtracted by the fix, e.g. by rescaling the
velocity of atoms. The sign convention is that subtracted energy is
positive, added energy is negative. This must be the total energy
added to the entire system, i.e. an "extensive" quantity, not a
per-atom energy. Cumulative means the summed energy since the fix
was instantiated, even across multiple runs. This is because the
energy is used by the *econserve* thermodynamic keyword to check
that the fix is conserving the total energy of the system,
i.e. potential energy + kinetic energy + coupling energy = a
constant.
And here is how the code operates:
* The Modify class makes a list of all fixes that set *ecouple_flag* = 1.
* The :doc:`thermo_style custom <thermo_style>` command defines
*ecouple* and *econserve* keywords.
* These keywords sum the energy contributions from all the
*ecouple_flag* = 1 fixes by invoking the energy_couple() method in
the Modify class, which calls the compute_scalar() method of each
fix in the list.
------------------
Next, here is how a fix contributes to the instantaneous energy and
virial of the system. First, it sets any or all of these flags to a
value of 1 in their constructor:
* *energy_global_flag* to contribute to global energy, example: :doc:`fix indent <fix_indent>`
* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`
The fix must also do the following:
* For global energy, implement a compute_scalar() method that returns
the energy added or subtracted on this timestep. Here the sign
convention is that added energy is positive, subtracted energy is
negative.
* For peratom energy, invoke the ev_init(eflag,vflag) function each
time the fix is invoked, which initializes per-atom energy storage.
The value of eflag may need to be stored from an earlier call to the
fix during the same timestep. See how the :doc:`fix cmap
<fix_cmap>` command does this in src/MOLECULE/fix_cmap.cpp. When an
energy for one or more atoms is calculated, invoke the ev_tally()
function to tally the contribution to each atom. Both the ev_init()
and ev_tally() methods are in the parent Fix class.
* For global and/or peratom virial, invoke the v_init(vflag) function
each time the fix is invoked, which initializes virial storage.
When forces on one or more atoms are calculated, invoke the
v_tally() function to tally the contribution. Both the v_init() and
v_tally() methods are in the parent Fix class. Note that there are
several variants of v_tally(); choose the one appropriate to your
fix.
.. note::
The ev_init() and ev_tally() methods also account for global and
peratom virial contributions. Thus you do not need to invoke the
v_init() and v_tally() methods, if the fix also calculates peratom
energies.
The fix must also specify whether (by default) to include or exclude
these contributions to the global/peratom energy/virial of the system.
For the fix to include the contributions, set either of both of these
variables in the constructor:
* *thermo_energy* = 1, for global and peratom energy
* *thermo_virial* = 1, for global and peratom virial
Note that these variables are zeroed in fix.cpp. Thus if you don't
set the variables, the contributions will be excluded (by default)
However, the user has ultimate control over whether to include or
exclude the contributions of the fix via the :doc:`fix modify
<fix_modify>` command:
* fix modify *energy yes* to include global and peratom energy contributions
* fix modify *virial yes* to include global and peratom virial contributions
If the fix contributes to any of the global/peratom energy/virial
values for the system, it should be explained on the fix doc page,
along with the default values for the *energy yes/no* and *virial
yes/no* settings of the :doc:`fix modify <fix_modify>` command.
Finally, these 4 contributions are included in the output of 4
computes:
* global energy in :doc:`compute pe <compute_pe>`
* peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
* global virial in :doc:`compute pressure <compute_pressure>`
* peratom virial in :doc:`compute stress/atom <compute_stress_atom>`
These computes invoke a method of the Modify class to include
contributions from fixes that have the corresponding flags set,
e.g. *energy_peratom_flag* and *thermo_energy* for :doc:`compute
pe/atom <compute_pe_atom>`.
Note that each compute has an optional keyword to either include or
exclude all contributions from fixes. Also note that :doc:`compute pe
<compute_pe>` and :doc:`compute pressure <compute_pressure>` are what
is used (by default) by :doc:`thermodynamic output <thermo_style>` to
calculate values for its *pe* and *press* keywords.
KSpace PPPM FFT grids
^^^^^^^^^^^^^^^^^^^^^
The various :doc:`KSpace PPPM <kspace_style>` styles in LAMMPS use
FFTs to solve Poisson's equation. This subsection describes:
* how FFT grids are defined
* how they are decomposed across processors
* how they are indexed by each processor
* how particle charge and electric field values are mapped to/from
the grid
An FFT grid cell is a 3d volume; grid points are corners of a grid
cell and the code stores values assigned to grid points in vectors or
3d arrays. A global 3d FFT grid has points indexed 0 to N-1 inclusive
in each dimension.
Each processor owns two subsets of the grid, each subset is
brick-shaped. Depending on how it is used, these subsets are
allocated as a 1d vector or 3d array. Either way, the ordering of
values within contiguous memory x fastest, then y, z slowest.
For the ``3d decomposition`` of the grid, the global grid is
partitioned into bricks that correspond to the sub-domains of the
simulation box that each processor owns. Often, this is a regular 3d
array (Px by Py by Pz) of bricks, where P = number of processors =
Px * Py * Pz. More generally it can be a tiled decomposition, where
each processor owns a brick and the union of all the bricks is the
global grid. Tiled decompositions are produced by load balancing with
the RCB algorithm; see the :doc:`balance rcb <balance>` command.
For the ``FFT decompostion`` of the grid, each processor owns a brick
that spans the entire x dimension of the grid while the y and z
dimensions are partitioned as a regular 2d array (P1 by P2), where P =
P1 * P2.
The following indices store the inclusive bounds of the brick a
processor owns, within the global grid:
.. parsed-literal::
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
dimension, where N is the grid size.
The ``out`` indices index an array which stores the ``in`` subset of
the grid plus ghost cells that surround it. These indices can thus be
< 0 or >= N.
The number of ghost cells a processor owns in each of the 6 directions
is a function of:
.. parsed-literal::
neighbor skin distance (since atoms can move outside a proc subdomain)
qdist = offset or charge from atom due to TIP4P fictitious charge
order = mapping stencil size
shift = factor used when order is an even number (see below)
Here is an explanation of how the PPPM variables ``order``,
``nlower`` / ``nupper``, ``shift``, and ``OFFSET`` work. They are the
relevant variables that determine how atom charge is mapped to grid
points and how field values are mapped from grid points to atoms:
.. parsed-literal::
order = # of nearby grid points in each dim that atom charge/field are mapped to/from
nlower,nupper = extent of stencil around the grid point an atom is assigned to
OFFSET = large integer added/subtracted when mapping to avoid int(-0.75) = 0 when -1 is the desired result
The particle_map() method assigns each atom to a grid point.
If order is even, say 4:
.. parsed-literal::
atom is assigned to grid point to its left (in each dim)
shift = OFFSET
nlower = -1, nupper = 2, which are offsets from assigned grid point
window of mapping grid pts is thus 2 grid points to left of atom, 2 to right
If order is odd, say 5:
.. parsed-literal::
atom is assigned to left/right grid pt it is closest to (in each dim)
shift = OFFSET + 0.5
nlower = 2, nupper = 2
if point is in left half of cell, then window of affected grid pts is 3 grid points to left of atom, 2 to right
if point is in right half of cell, then window of affected grid pts is 2 grid points to left of atom, 3 to right
These settings apply to each dimension, so that if order = 5, an
atom's charge is mapped to 125 grid points that surround the atom.

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@ -1,68 +1,75 @@
Source files
------------
The source files of the LAMMPS code are found in two
directories of the distribution: ``src`` and ``lib``.
Most of the code is C++ but there are small numbers of files
in several other languages.
The source files of the LAMMPS code are found in two directories of the
distribution: ``src`` and ``lib``. Most of the code is written in C++
but there are small a number of files in several other languages like C,
Fortran, Shell script, or Python.
The core of the code is located in the
``src`` folder and its sub-directories.
A sizable number of these files are in the ``src`` directory
itself, but there are plenty of :doc:`packages <Packages>`, which can be
included or excluded when LAMMPS is built. See the :doc:`Include
packages in build <Build_package>` section of the manual for more
information about that part of the build process. LAMMPS currently
supports building with :doc:`conventional makefiles <Build_make>` and
through :doc:`CMake <Build_cmake>` which differ in how packages are
enabled or disabled for a LAMMPS binary. The source files for each
The core of the code is located in the ``src`` folder and its
sub-directories. A sizable number of these files are in the ``src``
directory itself, but there are plenty of :doc:`packages <Packages>`,
which can be included or excluded when LAMMPS is built. See the
:doc:`Include packages in build <Build_package>` section of the manual
for more information about that part of the build process. LAMMPS
currently supports building with :doc:`conventional makefiles
<Build_make>` and through :doc:`CMake <Build_cmake>`. Those procedures
differ in how packages are enabled or disabled for inclusion into a
LAMMPS binary so they cannot be mixed. The source files for each
package are in all-uppercase sub-directories of the ``src`` folder, for
example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS``
sub-directory is not a package but contains a dummy MPI library, that is
used when building a serial version of the code. The ``src/MAKE``
directory contains makefiles with settings and flags for a variety of
configuration and machines for the build process with traditional
makefiles.
directory and its sub-directories contain makefiles with settings and
flags for a variety of configuration and machines for the build process
with traditional makefiles.
The ``lib`` directory contains the source code for several supporting
libraries or files with configuration settings to use globally installed
libraries, that are required by some of the optional packages.
Each sub-directory, like ``lib/poems`` or ``lib/gpu``, contains the
source files, some of which are in different languages such as Fortran
or CUDA. These libraries are linked to during a LAMMPS build, if the
corresponding package is installed.
libraries, that are required by some of the optional packages. They may
include python scripts that can transparently download additional source
code on request. Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
contains the source files, some of which are in different languages such
as Fortran or CUDA. These libraries included in the LAMMPS build,
if the corresponding package is installed.
LAMMPS C++ source files almost always come in pairs, such as
``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
Each pair of files defines a C++
class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains
the code invoked by the :doc:`run <run>` command in a LAMMPS input script.
As this example illustrates, source file and class names often have a
one-to-one correspondence with a command used in a LAMMPS input script.
Some source files and classes do not have a corresponding input script
Each pair of files defines a C++ class, for example the
:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
:doc:`run <run>` command in a LAMMPS input script. As this example
illustrates, source file and class names often have a one-to-one
correspondence with a command used in a LAMMPS input script. Some
source files and classes do not have a corresponding input script
command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
class. They are discussed in the next section.
A small number of C++ classes and utility functions are implemented with
only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
The names of all source files are in lower case and may use the
underscore character '_' to separate words. Outside of bundled libraries
which may have different conventions, all C and C++ header files have a
``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
``.c`` extension. A small number of C++ classes and utility functions
are implemented with only a ``.h`` file. Examples are the Pointers and
Commands classes or the MathVec functions.
Class topology
--------------
Though LAMMPS has a lot of source files and classes, its class topology
is relative flat, as outlined in the :ref:`class-topology` figure. Each
name refers to a class and has a pair of associated source files in the
``src`` folder, for example the class :cpp:class:`LAMMPS_NS::Memory`
corresponds to the files ``memory.cpp`` and ``memory.h``, or the class
:cpp:class:`LAMMPS_NS::AtomVec` corresponds to the files
``atom_vec.cpp`` and ``atom_vec.h``. Full lines in the figure represent
compositing: that is the class to the left holds a pointer to an
instance of the class to the right. Dashed lines instead represent
inheritance: the class to the right is derived from the class on the
left. Classes with a red boundary are not instantiated directly, but
they represent the base classes for "styles". Those "styles" make up
the bulk of the LAMMPS code and only a few typical examples are included
in the figure for demonstration purposes.
is not very deep, which can be seen from the :ref:`class-topology`
figure. In that figure, each name refers to a class and has a pair of
associated source files in the ``src`` folder, for example the class
:cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``. Full
lines in the figure represent compositing: that is the class at the base
of the arrow holds a pointer to an instance of the class at the tip.
Dashed lines instead represent inheritance: the class to the tip of the
arrow is derived from the class at the base. Classes with a red boundary
are not instantiated directly, but they represent the base classes for
"styles". Those "styles" make up the bulk of the LAMMPS code and only
a few representative examples are included in the figure so it remains
readable.
.. _class-topology:
.. figure:: JPG/lammps-classes.png
@ -82,69 +89,76 @@ in the figure for demonstration purposes.
derived classes, which may also hold instances of other classes.
The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
represents what is referred to an "instance" of LAMMPS. It is a
composite holding references to instances of other core classes
represents what is generally referred to an "instance" of LAMMPS. It is
a composite holding pointers to instances of other core classes
providing the core functionality of the MD engine in LAMMPS and through
them abstractions of the required operations. The constructor of the
LAMMPS class will instantiate those instances, process the command line
flags, initialize MPI (if not already done) and set up file pointers for
input and output. The destructor will shut everything down and free all
input and output. The destructor will shut everything down and free all
associated memory. Thus code for the standalone LAMMPS executable in
``main.cpp`` simply initializes MPI, instantiates a single instance of
LAMMPS, and passes it the command line flags and input script. It
LAMMPS while passing it the command line flags and input script. It
deletes the LAMMPS instance after the method reading the input returns
and shuts down the MPI environment before it exits the executable.
The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
:ref:`class-topology` figure, it holds references to members of the
`LAMMPS_NS::LAMMPS`, so that all classes derived from
:cpp:class:`LAMMPS_NS::Pointers` have direct access to those reference.
From the class topology all classes with blue boundary are referenced in
this class and all classes in the second and third columns, that are not
listed as derived classes are instead derived from
:cpp:class:`LAMMPS_NS::Pointers`.
:ref:`class-topology` figure for clarity. It holds references to many
of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
reference. From the class topology all classes with blue boundary are
referenced in the Pointers class and all classes in the second and third
columns, that are not listed as derived classes are instead derived from
:cpp:class:`LAMMPS_NS::Pointers`. To initialize the pointer references
in Pointers, a pointer to the LAMMPS class instance needs to be passed
to the constructor and thus all constructors for classes derived from it
must do so and pass this pointer to the constructor for Pointers.
Since all storage is encapsulated, the LAMMPS class can also be
instantiated multiple times by a calling code, and that can be either
simultaneously or consecutively. When running in parallel with MPI,
care has to be taken, that suitable communicators are used to not
create conflicts between different instances.
Since all storage is supposed to be encapsulated (there are a few
exceptions), the LAMMPS class can also be instantiated multiple times by
a calling code. Outside of the aforementioned exceptions, those LAMMPS
instances can be used alternately. As of the time of this writing
(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
execution. When running in parallel with MPI, care has to be taken,
that suitable copies of communicators are used to not create conflicts
between different instances.
The LAMMPS class currently holds instances of 19 classes representing
different core functionalities There are a handful of virtual parent
classes in LAMMPS that define what LAMMPS calls ``styles``. They are
shaded red in the :ref:`class-topology` figure. Each of these are
The LAMMPS class currently (early 2021) holds instances of 19 classes
representing the core functionality. There are a handful of virtual
parent classes in LAMMPS that define what LAMMPS calls ``styles``. They
are shaded red in the :ref:`class-topology` figure. Each of these are
parents of a number of child classes that implement the interface
defined by the parent class. There are two main categories of these
``styles``: some may only have one instance active at a time (e.g. atom,
pair, bond, angle, dihedral, improper, kspace, comm) and there is a
dedicated pointer variable in the composite class that manages them.
dedicated pointer variable for each of them in the composite class.
Setups that require a mix of different such styles have to use a
*hybrid* class that manages and forwards calls to the corresponding
sub-styles for the designated subset of atoms or data. or the composite
class may have lists of class instances, e.g. Modify handles lists of
compute and fix styles, while Output handles dumps class instances.
*hybrid* class that takes the place of the one allowed instance and then
manages and forwards calls to the corresponding sub-styles for the
designated subset of atoms or data. The composite class may also have
lists of class instances, e.g. Modify handles lists of compute and fix
styles, while Output handles a list of dump class instances.
The exception to this scheme are the ``command`` style classes. These
implement specific commands that can be invoked before, after, or between
runs or are commands which launch a simulation. For these an instance
of the class is created, its command() method called and then, after
completion, the class instance deleted. Examples for this are the
create_box, create_atoms, minimize, run, or velocity command styles.
The exception to this scheme are the ``command`` style classes. These
implement specific commands that can be invoked before, after, or in
between runs. For these an instance of the class is created, its
command() method called and then, after completion, the class instance
deleted. Examples for this are the create_box, create_atoms, minimize,
run, set, or velocity command styles.
For all those ``styles`` certain naming conventions are employed: for
the fix nve command the class is called FixNVE and the files are
the fix nve command the class is called FixNVE and the source files are
``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``. Style names
FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``. Style names
are lower case and without spaces or special characters. A suffix or
multiple appended with a forward slash '/' denotes a variant of the
corresponding class without the suffix. To connect the style name and
the class name, LAMMPS uses macros like the following ATOM\_CLASS,
PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, FIX\_CLASS, COMPUTE\_CLASS,
or DUMP\_CLASS in the corresponding header file. During compilation
files with the pattern ``style_name.h`` are created that contain include
statements including all headers of all styles of a given type that
are currently active (or "installed).
words are appended with a forward slash '/' which denotes a variant of
the corresponding class without the suffix. To connect the style name
and the class name, LAMMPS uses macros like: ``AtomStyle()``,
``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
corresponding header file. During configuration or compilation files
with the pattern ``style_<name>.h`` are created that consist of a list
of include statements including all headers of all styles of a given
type that are currently active (or "installed).
More details on individual classes in the :ref:`class-topology` are as
@ -152,20 +166,20 @@ follows:
- The Memory class handles allocation of all large vectors and arrays.
- The Error class prints all error and warning messages.
- The Error class prints all (terminal) error and warning messages.
- The Universe class sets up partitions of processors so that multiple
simulations can be run, each on a subset of the processors allocated
for a run, e.g. by the mpirun command.
- The Universe class sets up one or more partitions of processors so
that one or multiple simulations can be run, on the processors
allocated for a run, e.g. by the mpirun command.
- The Input class reads and processes input input strings and files,
stores variables, and invokes :doc:`commands <Commands_all>`.
- As discussed above, command style classes are directly derived from
the Pointers class. They provide input script commands that perform
one-time operations before/after/between simulations or which invoke a
simulation. They are instantiated from within the Input class,
invoked, then immediately destructed.
- Command style classes are derived from the Command class. They provide
input script commands that perform one-time operations
before/after/between simulations or which invoke a simulation. They
are usually instantiated from within the Input class, its ``command``
method invoked, and then immediately destructed.
- The Finish class is instantiated to print statistics to the screen
after a simulation is performed, by commands like run and minimize.
@ -241,7 +255,8 @@ follows:
.. TODO section on "Spatial decomposition and parallel operations"
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
.. atoms, 6-way communication with pack/unpack functions,
.. PBC as part of the communication
.. PBC as part of the communication, forward and reverse communication
.. rendezvous communication, ring communication.
.. TODO section on "Fixes, Computes, and Variables"
.. how and when data is computed and provided and how it is

251
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@ -0,0 +1,251 @@
Writing plugins
---------------
Plugins provide a mechanism to add functionality to a LAMMPS executable
without recompiling LAMMPS. The functionality for this and the
:doc:`plugin command <plugin>` are implemented in the
:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
Plugins use the operating system's capability to load dynamic shared
object (DSO) files in a way similar shared libraries and then reference
specific functions in those DSOs. Any DSO file with plugins has to include
an initialization function with a specific name, "lammpsplugin_init", that
has to follow specific rules described below. When loading the DSO with
the "plugin" command, this function is looked up and called and will then
register the contained plugin(s) with LAMMPS.
From the programmer perspective this can work because of the object
oriented design of LAMMPS where all pair style commands are derived from
the class Pair, all fix style commands from the class Fix and so on and
usually only functions present in those base classes are called
directly. When a :doc:`pair_style` command or :doc:`fix` command is
issued a new instance of such a derived class is created. This is done
by a so-called factory function which is mapped to the style name. Thus
when, for example, the LAMMPS processes the command ``pair_style lj/cut
2.5``, LAMMPS will look up the factory function for creating the
``PairLJCut`` class and then execute it. The return value of that
function is a ``Pair *`` pointer and the pointer will be assigned to the
location for the currently active pair style.
A DSO file with a plugin thus has to implement such a factory function
and register it with LAMMPS so that it gets added to the map of available
styles of the given category. To register a plugin with LAMMPS an
initialization function has to be present in the DSO file called
``lammpsplugin_init`` which is called with three ``void *`` arguments:
a pointer to the current LAMMPS instance, a pointer to the opened DSO
handle, and a pointer to the registration function. The registration
function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
with information about the plugin and a pointer to the current LAMMPS
instance. Please see below for an example of how the registration is
done.
Members of ``lammpsplugin_t``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
:widths: auto
* - Member
- Description
* - version
- LAMMPS Version string the plugin was compiled for
* - style
- Style of the plugin (pair, bond, fix, command, etc.)
* - name
- Name of the plugin style
* - info
- String with information about the plugin
* - author
- String with the name and email of the author
* - creator.v1
- Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
* - creator.v2
- Pointer to factory function for compute, fix, or region styles
* - handle
- Pointer to the open DSO file handle
Only one of the three alternate creator entries can be used at a time
and which of those is determined by the style of plugin. The
"creator.v1" element is for factory functions of supported styles
computing forces (i.e. command, pair, bond, angle, dihedral, or
improper styles) and the function takes as single argument the pointer
to the LAMMPS instance. The factory function is cast to the
``lammpsplugin_factory1`` type before assignment. The "creator.v2"
element is for factory functions creating an instance of a fix, compute,
or region style and takes three arguments: a pointer to the LAMMPS
instance, an integer with the length of the argument list and a ``char
**`` pointer to the list of arguments. The factory function pointer
needs to be cast to the ``lammpsplugin_factory2`` type before
assignment.
Pair style example
^^^^^^^^^^^^^^^^^^
As an example, a hypothetical pair style plugin "morse2" implemented in
a class ``PairMorse2`` in the files ``pair_morse2.h`` and
``pair_morse2.cpp`` with the factory function and initialization
function would look like this:
.. code-block:: C++
#include "lammpsplugin.h"
#include "version.h"
#include "pair_morse2.h"
using namespace LAMMPS_NS;
static Pair *morse2creator(LAMMPS *lmp)
{
return new PairMorse2(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
lammpsplugin_t plugin;
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "morse2";
plugin.info = "Morse2 variant pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
The factory function in this example is called ``morse2creator()``. It
receives a pointer to the LAMMPS class as only argument and thus has to
be assigned to the *creator.v1* member of the plugin struct and cast to
the ``lammpsplugin_factory1`` function pointer type. It returns a
pointer to the allocated class instance derived from the ``Pair`` class.
This function may be declared static to avoid clashes with other
plugins. The name of the derived class, ``PairMorse2``, however must be
unique inside the entire LAMMPS executable.
Fix style example
^^^^^^^^^^^^^^^^^
If the factory function would be for a fix or compute, which take three
arguments (a pointer to the LAMMPS class, the number of arguments and the
list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
Below is an example for that:
.. code-block:: C++
#include "lammpsplugin.h"
#include "version.h"
#include "fix_nve2.h"
using namespace LAMMPS_NS;
static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixNVE2(lmp,argc,argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
lammpsplugin_t plugin;
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "nve2";
plugin.info = "NVE2 variant fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
Command style example
^^^^^^^^^^^^^^^^^^^^^
Command styles also use the first variant of factory function as
demonstrated in the following example, which also shows that the
implementation of the plugin class may be within the same source
file as the plugin interface code:
.. code-block:: C++
#include "lammpsplugin.h"
#include "comm.h"
#include "error.h"
#include "command.h"
#include "version.h"
#include <cstring>
namespace LAMMPS_NS {
class Hello : public Command {
public:
Hello(class LAMMPS *lmp) : Command(lmp) {};
void command(int, char **);
};
}
using namespace LAMMPS_NS;
void Hello::command(int argc, char **argv)
{
if (argc != 1) error->all(FLERR,"Illegal hello command");
if (comm->me == 0)
utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
}
static void hellocreator(LAMMPS *lmp)
{
return new Hello(lmp);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
plugin.version = LAMMPS_VERSION;
plugin.style = "command";
plugin.name = "hello";
plugin.info = "Hello world command v1.1";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
plugin.handle = handle;
(*register_plugin)(&plugin,lmp);
}
Additional Details
^^^^^^^^^^^^^^^^^^
The initialization function **must** be called ``lammpsplugin_init``, it
**must** have C bindings and it takes three void pointers as arguments.
The first is a pointer to the LAMMPS class that calls it and it needs to
be passed to the registration function. The second argument is a
pointer to the internal handle of the DSO file, this needs to be added
to the plugin info struct, so that the DSO can be closed and unloaded
when all its contained plugins are unloaded. The third argument is a
function pointer to the registration function and needs to be stored
in a variable of ``lammpsplugin_regfunc`` type and then called with a
pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
instance as arguments to register a single plugin. There may be multiple
calls to multiple plugins in the same initialization function.
To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
with relevant info: current LAMMPS version string, kind of style, name of
style, info string, author string, pointer to factory function, and the
DSO handle. The registration function is called with a pointer to the address
of this struct and the pointer of the LAMMPS class. The registration function
will then add the factory function of the plugin style to the respective
style map under the provided name. It will also make a copy of the struct
in a list of all loaded plugins and update the reference counter for loaded
plugins from this specific DSO file.
The pair style itself (i.e. the PairMorse2 class in this example) can be
written just like any other pair style that is included in LAMMPS. For
a plugin, the use of the ``PairStyle`` macro in the section encapsulated
by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
name to the style name is done by the plugin registration function with
the information from the ``lammpsplugin_t`` struct. It may be included
in case the new code is intended to be later included in LAMMPS directly.

45
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@ -4,10 +4,10 @@ Adding tests for unit testing
This section discusses adding or expanding tests for the unit test
infrastructure included into the LAMMPS source code distribution.
Unlike example inputs, unit tests focus on testing the "local" behavior
of individual features, tend to run very fast, and should be set up to
cover as much of the added code as possible. When contributing code to
the distribution, the LAMMPS developers will appreciate if additions
to the integrated unit test facility are included.
of individual features, tend to run fast, and should be set up to cover
as much of the added code as possible. When contributing code to the
distribution, the LAMMPS developers will appreciate if additions to the
integrated unit test facility are included.
Given the complex nature of MD simulations where many operations can
only be performed when suitable "real" simulation environment has been
@ -50,6 +50,9 @@ available:
* - File name:
- Test name:
- Description:
* - ``test_argutils.cpp``
- ArgInfo
- Tests for ``ArgInfo`` class used by LAMMPS
* - ``test_fmtlib.cpp``
- FmtLib
- Tests for ``fmtlib::`` functions used by LAMMPS
@ -155,23 +158,27 @@ have the desired effect:
{
ASSERT_EQ(lmp->update->ntimestep, 0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 10");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 10");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 10);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("reset_timestep 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
BEGIN_HIDE_OUTPUT();
command("reset_timestep 0");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->update->ntimestep, 0);
TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
}
Please note the use of the (global) verbose variable to control whether
the LAMMPS command will be silent by capturing the output or not. In
the default case, verbose == false, the test output will be compact and
not mixed with LAMMPS output. However setting the verbose flag (via
setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
helpful to understand why tests fail unexpectedly.
Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
functions that will capture output from running LAMMPS. This is normally
discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called
@ -210,6 +217,12 @@ The following test programs are currently available:
* - ``test_lattice_region.cpp``
- LatticeRegion
- Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
* - ``test_groups.cpp``
- GroupTest
- Tests to validate the :doc:`group <group>` command
* - ``test_variables.cpp``
- VariableTest
- Tests to validate the :doc:`variable <variable>` command
* - ``test_kim_commands.cpp``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`

79
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@ -12,11 +12,18 @@ reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
These are wrappers around the corresponding C library calls like
``fgets()`` or ``fread()``. They will check if there were errors
on reading or an unexpected end-of-file state was reached. In that
case, the functions will stop the calculation with an error message,
indicating the name of the problematic file, if possible.
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
were errors on reading or an unexpected end-of-file state was reached.
In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
terminated with a newline character and the entire buffer with a
NULL character.
----------
@ -26,6 +33,9 @@ indicating the name of the problematic file, if possible.
.. doxygenfunction:: sfread
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
----------
String to number conversions with validity check
@ -71,12 +81,21 @@ and parsing files or arguments.
----------
.. doxygenfunction:: strdup
:project: progguide
.. doxygenfunction:: trim
:project: progguide
.. doxygenfunction:: trim_comment
:project: progguide
.. doxygenfunction:: has_utf8
:project: progguide
.. doxygenfunction:: utf8_subst
:project: progguide
.. doxygenfunction:: count_words(const char *text)
:project: progguide
@ -92,9 +111,15 @@ and parsing files or arguments.
.. doxygenfunction:: split_words
:project: progguide
.. doxygenfunction:: split_lines
:project: progguide
.. doxygenfunction:: strmatch
:project: progguide
.. doxygenfunction:: strfind
:project: progguide
.. doxygenfunction:: is_integer
:project: progguide
@ -286,6 +311,50 @@ This code example should produce the following output:
----------
Argument parsing classes
---------------------------
The purpose of argument parsing classes it to simplify and unify how
arguments of commands in LAMMPS are parsed and to make abstractions of
repetitive tasks.
The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
for parsing references to compute or fix styles or variables. These
would start with a "c\_", "f\_", "v\_" followed by the ID or name of
than instance and may be postfixed with one or two array indices
"[<number>]" with numbers > 0.
A typical code segment would look like this:
.. code-block:: C++
:caption: Usage example for ArgInfo class
int nvalues = 0;
for (iarg = 0; iarg < nargnew; iarg++) {
ArgInfo argi(arg[iarg]);
which[nvalues] = argi.get_type();
argindex[nvalues] = argi.get_index1();
ids[nvalues] = argi.copy_name();
if ((which[nvalues] == ArgInfo::UNKNOWN)
|| (which[nvalues] == ArgInfo::NONE)
|| (argi.get_dim() > 1))
error->all(FLERR,"Illegal compute XXX command");
nvalues++;
}
----------
.. doxygenclass:: LAMMPS_NS::ArgInfo
:project: progguide
:members:
----------
File reader classes
-------------------

1
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@ -91,6 +91,7 @@ documentation for the formula it computes.
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`bond_style <bond_morse>` morse
* :doc:`angle_style <angle_cosine_squared>` cosine/squared
* :doc:`angle_style <angle_harmonic>` harmonic
* :doc:`angle_style <angle_cosine>` cosine
* :doc:`angle_style <angle_cosine_periodic>` cosine/periodic

10
doc/src/Howto_cmake.rst
View File

@ -296,6 +296,8 @@ Some common CMake variables
- Description
* - ``CMAKE_INSTALL_PREFIX``
- root directory of install location for ``make install`` (default: ``$HOME/.local``)
* - ``LAMMPS_INSTALL_RPATH``
- set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
* - ``CMAKE_BUILD_TYPE``
- controls compilation options:
one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``
@ -409,10 +411,10 @@ interface (``ccmake`` or ``cmake-gui``).
.. note::
Using a preset to select a compiler package (``clang.cmake``,
``gcc.cmake``, or ``intel.cmake``) are an exception to the option
of updating the configuration incrementally, as they will trigger
a reset of cached internal CMake settings and thus reset them to
their default values.
``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
are an exception to the mechanism of updating the configuration incrementally,
as they will trigger a reset of cached internal CMake settings and thus
reset settings to their default values.
Compilation and build targets
-----------------------------

5
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@ -42,10 +42,11 @@ screening. It may be necessary to use the *extra/special/per/atom*
keyword of the :doc:`read_data <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
group.
There are two ways to thermostat the Drude particles at a low
There are three ways to thermostat the Drude particles at a low
temperature: use either :doc:`fix langevin/drude <fix_langevin_drude>`
for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
thermostat. The former requires use of the command :doc:`comm_modify vel yes <comm_modify>`. The latter requires two separate integration
thermostat, or :doc:`fix tgnvt/drude <fix_tgnh_drude>` for a temperature-grouped Nose-Hoover thermostat.
The first and third require use of the command :doc:`comm_modify vel yes <comm_modify>`. The second requires two separate integration
fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
command *comm_modify vel yes*.

46
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@ -221,6 +221,14 @@ modification of forces but no position/velocity updates), the fix
fix NVE all nve
To avoid the flying ice cube artifact, where the atoms progressively freeze and the
center of mass of the whole system drifts faster and faster, the *fix momentum*
can be used. For instance:
.. code-block:: LAMMPS
fix MOMENTUM all momentum 100 linear 1 1 1
Finally, do not forget to update the atom type elements if you use
them in a *dump_modify ... element ...* command, by adding the element
type of the DPs. Here for instance
@ -376,14 +384,7 @@ For our phenol example, the groups would be defined as
Note that with the fixes *drude/transform*\ , it is not required to
specify *comm_modify vel yes* because the fixes do it anyway (several
times and for the forces also). To avoid the flying ice cube artifact
:ref:`(Lamoureux and Roux) <Lamoureux2>`, where the atoms progressively freeze and the
center of mass of the whole system drifts faster and faster, the *fix
momentum* can be used. For instance:
.. code-block:: LAMMPS
fix MOMENTUM all momentum 100 linear 1 1 1
times and for the forces also).
It is a bit more tricky to run a NPT simulation with Nose-Hoover
barostat and thermostat. First, the volume should be integrated only
@ -404,6 +405,31 @@ instructions for thermostatting and barostatting will look like
fix NVT DRUDES nvt temp 1. 1. 20
fix INVERSE all drude/transform/inverse
Another option for thermalizing the Drude model is to use the
temperature-grouped Nose-Hoover (TGNH) thermostat proposed by :ref:`(Son) <TGNH-SON>`.
This is implemented as :doc:`fix tgnvt/drude <fix_tgnh_drude>` and :doc:`fix tgnpt/drude <fix_tgnh_drude>`.
It separates the kinetic energy into three contributions:
the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs,
and the relative motion of atom-Drude pairs.
An independent Nose-Hoover chain is applied to each type of motion.
When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with :doc:`thermo_style` command.
NVT simulation with TGNH thermostat
.. code-block:: LAMMPS
comm_modify vel yes
fix TGNVT all tgnvt/drude temp 300. 300. 100 1. 20
thermo_style custom f_TGNVT[1] f_TGNVT[2] f_TGNVT[3]
NPT simulation with TGNH thermostat
.. code-block:: LAMMPS
comm_modify vel yes
fix TGNPT all tgnpt/drude temp 300. 300. 100 1. 20 iso 1. 1. 500
thermo_style custom f_TGNPT[1] f_TGNPT[2] f_TGNPT[3]
----------
**Rigid bodies**
@ -480,3 +506,7 @@ NPT ensemble using Nose-Hoover thermostat:
**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
Let, 418, 245-249 (2006)
.. _TGNH-Son:
**(Son)** Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).

10
doc/src/Howto_granular.rst
View File

@ -18,12 +18,13 @@ This compute
calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
Use one of these 3 pair potentials, which compute forces and torques
Use one of these 4 pair potentials, which compute forces and torques
between interacting pairs of particles:
* :doc:`pair_style <pair_style>` gran/history
* :doc:`pair_style <pair_style>` gran/no_history
* :doc:`pair_style <pair_style>` gran/hertzian
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/no_history <pair_gran>`
* :doc:`pair_style gran/hertzian <pair_gran>`
* :doc:`pair_style granular <pair_granular>`
These commands implement fix options specific to granular systems:
@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
* :doc:`fix pour <fix_pour>`
* :doc:`fix viscous <fix_viscous>`
* :doc:`fix wall/gran <fix_wall_gran>`
* :doc:`fix wall/gran/region <fix_wall_gran_region>`
The fix style *freeze* zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style

4
doc/src/Howto_pylammps.rst
View File

@ -9,8 +9,8 @@ Overview
``PyLammps`` is a Python wrapper class for LAMMPS which can be created
on its own or use an existing lammps Python object. It creates a simpler,
more "pythonic" interface to common LAMMPS functionality, in contrast to
the ``lammps.py`` wrapper for the C-style LAMMPS library interface which
is written using `Python ctypes <ctypes_>`_. The ``lammps.py`` wrapper
the ``lammps`` wrapper for the C-style LAMMPS library interface which
is written using `Python ctypes <ctypes_>`_. The ``lammps`` wrapper
is discussed on the :doc:`Python_head` doc page.
Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable

4
doc/src/Howto_spins.rst
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@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances.
The command :doc:`fix precession/spin <fix_precession_spin>` allows to
apply a constant magnetic torque on all the spins in the system. This
torque can be an external magnetic field (Zeeman interaction), or an
uniaxial magnetic anisotropy.
torque can be an external magnetic field (Zeeman interaction), and an
uniaxial or cubic magnetic anisotropy.
A Langevin thermostat can be applied to those magnetic spins using
:doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat

70
doc/src/Install_git.rst
View File

@ -86,33 +86,59 @@ check out any other desired branch) first.
Once you have updated your local files with a ``git pull`` (or ``git
checkout``), you still need to re-build LAMMPS if any source files have
changed. To do this, you should cd to the src directory and type:
changed. How to do this depends on the build system you are using.
.. code-block:: bash
.. tabs::
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
.. tab:: CMake build
just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
Change to your build folder and type:
.. warning::
.. code-block:: bash
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The version in
the source directory is merely a copy and will be wiped out if you type "make
package-update".
cmake . --build
.. warning::
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
The GitHub servers support both the "git://" and
"https://" access protocols for anonymous read-only access. If you
have a correspondingly configured GitHub account, you may also use
SSH access with the URL "git@github.com:lammps/lammps.git".
.. code-block:: bash
The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
Just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".
.. admonition:: Git protocols
:class: note
The servers at github.com support the "git://" and "https://" access
protocols for anonymous, read-only access. If you have a suitably
configured GitHub account, you may also use SSH protocol with the
URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
richard.berger at temple.edu).

62
doc/src/Install_patch.rst
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@ -43,24 +43,54 @@ up to date.
* A list of updated files print out to the screen. The -b switch
creates backup files of your originals (e.g. src/force.cpp.orig), so
you can manually undo the patch if something goes wrong.
* Type the following from the src directory, to enforce consistency
between the src and package directories. This is OK to do even if you
don't use one or more packages. If you are applying several patches
successively, you only need to type this once at the end. The purge
command removes deprecated src files if any were removed by the patch
from package sub-directories.
.. code-block:: bash
* Once you have updated your local files you need to re-build LAMMPS.
If you are applying several patches successively, you only need to
do the rebuild once at the end. How to do it depends on the build
system you are using.
$ make purge
$ make package-update
.. tabs::
* Re-build LAMMPS via the "make" command.
.. tab:: CMake build
.. warning::
Change to your build folder and type:
If you wish to edit/change a source file that is part of a package,
you should edit the version of the file inside the package folder in
src, and then re-install or update the package. The version in the
src directory is merely a copy and will be wiped out when you type
"make package-update".
.. code-block:: bash
cmake . --build
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
.. code-block:: bash
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
to enforce consistency of the source between the src folder
and package directories. This is OK to do even if you don't
use any packages. The "make purge" command removes any deprecated
src files if they were removed by the patch from a package
sub-directory.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".

17
doc/src/Install_tarball.rst
View File

@ -33,22 +33,19 @@ in its name, e.g. lammps-23Jun18.
----------
You can also download a zip file via the "Clone or download" button on
the `LAMMPS GitHub site <git_>`_. The file name will be lammps-master.zip
which can be unzipped with the following command, to create
a lammps-master dir:
You can also download a compressed tar or zip archives from the
"Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
The file name will be lammps-<version>.zip which can be unzipped
with the following command, to create a lammps-<version> dir:
.. code-block:: bash
$ unzip lammps*.zip
This version is the most up-to-date LAMMPS development version. It
will have the date of the most recent patch release (see the file
src/version.h). But it will also include any new bug-fixes or
features added since the last patch release. They will be included in
the next patch release tarball.
This version corresponds to the selected LAMMPS patch or stable
release.
.. _git: https://github.com/lammps/lammps
.. _git: https://github.com/lammps/lammps/releases
----------

19
doc/src/Intro_citing.rst
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@ -38,17 +38,18 @@ In addition there are DOIs for individual stable releases. Currently there are:
Home page
^^^^^^^^^
The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
location for information about LAMMPS and more detailed lists of publications
using LAMMPS and contributing features.
The LAMMPS website at `https://lammps.sandia.gov/
<https://lammps.sandia.gov>`_ is the canonical location for information
about LAMMPS and its features.
Citing contributions
^^^^^^^^^^^^^^^^^^^^
LAMMPS has many features and uses previously published methods and
algorithms or novel features. It also includes potential parameter
filed for specific models. You can look up relevant publications either
in the LAMMPS output to the screen, the ``log.cite`` file (which is
populated with references to relevant papers through embedding them into
the source code) and in the documentation of the :doc:`corresponding commands
LAMMPS has many features and that use either previously published
methods and algorithms or novel features. It also includes potential
parameter filed for specific models. Where available, a reminder about
references for optional features used in a specific run is printed to
the screen and log file. Style and output location can be selected with
the :ref:`-cite command-line switch <cite>`. Additional references are
given in the documentation of the :doc:`corresponding commands
<Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

2
doc/src/Intro_features.rst
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@ -85,7 +85,7 @@ commands)
* water potentials: TIP3P, TIP4P, SPC
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials

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@ -14,6 +14,7 @@ This section documents the following functions:
- :cpp:func:`lammps_config_has_package`
- :cpp:func:`lammps_config_package_count`
- :cpp:func:`lammps_config_package_name`
- :cpp:func:`lammps_config_accelerator`
- :cpp:func:`lammps_has_style`
- :cpp:func:`lammps_style_count`
- :cpp:func:`lammps_style_name`
@ -126,6 +127,11 @@ approach.
-----------------------
.. doxygenfunction:: lammps_config_accelerator
:project: progguide
-----------------------
.. doxygenfunction:: lammps_has_style
:project: progguide

2
doc/src/Library_scatter.rst
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@ -76,7 +76,7 @@ It documents the following functions:
-----------------------
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand)
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
:project: progguide

17
doc/src/Modify_command.rst
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@ -1,14 +1,15 @@
Input script command style
==========================
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
fashion. When such a command is encountered in the LAMMPS input
script, LAMMPS simply creates a class with the corresponding name,
invokes the "command" method of the class, and passes it the arguments
from the input script. The command method can perform whatever
operations it wishes on LAMMPS data structures.
New commands can be added to LAMMPS input scripts by adding new classes
that are derived from the Command class and thus must have a "command"
method. For example, the create_atoms, read_data, velocity, and run
commands are all implemented in this fashion. When such a command is
encountered in the LAMMPS input script, LAMMPS simply creates a class
instance with the corresponding name, invokes the "command" method of
the class, and passes it the arguments from the input script. The
command method can perform whatever operations it wishes on LAMMPS data
structures.
The single method your new class must define is as follows:

26
doc/src/Modify_contribute.rst
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@ -206,16 +206,22 @@ packages in the src directory for examples. If you are uncertain, please ask.
algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the \*.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the
constructor of the class. Whenever a user invokes your feature from
their input script, this will cause LAMMPS to output the citation to a
log.cite file and prompt the user to examine the file. Note that you
should only use this for a paper you or your group authored.
E.g. adding a cite in the code for a paper by Nose and Hoover if you
write a fix that implements their integrator is not the intended
usage. That kind of citation should just be in the doc page you
provide.
A LaTeX citation is stored in a variable at the top of the file and
a single line of code registering this variable is added to the
constructor of the class. If there is additional functionality (which
may have been added later) described in a different publication,
additional citation descriptions may be added for as long as they
are only registered when the corresponding keyword activating this
functionality is used. With these options it is possible to have
LAMMPS output a specific citation reminder whenever a user invokes
your feature from their input script. Note that you should only use
this for the most relevant paper for a feature and a publication that
you or your group authored. E.g. adding a citation in the code for
a paper by Nose and Hoover if you write a fix that implements their
integrator is not the intended usage. That kind of citation should
just be included in the documentation page you provide describing
your contribution. If you are not sure what the best option would
be, please contact the LAMMPS developers for advice.
Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the

120
doc/src/Packages_details.rst
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@ -50,6 +50,7 @@ page gives those details.
* :ref:`MSCG <PKG-MSCG>`
* :ref:`OPT <PKG-OPT>`
* :ref:`PERI <PKG-PERI>`
* :ref:`PLUGIN <PKG-PLUGIN>`
* :ref:`POEMS <PKG-POEMS>`
* :ref:`PYTHON <PKG-PYTHON>`
* :ref:`QEQ <PKG-QEQ>`
@ -89,6 +90,7 @@ page gives those details.
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
* :ref:`USER-OMP <PKG-USER-OMP>`
* :ref:`USER-PACE <PKG-USER-PACE>`
* :ref:`USER-PHONON <PKG-USER-PHONON>`
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
* :ref:`USER-PTM <PKG-USER-PTM>`
@ -367,17 +369,19 @@ KIM package
**Contents:**
This package contains a set of commands that serve as a wrapper on the
This package contains a command with a set of sub-commands that serve as a
wrapper on the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository of interatomic models (IMs) enabling compatible ones to be used in
LAMMPS simulations.
This includes :doc:`kim_init <kim_commands>`, and
:doc:`kim_interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
This includes :doc:`kim init <kim_commands>`, and
:doc:`kim interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
queries for material property predictions of OpenKIM IMs, a
:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
properties computed in LAMMPS to standard KIM property instance format.
Support for KIM IMs that conform to the
@ -386,8 +390,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
.. note::
The command *pair_style kim* is called by *kim_interactions* and
is not recommended to be directly used in input scripts.
The command *pair_style kim* is called by *kim interactions* and is not
recommended to be directly used in input scripts.
To use this package you must have the KIM API library available on your
system. The KIM API is available for download on the
@ -404,7 +408,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
Daniel Karls (U Minnesota) contributed to the
:doc:`kim_commands <kim_commands>` interface in close collaboration with
:doc:`kim command <kim_commands>` interface in close collaboration with
Ryan Elliott.
**Install:**
@ -414,7 +418,7 @@ This package has :ref:`specific installation instructions <kim>` on the
**Supporting info:**
* :doc:`kim_commands <kim_commands>`
* :doc:`kim command <kim_commands>`
* :doc:`pair_style kim <pair_kim>`
* src/KIM: filenames -> commands
* src/KIM/README
@ -582,7 +586,7 @@ MC package
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjunction with dynamics.
(GCMC) or similar processes in conjunction with dynamics.
**Supporting info:**
@ -590,8 +594,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix atom/swap <fix_atom_swap>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/create <fix_bond_create>`
* :doc:`fix bond/create/angle <fix_bond_create>`
* :doc:`fix bond/swap <fix_bond_swap>`
* :doc:`fix charge/regulation <fix_charge_regulation>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc
@ -662,19 +670,31 @@ MLIAP package
**Contents:**
A general interface for machine-learning interatomic potentials.
A general interface for machine-learning interatomic potentials, including PyTorch.
**Install:**
To use this package, also the :ref:`SNAP package <PKG-SNAP>` needs to be installed.
To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
to be installed. To make the *mliappy* model available, also the
:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
must be installed.
**Author:** Aidan Thompson (Sandia).
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
**Supporting info:**
* src/MLIAP: filenames -> commands
* src/MLIAP/README
* :doc:`pair_style mliap <pair_mliap>`
* examples/mliap
* :doc:`compute_style mliap <compute_mliap>`
* examples/mliap (see README)
When built with the *mliappy* model this package includes an extension for
coupling with Python models, including PyTorch. In this case, the Python
interpreter linked to LAMMPS will need the ``cython`` and ``numpy`` modules
installed. The provided examples build models with PyTorch, which would
therefore also needs to be installed to run those examples.
----------
@ -829,6 +849,28 @@ Foster (UTSA).
----------
.. _PKG-PLUGIN:
PLUGIN package
--------------
**Contents:**
A :doc:`plugin <plugin>` command that can load and unload several
kind of styles in LAMMPS from shared object files at runtime without
having to recompile and relink LAMMPS.
**Authors:** Axel Kohlmeyer (Temple U)
**Supporting info:**
* src/PLUGIN: filenames -> commands
* :doc:`plugin command <plugin>`
* :doc:`Information on writing plugins <Developer_plugins>`
* examples/plugin
----------
.. _PKG-POEMS:
POEMS package
@ -1312,6 +1354,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
----------
.. _PKG-USER-PACE:
USER-PACE package
-------------------
**Contents:**
A pair style for the Atomic Cluster Expansion potential (ACE).
ACE is a methodology for deriving a highly accurate classical potential
fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
package provides an efficient implementation for running simulations
with ACE potentials.
**Authors:**
This package was written by Yury Lysogorskiy^1,
Cas van der Oord^2, Anton Bochkarev^1,
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
**Install:**
This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-PACE: filenames -> commands
* :doc:`pair_style pace <pair_pace>`
* examples/USER/pace
----------
.. _PKG-USER-PLUMED:
USER-PLUMED package
@ -1418,8 +1500,8 @@ oscillators as a model of polarization. See the :doc:`Howto drude <Howto_drude>
for an overview of how to use the package. There are auxiliary tools
for using this package in tools/drude.
**Authors:** Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
**Authors:** Alain Dequidt (U Clermont Auvergne), Julien
Devemy (CNRS), and Agilio Padua (ENS de Lyon).
**Supporting info:**
@ -1486,7 +1568,7 @@ methods for performing FEP simulations by using a :doc:`fix adapt/fep <fix_adapt
which have a "soft" in their style name. There are auxiliary tools
for using this package in tools/fep; see its README file.
**Author:** Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
**Author:** Agilio Padua (ENS de Lyon)
**Supporting info:**
@ -2442,6 +2524,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`bond_style mm3 <bond_mm3>`
* :doc:`improper_style distharm <improper_distharm>`
* :doc:`improper_style sqdistharm <improper_sqdistharm>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff

2
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View File

@ -71,6 +71,8 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PLUGIN <PKG-PLUGIN>` | Plugin loader command | :doc:`plugin <plugin>` | plugins | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`POEMS <PKG-POEMS>` | coupled rigid body motion | :doc:`fix poems <fix_poems>` | rigid | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PYTHON <PKG-PYTHON>` | embed Python code in an input script | :doc:`python <python>` | python | sys |

2
doc/src/Packages_user.rst
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@ -81,6 +81,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |

2
doc/src/Python_atoms.rst
View File

@ -50,7 +50,7 @@ against invalid accesses.
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
.. tab:: PyLammps/IPyLammps API

4
doc/src/Python_config.rst
View File

@ -39,7 +39,9 @@ about compile time settings and included packages and styles.
* :py:attr:`lammps.has_jpeg_support <lammps.lammps.has_jpeg_support>`
* :py:attr:`lammps.has_ffmpeg_support <lammps.lammps.has_ffmpeg_support>`
* :py:attr:`lammps.installed_packages <lammps.lammps.installed_pages>`
* :py:attr:`lammps.installed_packages <lammps.lammps.installed_packages>`
* :py:meth:`lammps.get_accelerator_config <lammps.lammps.accelerator_config>`
* :py:meth:`lammps.has_style() <lammps.lammps.has_style()>`
* :py:meth:`lammps.available_styles() <lammps.lammps.available_styles()>`

2
doc/src/Python_ext.rst
View File

@ -9,7 +9,7 @@ This means you can extend the Python wrapper by following these steps:
* Add a new interface function to ``src/library.cpp`` and
``src/library.h``.
* Rebuild LAMMPS as a shared library.
* Add a wrapper method to ``python/lammps.py`` for this interface
* Add a wrapper method to ``python/lammps/core.py`` for this interface
function.
* Define the corresponding ``argtypes`` list and ``restype``
in the ``lammps.__init__()`` function.

11
doc/src/Python_formats.rst Normal file
View File

@ -0,0 +1,11 @@
Output Readers
==============
.. py:module:: lammps.formats
The Python package contains the :py:mod:`lammps.formats` module, which
provides classes to post-process some of the output files generated by LAMMPS.
.. automodule:: lammps.formats
:members:
:noindex:

1
doc/src/Python_head.rst
View File

@ -13,6 +13,7 @@ together.
Python_module
Python_ext
Python_call
Python_formats
Python_examples
Python_error
Python_trouble

186
doc/src/Python_install.rst
View File

@ -8,9 +8,9 @@ module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`. It is also recommended to
compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
Two files are necessary for Python to be able to invoke LAMMPS code:
Two components are necessary for Python to be able to invoke LAMMPS code:
* The LAMMPS Python Module (``lammps.py``) from the ``python`` folder
* The LAMMPS Python Package (``lammps``) from the ``python`` folder
* The LAMMPS Shared Library (``liblammps.so``, ``liblammps.dylib`` or
``liblammps.dll``) from the folder where you compiled LAMMPS.
@ -25,10 +25,10 @@ Installing the LAMMPS Python Module and Shared Library
======================================================
Making LAMMPS usable within Python and vice versa requires putting the
LAMMPS Python module file (``lammps.py``) into a location where the
LAMMPS Python package (``lammps``) into a location where the
Python interpreter can find it and installing the LAMMPS shared library
into a folder that the dynamic loader searches or into the same folder
where the ``lammps.py`` file is. There are multiple ways to achieve
into a folder that the dynamic loader searches or inside of the installed
``lammps`` package folder. There are multiple ways to achieve
this.
#. Do a full LAMMPS installation of libraries, executables, selected
@ -36,13 +36,13 @@ this.
available via CMake), which can also be either system-wide or into
user specific folders.
#. Install both files into a Python ``site-packages`` folder, either
#. Install both components into a Python ``site-packages`` folder, either
system-wide or in the corresponding user-specific folder. This way no
additional environment variables need to be set, but the shared
library is otherwise not accessible.
#. Do an installation into a virtual environment. This can either be
an installation of the python module only or a full installation.
#. Do an installation into a virtual environment. This can either be an
installation of the Python package only or a full installation of LAMMPS.
#. Leave the files where they are in the source/development tree and
adjust some environment variables.
@ -69,7 +69,7 @@ this.
cd build
# configure LAMMPS compilation
cmake -C cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
# compile LAMMPS
@ -81,40 +81,42 @@ this.
This leads to an installation to the following locations:
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===========================================================+=============================================================+
| LAMMPS Python Module | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/`` (32bit) | |
| | * ``$HOME/.local/lib64/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$HOME/.local/bin/`` | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$HOME/.local/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$HOME/.local/bin/`` | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
For a system-wide installation you need to set
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
``/usr/local``). The installation step (**not** the
``/usr/local``); the default is ``${HOME}/.local``. The
installation step for a system folder installation (**not** the
configuration/compilation) needs to be done with superuser
privilege, e.g. by using ``sudo cmake --install .``. The
installation folders will then by changed to:
installation folders will then be changed to (assuming ``/usr`` as
prefix):
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===================================================+=============================================================+
| LAMMPS Python Module | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/`` (32bit) | |
| | * ``/usr/lib64/`` (64bit) | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``/usr/bin/`` | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``/usr/share/lammps/potentials/`` | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=========================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/`` (32bit) | |
| | * ``/usr/lib64/`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``/usr/bin/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``/usr/share/lammps/potentials/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
To be able to use the "user" installation you have to ensure that
the folder containing the LAMMPS shared library is either included
@ -146,7 +148,7 @@ this.
necessary due to files installed in system folders that are loaded
automatically when a login shell is started.
.. tab:: Python module only
.. tab:: Python package only
Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
:doc:`traditional make <Build_make>` procedure in :ref:`shared
@ -157,37 +159,37 @@ this.
make install-python
This will try to install (only) the shared library and the python
module into a system folder and if that fails (due to missing
This will try to install (only) the shared library and the Python
package into a system folder and if that fails (due to missing
write permissions) will instead do the installation to a user
folder under ``$HOME/.local``. For a system-wide installation you
would have to gain superuser privilege, e.g. though ``sudo``
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===========================================================+=============================================================+
| LAMMPS Python Module | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
For a system-wide installation those folders would then become.
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===================================================+=============================================================+
| LAMMPS Python Module | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+---------------------------------------------------+-------------------------------------------------------------+
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=========================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
No environment variables need to be set for those, as those
folders are searched by default by Python or the LAMMPS Python
module.
package.
For the traditional make process you can override the python
version to version x.y when calling ``make`` with
@ -199,9 +201,9 @@ this.
.. code-block:: bash
$ python install.py -m <python module> -l <shared library> -v <version.h file> [-d <pydir>]
$ python install.py -p <python package> -l <shared library> -v <version.h file> [-d <pydir>]
* The ``-m`` flag points to the ``lammps.py`` python module file to be installed,
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
* the ``-v`` flag points to the ``version.h`` file in the LAMMPS source
* and the optional ``-d`` flag to a custom (legacy) installation folder
@ -249,38 +251,38 @@ this.
When using CMake to build LAMMPS, you need to set
``CMAKE_INSTALL_PREFIX`` to the value of the ``$VIRTUAL_ENV``
environment variable during the configuration step. For the
traditional make procedure, not additional steps are needed.
After compiling LAMMPS you can do a "Python module only"
traditional make procedure, no additional steps are needed.
After compiling LAMMPS you can do a "Python package only"
installation with ``make install-python`` and the LAMMPS Python
module and the shared library file are installed into the
package and the shared library file are installed into the
following locations:
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
If you do a full installation (CMake only) with "install", this
leads to the following installation locations:
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+===========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | |
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | |
+------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
In that case you need to modify the ``$HOME/myenv/bin/activate``
script in a similar fashion you need to update your
@ -296,15 +298,15 @@ this.
echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
# MacOS
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
.. tab:: In place usage
You can also :doc:`compile LAMMPS <Build>` as usual in
:ref:`"shared" mode <exe>` leave the shared library and Python
module files inside the source/compilation folders. Instead of
package inside the source/compilation folders. Instead of
copying the files where they can be found, you need to set the environment
variables ``PYTHONPATH`` (for the Python module) and
variables ``PYTHONPATH`` (for the Python package) and
``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH`` on MacOS
For Bourne shells (bash, ksh and similar) the commands are:
@ -325,6 +327,10 @@ this.
You can make those changes permanent by editing your ``$HOME/.bashrc``
or ``$HOME/.login`` files, respectively.
.. note::
The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
To verify if LAMMPS can be successfully started from Python, start the
Python interpreter, load the ``lammps`` Python module and create a
@ -346,7 +352,7 @@ output similar to the following:
.. note::
Unless you opted for "In place use", you will have to rerun the installation
any time you recompile LAMMPS to ensure the latest Python module and shared
any time you recompile LAMMPS to ensure the latest Python package and shared
library are installed and used.
.. note::

43
doc/src/Python_module.rst
View File

@ -3,12 +3,12 @@ The ``lammps`` Python module
.. py:module:: lammps
The LAMMPS Python interface is implemented as a module called
:py:mod:`lammps` in the ``lammps.py`` file in the ``python`` folder of
the LAMMPS source code distribution. After compilation of LAMMPS, the
module can be installed into a Python system folder or a user folder
with ``make install-python``. Components of the module can then loaded
into a Python session with the ``import`` command.
The LAMMPS Python interface is implemented as a module called :py:mod:`lammps`
which is defined in the ``lammps`` package in the ``python`` folder of the
LAMMPS source code distribution. After compilation of LAMMPS, the module can
be installed into a Python system folder or a user folder with ``make
install-python``. Components of the module can then loaded into a Python
session with the ``import`` command.
There are multiple Python interface classes in the :py:mod:`lammps` module:
@ -26,6 +26,23 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
.. _mpi4py_url: https://mpi4py.readthedocs.io
.. admonition:: Version check
:class: note
The :py:mod:`lammps` module stores the version number of the LAMMPS
version it is installed from. When initializing the
:py:class:`lammps <lammps.lammps>` class, this version is checked to
be the same as the result from :py:func:`lammps.version`, the version
of the LAMMPS shared library that the module interfaces to. If the
they are not the same an AttributeError exception is raised since a
mismatch of versions (e.g. due to incorrect use of the
``LD_LIBRARY_PATH`` or ``PYTHONPATH`` environment variables can lead
to crashes or data corruption and otherwise incorrect behavior.
.. automodule:: lammps
:members:
:noindex:
----------
The ``lammps`` class API
@ -44,7 +61,7 @@ functions. Below is a detailed documentation of the API.
.. autoclass:: lammps.lammps
:members:
.. autoclass:: lammps.numpy_wrapper
.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
:members:
----------
@ -117,23 +134,23 @@ Style Constants
to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
for the equivalent constants in the C library interface. Used in
:py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_type_constants:
Type Constants
--------------
.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
:type: int
Constants in the :py:mod:`lammps` module to select what type of data
to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST`
for the equivalent constants in the C library interface. Used in
:py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_vartype_constants:
@ -153,6 +170,6 @@ Classes representing internal objects
:members:
:no-undoc-members:
.. autoclass:: lammps.NumPyNeighList
.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
:members:
:no-undoc-members:

41
doc/src/Python_neighbor.rst
View File

@ -1,6 +1,43 @@
Neighbor list access
====================
Access to neighbor lists is handled through a couple of wrapper classes
that allows to treat it like either a python list or a NumPy array. The
access procedure is similar to that of the C-library interface: use one
of the "find" functions to look up the index of the neighbor list in the
global table of neighbor lists and then get access to the neighbor list
data. The code sample below demonstrates reading the neighbor list data
using the NumPy access method.
.. code-block:: python
from lammps import lammps
import numpy as np
lmp = lammps()
lmp.commands_string("""
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
run 0 post no""")
# look up the neighbor list
nlidx = lmp.find_pair_neighlist('lj/cut')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("half neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
idx, nlist = nl.get(i)
print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
if nlist.size > 0:
for n in np.nditer(nlist):
print(" atom {} with ID {}".format(n,tags[n]))
**Methods:**
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index
@ -14,5 +51,5 @@ Neighbor list access
**NumPy Methods:**
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

12
doc/src/Python_objects.rst
View File

@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
Python subscripting. The values will be zero for atoms not in the
specified group.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
**NumPy Methods**:
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API

10
doc/src/Python_overview.rst
View File

@ -2,9 +2,9 @@ Overview
========
The LAMMPS distribution includes a ``python`` directory with the Python
code needed to run LAMMPS from Python. The ``python/lammps.py``
contains :doc:`the "lammps" Python <Python_module>` that wraps the
LAMMPS C-library interface. This file makes it is possible to do the
code needed to run LAMMPS from Python. The ``python/lammps`` package
contains :doc:`the "lammps" Python module <Python_module>` that wraps the
LAMMPS C-library interface. This module makes it is possible to do the
following either from a Python script, or interactively from a Python
prompt:
@ -20,8 +20,8 @@ have a version of Python that extends Python to enable multiple
instances of Python to read what you type.
To do all of this, you must build LAMMPS in :ref:`"shared" mode <exe>`
and make certain that your Python interpreter can find the ``lammps.py``
file and the LAMMPS shared library file.
and make certain that your Python interpreter can find the ``lammps``
Python package and the LAMMPS shared library file.
.. _ctypes: https://docs.python.org/3/library/ctypes.html

2
doc/src/Python_trouble.rst
View File

@ -33,7 +33,7 @@ the constructor call as follows (see :ref:`python_create_lammps` for more detail
>>> lmp = lammps(name='mpi')
You can also test the load directly in Python as follows, without
first importing from the lammps.py file:
first importing from the ``lammps`` module:
.. code-block:: python

26
doc/src/Run_options.rst
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@ -11,6 +11,7 @@ letter abbreviation can be used:
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
* :ref:`-pk or -package <package>`
* :ref:`-p or -partition <partition>`
@ -220,14 +221,31 @@ links with from the lib/message directory. See the
----------
.. _cite:
**-cite style or file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are
"both", "none", "screen", or "log". Any flag will be considered a file
name to write the detailed citation info to. Default is the "log" style
where there is a short summary in the screen output and detailed citations
in BibTeX format in the logfile. The option "both" selects the detailed
output for both, "none", the short output for both, and "screen" will
write the detailed info to the screen and the short version to the log
file. If a dedicated citation info file is requested, the screen and
log file output will be in the short format (same as with "none").
See the :doc:`citation page <Intro_citing>` for more details on
how to correctly reference and cite LAMMPS.
----------
.. _nocite:
**-nocite**
Disable writing the log.cite file which is normally written to list
references for specific cite-able features used during a LAMMPS run.
See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
details.
Disable generating a citation reminder (see above) at all.
----------

64
doc/src/Speed_gpu.rst
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@ -1,11 +1,14 @@
GPU package
===========
The GPU package was developed by Mike Brown while at SNL and ORNL
and his collaborators, particularly Trung Nguyen (now at Northwestern).
It provides GPU versions of many pair styles and for parts of the
:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
It has the following general features:
The GPU package was developed by Mike Brown while at SNL and ORNL (now
at Intel Corp.) and his collaborators, particularly Trung Nguyen (now at
Northwestern). Support for AMD GPUs via HIP was added by Vsevolod Nikolskiy
and coworkers at HSE University.
The GPU package provides GPU versions of many pair styles and for
parts of the :doc:`kspace_style pppm <kspace_style>` for long-range
Coulombics. It has the following general features:
* It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
@ -24,8 +27,9 @@ It has the following general features:
force vectors.
* LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality is supported on a variety of hardware.
either Nvidia support, AMD support, or more general OpenCL support
(for Nvidia GPUs, AMD GPUs, Intel GPUs, and multi-core CPUs).
so that the same functionality is supported on a variety of hardware.
**Required hardware/software:**
@ -45,12 +49,23 @@ to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
In OpenCL mode, the acceleration depends on having an `OpenCL Installable Client Driver (ICD) <https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader>`_
installed. There can be multiple of them for the same or different hardware
(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
as 'platforms'. The GPU library will select the **first** suitable platform,
but this can be overridden using the device option of the :doc:`package <package>`
as 'platforms'. The GPU library will try to auto-select the best suitable platform,
but this can be overridden using the platform option of the :doc:`package <package>`
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
platforms and devices with a suitable ICD available.
To compute and use this package in HIP mode, you have to have the AMD ROCm
To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI
HPC Toolkit can be installed using linux package managers. The latter also
provides optimized C++, MPI, and many other libraries and tools. See:
* https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html
If you do not have a discrete GPU card installed, this package can still provide
significant speedups on some CPUs that include integrated GPUs. Additionally, for
many macs, OpenCL is already included with the OS and Makefiles are available
in the lib/gpu directory.
To compile and use this package in HIP mode, you have to have the AMD ROCm
software installed. Versions of ROCm older than 3.5 are currently deprecated
by AMD.
@ -75,10 +90,20 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
The GPU package also has limited support for OpenMP for both
multi-threading and vectorization of routines that are run on the CPUs.
This requires that the GPU library and LAMMPS are built with flags to
enable OpenMP support (e.g. -fopenmp). Some styles for time integration
are also available in the GPU package. These run completely on the CPUs
in full double precision, but exploit multi-threading and vectorization
for faster performance.
Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will
automatically append "gpu" to styles that support it. Use the "-pk
gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
GPUs/node to use.
GPUs/node to use. If Ng is 0, the number is selected automatically as
the number of matching GPUs that have the highest number of compute
cores.
.. code-block:: bash
@ -87,8 +112,8 @@ GPUs/node to use.
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
Note that if the "-sf gpu" switch is used, it also issues a default
:doc:`package gpu 1 <package>` command, which sets the number of
GPUs/node to 1.
:doc:`package gpu 0 <package>` command, which will result in
automatic selection of the number of GPUs to use.
Using the "-pk" switch explicitly allows for setting of the number of
GPUs/node to use and additional options. Its syntax is the same as
@ -138,6 +163,13 @@ Likewise, you should experiment with the precision setting for the GPU
library to see if single or mixed precision will give accurate
results, since they will typically be faster.
MPI parallelism typically outperforms OpenMP parallelism, but in some
cases using fewer MPI tasks and multiple OpenMP threads with the GPU
package can give better performance. 3-body potentials can often perform
better with multiple OMP threads because the inter-process communication
is higher for these styles with the GPU package in order to allow
deterministic results.
**Guidelines for best performance:**
* Using multiple MPI tasks per GPU will often give the best performance,
@ -161,6 +193,12 @@ results, since they will typically be faster.
:doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
:doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
calculations will not be included in the "Pair" time.
* Since only part of the pppm kspace style is GPU accelerated, it
may be faster to only use GPU acceleration for Pair styles with
long-range electrostatics. See the "pair/only" keyword of the
package command for a shortcut to do that. The work between kspace
on the CPU and non-bonded interactions on the GPU can be balanced
through adjusting the coulomb cutoff without loss of accuracy.
* When the *mode* setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time. An additional breakdown of the

21
doc/src/Speed_kokkos.rst
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@ -26,6 +26,15 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
.. admonition:: C++14 support
:class: note
Kokkos requires using a compiler that supports the c++14 standard. For
some compilers, it may be necessary to add a flag to enable c++14 support.
For example, the GNU compiler uses the -std=c++14 flag. For a list of
compilers that have been tested with the Kokkos library, see the Kokkos
`README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
.. admonition:: NVIDIA CUDA support
:class: note
@ -38,14 +47,14 @@ produce an executable compatible with a specific hardware.
:class: note
Kokkos with CUDA currently implicitly assumes that the MPI library is
CUDA-aware. This is not always the case, especially when using
GPU-aware. This is not always the case, especially when using
pre-compiled MPI libraries provided by a Linux distribution. This is
not a problem when using only a single GPU with a single MPI
rank. When running with multiple MPI ranks, you may see segmentation
faults without CUDA-aware MPI support. These can be avoided by adding
the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the
faults without GPU-aware MPI support. These can be avoided by adding
the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
LAMMPS command line or by using the command :doc:`package kokkos
cuda/aware off <package>` in the input file.
gpu/aware off <package>` in the input file.
.. admonition:: AMD GPU support
:class: note
@ -242,8 +251,8 @@ case, also packing/unpacking communication buffers on the host may give
speedup (see the KOKKOS :doc:`package <package>` command). Using CUDA MPS
is recommended in this scenario.
Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
avoided by using :doc:`-pk kokkos cuda/aware no <package>`. As above for
Using a GPU-aware MPI library is highly recommended. GPU-aware MPI use can be
avoided by using :doc:`-pk kokkos gpu/aware off <package>`. As above for
multi-core CPUs (and no GPU), if N is the number of physical cores/node,
then the number of MPI tasks/node should not exceed N.

8
doc/src/Speed_packages.rst
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@ -16,7 +16,7 @@ These are the accelerator packages currently in LAMMPS, either as
standard or user packages:
+-----------------------------------------+-------------------------------------------------------+
| :doc:`GPU Package <Speed_gpu>` | for NVIDIA GPUs as well as OpenCL support |
| :doc:`GPU Package <Speed_gpu>` | for GPUs via CUDA, OpenCL, or ROCm HIP |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
+-----------------------------------------+-------------------------------------------------------+
@ -43,7 +43,7 @@ three kinds of hardware, via the listed packages:
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| NVIDIA/AMD GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
| GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi/AVX | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
@ -154,8 +154,8 @@ Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
* Styles with a "gpu" suffix are part of the GPU package and can be run
on NVIDIA or AMD GPUs. The speed-up on a GPU depends on a variety of
factors, discussed in the accelerator sections.
on Intel, NVIDIA, or AMD GPUs. The speed-up on a GPU depends on a
variety of factors, discussed in the accelerator sections.
* Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,

39
doc/src/Tools.rst
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@ -93,6 +93,7 @@ Miscellaneous tools
* :ref:`i-pi <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`singularity <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -267,7 +268,7 @@ data file in the required format.
See the header of the polarizer.py file for details.
The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
at ens-lyon.fr, alain.dequidt at uca.fr
----------
@ -341,8 +342,7 @@ The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.
The scripts were contributed by Agilio Padua (Universite Blaise
Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr.
See README file in the tools/fep directory.
@ -642,6 +642,39 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
----------
.. _magic:
Magic patterns for the "file" command
-------------------------------------
.. versionadded:: 10Mar2021
The file ``magic`` contains patterns that are used by the
`file program <https://en.wikipedia.org/wiki/File_(command)>`_
available on most Unix-like operating systems which enables it
to detect various LAMMPS files and print some useful information
about them. To enable these patterns, append or copy the contents
of the file to either the file ``.magic`` in your home directory
or (as administrator) to ``/etc/magic`` (for a system-wide
installation). Afterwards the ``file`` command should be able to
detect most LAMMPS restarts, dump, data and log files. Examples:
.. code-block:: bash
$ file *.*
dihedral-quadratic.restart: LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
mol-pair-wf_cut.restart: LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
atom.bin: LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
custom.bin: LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
bn1.lammpstrj: LAMMPS text mode dump, First time step: 5000
data.fourmol: LAMMPS data file written by LAMMPS
pnc.data: LAMMPS data file written by msi2lmp
data.spce: LAMMPS data file written by TopoTools
B.data: LAMMPS data file written by OVITO
log.lammps: LAMMPS log file written by version 10 Feb 2021
----------
.. _matlab:
matlab tool

22
doc/src/angle_cosine_periodic.rst
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@ -24,20 +24,17 @@ Examples
Description
"""""""""""
The *cosine/periodic* angle style uses the following potential, which
is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
particularly for organometallic systems where :math:`n` = 4 might be used
The *cosine/periodic* angle style uses the following potential, which may be
particularly used for organometallic systems where :math:`n` = 4 might be used
for an octahedral complex and :math:`n` = 3 might be used for a trigonal
center:
.. math::
E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
@ -47,10 +44,9 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`B` = 1 or -1
* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
Note that the prefactor :math:`C` is specified and not the overall force
constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear
geometry.
Note that the prefactor :math:`C` is specified as coefficient and not the overall force
constant :math:`K = \frac{2 C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the
linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry.
----------
@ -75,9 +71,3 @@ Default
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

14
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@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential
E = K [\cos(\theta) - \cos(\theta_0)]^2
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. Note that the usual 1/2 factor is included in :math:`K`.
, which is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
is a prefactor. Note that the usual 1/2 factor is included in :math:`K`.
See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@ -66,3 +69,10 @@ Default
"""""""
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

2
doc/src/atom_style.rst
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@ -27,7 +27,7 @@ Syntax
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
*hybrid* args = list of one or more sub-styles, each with their args
* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk*
* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk*
Examples
""""""""

6
doc/src/balance.rst
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@ -257,7 +257,7 @@ factor, similar to how the :doc:`fix balance shift <fix_balance>`
command operates.
The *dimstr* argument is a string of characters, each of which must be
an "x" or "y" or "z". Eacn character can appear zero or one time,
an "x" or "y" or "z". Each character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.
@ -285,10 +285,10 @@ plane gets closer to the target value.
After the balanced plane positions are determined, if any pair of
adjacent planes are closer together than the neighbor skin distance
(as specified by the :doc`neigh_modify <neigh_modify>` command), then
(as specified by the :doc:`neigh_modify <neigh_modify>` command), then
the plane positions are shifted to separate them by at least this
amount. This is to prevent particles being lost when dynamics are run
with processor subdomains that are too narrow in one or more
with processor sub-domains that are too narrow in one or more
dimensions.
Once the re-balancing is complete and final processor sub-domains

6
doc/src/comm_modify.rst
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@ -84,13 +84,15 @@ information is available, then also a heuristic based on that bond length
is computed. It is used as communication cutoff, if there is no pair
style present and no *comm_modify cutoff* command used. Otherwise a
warning is printed, if this bond based estimate is larger than the
communication cutoff used. A
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since in this case the communication
cutoffs are determined per atom type, a type specifier is needed and
cutoff for one or multiple types can be extended. Also ranges of types
using the usual asterisk notation can be given.
using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:

1
doc/src/commands_list.rst
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@ -77,6 +77,7 @@ Commands
pair_style
pair_write
partition
plugin
prd
print
processors

11
doc/src/compute_displace_atom.rst
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@ -46,11 +46,12 @@ the compute command was issued. The value of the displacement will be
.. note::
Initial coordinates are stored in "unwrapped" form, by using the
image flags associated with each atom. See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
See the Atoms section of the :doc:`read_data <read_data>` command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the :doc:`set image <set>` command.
image flags associated with each atom. See the :doc:`dump custom
<dump>` command for a discussion of "unwrapped" coordinates. See
the Atoms section of the :doc:`read_data <read_data>` command for a
discussion of image flags and how they are set for each atom. You
can reset the image flags (e.g. to 0) before invoking this compute
by using the :doc:`set image <set>` command.
.. note::

2
doc/src/compute_fep.rst
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@ -163,7 +163,7 @@ the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

19
doc/src/compute_mliap.rst
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@ -18,7 +18,7 @@ Syntax
.. parsed-literal::
*model* values = style
style = *linear* or *quadratic*
style = *linear* or *quadratic* or *mliappy*
*descriptor* values = style filename
style = *sna*
filename = name of file containing descriptor definitions
@ -56,13 +56,15 @@ and it is also straightforward to add new descriptor styles.
The compute *mliap* command must be followed by two keywords
*model* and *descriptor* in either order.
The *model* keyword is followed by a model style, currently limited to
either *linear* or *quadratic*.
The *model* keyword is followed by the model style (*linear*, *quadratic* or *mliappy*).
The *mliappy* model is only available
if lammps is built with MLIAPPY package.
The *descriptor* keyword is followed by a descriptor style, and additional arguments.
Currently the only descriptor style is *sna*, indicating the bispectrum component
descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
:doc:`pair_style snap <pair_snap>`.
The compute currently supports just one descriptor style, but it is
is straightforward to add new descriptor styles.
The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap <pair_snap>`,
including the linear, quadratic, and chem variants.
A single additional argument specifies the descriptor filename
containing the parameters and setting used by the SNAP descriptor.
The descriptor filename usually ends in the *.mliap.descriptor* extension.
@ -162,9 +164,10 @@ potentials, see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
Restrictions
""""""""""""
This compute is part of the MLIAP package. It is only enabled if
LAMMPS was built with that package. In addition, building LAMMPS with the MLIAP package
This compute is part of the MLIAP package. It is only enabled if LAMMPS
was built with that package. In addition, building LAMMPS with the MLIAP package
requires building LAMMPS with the SNAP package.
The *mliappy* model requires building LAMMPS with the PYTHON package.
See the :doc:`Build package <Build_package>` doc page for more info.
Related commands

6
doc/src/compute_orientorder_atom.rst
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@ -115,8 +115,8 @@ The optional keyword *chunksize* is only applicable when using the
the KOKKOS package and is ignored otherwise. This keyword controls
the number of atoms in each pass used to compute the bond-orientational
order parameters and is used to avoid running out of memory. For example
if there are 4000 atoms in the simulation and the *chunksize*
is set to 2000, the parameter calculation will be broken up
if there are 32768 atoms in the simulation and the *chunksize*
is set to 16384, the parameter calculation will be broken up
into two passes.
The value of :math:`Q_l` is set to zero for atoms not in the
@ -193,7 +193,7 @@ Default
The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
*degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 2000
*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 16384
----------

22
doc/src/compute_pressure.rst
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@ -46,13 +46,14 @@ system volume (or area in 2d). The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
many-body, and long-range interactions, where :math:`r_i` and
:math:`f_i` are the position and force vector of atom *i*, and the black
dot indicates a dot product. When periodic boundary conditions are
used, N' necessarily includes periodic image (ghost) atoms outside the
central box, and the position and force vectors of ghost atoms are thus
included in the summation. When periodic boundary conditions are not
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>`
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
also contribute to the virial term.
dot indicates a dot product. This is computed in parallel for each
sub-domain and then summed over all parallel processes. Thus N'
necessarily includes atoms from neighboring sub-domains (so-called ghost
atoms) and the position and force vectors of ghost atoms are thus
included in the summation. Only when running in serial and without
periodic boundary conditions is N' = N = the number of atoms in the
system. :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
shake <fix_shake>` command) may also contribute to the virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
@ -122,8 +123,11 @@ Output info
This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
options.
or vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` doc page for an overview of LAMMPS output options.
The ordering of values in the symmetric pressure tensor is as follows:
pxx, pyy, pzz, pxy, pxz, pyz.
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure

2
doc/src/compute_reduce_chunk.rst
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@ -30,7 +30,7 @@ Examples
.. code-block:: LAMMPS
compute 1 all reduce/chunk/atom mychunk min c_cluster
compute 1 all reduce/chunk mychunk min c_cluster
Description
"""""""""""

5
doc/src/compute_stress_atom.rst
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@ -216,6 +216,11 @@ an identical manner to compute *stress/atom*. See the :doc:`Howto
output <Howto_output>` doc page for an overview of LAMMPS output
options.
The ordering of the 6 columns for *stress/atom* is as follows: xx, yy,
zz, xy, xz, yz. The ordering of the 9 columns for
*centroid/stress/atom* is as follows: xx, yy, zz, xy, xz, yz, yx, zx,
zy.
The per-atom array values will be in pressure\*volume :doc:`units
<units>` as discussed above.

2
doc/src/compute_temp_chunk.rst
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@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
----------

10
doc/src/create_bonds.rst
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@ -125,6 +125,16 @@ cannot appear in the neighbor list, to avoid creation of duplicate
bonds. The neighbor list for all atom type pairs must also extend to
a distance that encompasses the *rmax* for new bonds to create.
.. note::
If you want to create bonds between pairs of 1-3 or 1-4 atoms in
the current bond topology, then you need to use :doc:`special_bonds
lj 0 1 1 <special_bonds>` to insure those pairs appear in the
neighbor list. They will not appear with the default special_bonds
settings which are zero for 1-2, 1-3, and 1-4 atoms. 1-3 or 1-4
atoms are those which are 2 hops or 3 hops apart in the bond
topology.
An additional requirement for this style is that your system must be
ready to perform a simulation. This means, for example, that all
:doc:`pair_style <pair_style>` coefficients be set via the

2
doc/src/create_box.rst
View File

@ -13,7 +13,7 @@ Syntax
* N = # of atom types to use in this simulation
* region-ID = ID of region to use as simulation domain
* zero or more keyword/value pairs may be appended
* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
.. parsed-literal::

2
doc/src/dihedral_style.rst
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@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
* :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
* :doc:`table <dihedral_table>` - tabulated dihedral
* :doc:`table/cut <dihedral_table_cut>` - tabulated dihedral with analytic cutoff
* :doc:`table/cut <dihedral_table>` - tabulated dihedral with analytic cutoff
----------

89
doc/src/dihedral_table.rst
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@ -1,19 +1,24 @@
.. index:: dihedral_style table
.. index:: dihedral_style table/omp
.. index:: dihedral_style table/cut
dihedral_style table command
============================
Accelerator Variants: *table/omp*
dihedral_style table/cut command
================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style table style Ntable
dihedral_style style interpolation Ntable
* style = *linear* or *spline* = method of interpolation
* style = *table* or *table/cut*
* interpolation = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples
@ -26,13 +31,21 @@ Examples
dihedral_coeff 1 file.table DIH_TABLE1
dihedral_coeff 2 file.table DIH_TABLE2
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
Description
"""""""""""
The *table* dihedral style creates interpolation tables of length
*Ntable* from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". The files are read
by the :doc:`dihedral_coeff <dihedral_coeff>` command.
The *table* and *table/cut* dihedral styles create interpolation tables
of length *Ntable* from dihedral potential and derivative values listed
in a file(s) as a function of the dihedral angle "phi". The files are
read by the :doc:`dihedral_coeff <dihedral_coeff>` command. For
dihedral style *table/cut* additionally an analytic cutoff that is
quadratic in the bond-angle (theta) is applied in order to regularize
the dihedral interaction.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
@ -51,16 +64,53 @@ interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
above.
For dihedral style *table* the following coefficients must be defined
for each dihedral type via the :doc:`dihedral_coeff <dihedral_coeff>`
command as in the example above.
* filename
* keyword
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
The filename specifies a file containing tabulated energy and derivative
values. The keyword specifies which section of the file to read. The
format of this file is the same for both dihedral styles and described
below.
For dihedral style *table/cut* the following coefficients must be
defined for each dihedral type via the :doc:`dihedral_coeff
<dihedral_coeff>` command as in the example above.
* style (aat)
* cutoff prefactor
* cutoff angle1
* cutoff angle2
* filename
* keyword
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
.. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
The cutoff specifies an prefactor to the cutoff function. While this
value would ordinarily equal 1 there may be situations where the value
should change.
The cutoff :math:`\theta_1` specifies the angle (in degrees) below which
the dihedral interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between :math:`\theta_1` and
:math:`\theta_2`, which is the angle at which the cutoff function drops
to zero. The value of zero effectively "turns off" the dihedral
interaction.
The filename specifies a file containing tabulated energy and derivative
values. The keyword specifies which section of the file to read. The
format of this file is the same for both dihedral styles and described
below.
----------
@ -182,18 +232,19 @@ that matches the specified keyword.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This dihedral style writes the settings for the "dihedral_style table"
command to :doc:`binary restart files <restart>`, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
These dihedral styles write the settings for the "dihedral_style table"
or "dihedral_style table/cut" command to :doc:`binary restart files
<restart>`, so a dihedral_style command does not need to specified in an
input script that reads a restart file. However, the coefficient
information loaded from the table file(s) is not stored in the restart
file, since it is tabulated in the potential files. Thus, suitable
dihedral_coeff commands do need to be specified in the restart input
script.
script after reading the restart file.
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
These dihedral styles can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.

229
doc/src/dihedral_table_cut.rst
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@ -1,229 +0,0 @@
.. index:: dihedral_style table/cut
dihedral_style table/cut command
================================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_style table/cut style Ntable
* style = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples
""""""""
.. code-block:: LAMMPS
dihedral_style table/cut spline 400
dihedral_style table/cut linear 1000
dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
Description
"""""""""""
The *table/cut* dihedral style creates interpolation tables of length
*Ntable* from dihedral potential and derivative values listed in a
file(s) as a function of the dihedral angle "phi". In addition, an
analytic cutoff that is quadratic in the bond-angle (theta) is applied
in order to regularize the dihedral interaction. The dihedral table
files are read by the :doc:`dihedral_coeff <dihedral_coeff>` command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
*Ntable* dihedral angles. During a simulation, these tables are used
to interpolate energy and force values on individual atoms as
needed. The interpolation is done in one of 2 styles: *linear* or
*spline*\ .
For the *linear* style, the dihedral angle (phi) is used to find 2
surrounding table values from which an energy or its derivative is
computed by linear interpolation.
For the *spline* style, cubic spline coefficients are computed and
stored at each of the *Ntable* evenly-spaced values in the
interpolated table. For a given dihedral angle (phi), the appropriate
coefficients are chosen from this list, and a cubic polynomial is used
to compute the energy and the derivative at this angle.
The following coefficients must be defined for each dihedral type via
the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
above.
* style (aat)
* cutoff prefactor
* cutoff angle1
* cutoff angle2
* filename
* keyword
The cutoff dihedral style uses a tabulated dihedral interaction with a
cutoff function:
.. math::
f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
The cutoff specifies an prefactor to the cutoff function. While this value
would ordinarily equal 1 there may be situations where the value should change.
The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral
interaction is unmodified, i.e. the cutoff function is 1.
The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is
the angle at which the cutoff function drops to zero. The value of zero effectively
"turns off" the dihedral interaction.
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
----------
The format of a tabulated file is as follows (without the
parenthesized comments). It can begin with one or more comment
or blank lines.
.. parsed-literal::
# Table of the potential and its negative derivative
DIH_TABLE1 (keyword is the first text on line)
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
(blank line)
1 -168.0 -1.40351172223 0.0423346818422
2 -156.0 -1.70447981034 0.00811786522531
3 -144.0 -1.62956100432 -0.0184129719987
...
30 180.0 -0.707106781187 0.0719306095245
# Example 2: table of the potential. Forces omitted
DIH_TABLE2
N 30 NOF CHECKU testU.dat CHECKF testF.dat
1 -168.0 -1.40351172223
2 -156.0 -1.70447981034
3 -144.0 -1.62956100432
...
30 180.0 -0.707106781187
A section begins with a non-blank line whose first character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
:doc:`dihedral_coeff <dihedral_coeff>` command. The next line lists (in
any order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
Following a blank line, the next N lines list the tabulated values. On
each line, the first value is the index from 1 to N, the second value is
the angle value, the third value is the energy (in energy units), and
the fourth is -dE/d(phi) also in energy units). The third term is the
energy of the 4-atom configuration for the specified angle. The fourth
term (when present) is the negative derivative of the energy with
respect to the angle (in degrees, or radians depending on whether the
user selected DEGREES or RADIANS). Thus the units of the last term
are still energy, not force. The dihedral angle values must increase
from one line to the next.
Dihedral table splines are cyclic. There is no discontinuity at 180
degrees (or at any other angle). Although in the examples above, the
angles range from -180 to 180 degrees, in general, the first angle in
the list can have any value (positive, zero, or negative). However
the *range* of angles represented in the table must be *strictly* less
than 360 degrees (2pi radians) to avoid angle overlap. (You may not
supply entries in the table for both 180 and -180, for example.) If
the user's table covers only a narrow range of dihedral angles,
strange numerical behavior can occur in the large remaining gap.
**Parameters:**
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the N
specified in the :doc:`dihedral_style table <dihedral_style>` command.
Let *Ntable* is the number of table entries requested dihedral_style
command, and let *Nfile* be the parameter following "N" in the
tabulated file ("30" in the sparse example above). What LAMMPS does
is a preliminary interpolation by creating splines using the *Nfile*
tabulated values as nodal points. It uses these to interpolate as
needed to generate energy and derivative values at *Ntable* different
points (which are evenly spaced over a 360 degree range, even if the
angles in the file are not). The resulting tables of length *Ntable*
are then used as described above, when computing energy and force for
individual dihedral angles and their atoms. This means that if you
want the interpolation tables of length *Ntable* to match exactly what
is in the tabulated file (with effectively nopreliminary
interpolation), you should set *Ntable* = *Nfile*\ . To insure the
nodal points in the user's file are aligned with the interpolated
table entries, the angles in the table should be integer multiples of
360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
choice of angle units).
The optional "NOF" keyword allows the user to omit the forces
(negative energy derivatives) from the table file (normally located in
the fourth column). In their place, forces will be calculated
automatically by differentiating the potential energy function
indicated by the third column of the table (using either linear or
spline interpolation).
The optional "DEGREES" keyword allows the user to specify angles in
degrees instead of radians (default).
The optional "RADIANS" keyword allows the user to specify angles in
radians instead of degrees. (Note: This changes the way the forces
are scaled in the fourth column of the data file.)
The optional "CHECKU" keyword is followed by a filename. This allows
the user to save all of the *Ntable* different entries in the
interpolated energy table to a file to make sure that the interpolated
function agrees with the user's expectations. (Note: You can
temporarily increase the *Ntable* parameter to a high value for this
purpose. "\ *Ntable*\ " is explained above.)
The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
It is followed by a filename, and it allows the user to check the
interpolated force table. This option is available even if the user
selected the "NOF" option.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds one
that matches the specified keyword.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This dihedral style writes the settings for the "dihedral_style table/cut"
command to :doc:`binary restart files <restart>`, so a dihedral_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
dihedral_coeff commands do need to be specified in the restart input
script.
Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`, :doc:`dihedral_style table <dihedral_table>`
Default
"""""""
none
.. _dihedralcut-Salerno:
**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

2
doc/src/dump.rst
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@ -349,7 +349,7 @@ the box size stored with the snapshot.
The *xtc* style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
`here <http://manual.gromacs.org/current/online/xtc.html>`_.
`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
The precision used in XTC files can be adjusted via the
:doc:`dump_modify <dump_modify>` command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC

8
doc/src/dump_modify.rst
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@ -308,9 +308,9 @@ performed with dump style *xtc*\ .
----------
The *format* keyword can be used to change the default numeric format
output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
The *format* keyword can be used to change the default numeric format output
by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
options can be used with the *atom* and *xyz* styles.
All the specified format strings are C-style formats, e.g. as used by
@ -362,7 +362,7 @@ settings, reverting all values to their default format.
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
dump_modify 1 format "%d %0.0f %0.0f"
dump_modify 1 format line "%d %0.0f %0.0f"
will output the two atom IDs for atoms in each bond as integers. If
the dump_modify command were omitted, they would appear as

3
doc/src/fix.rst
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@ -189,6 +189,7 @@ accelerated styles exist.
* :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
* :doc:`client/md <fix_client_md>` - MD client for client/server simulations
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
@ -364,6 +365,8 @@ accelerated styles exist.
* :doc:`temp/rescale <fix_temp_rescale>` - temperature control by velocity rescaling
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>` - temperature control by velocity rescaling in the electron force field model
* :doc:`tfmc <fix_tfmc>` - perform force-bias Monte Carlo with time-stamped method
* :doc:`tgnvt/drude <fix_tgnh_drude>` - NVT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
* :doc:`tgnpt/drude <fix_tgnh_drude>` - NPT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
* :doc:`thermal/conductivity <fix_thermal_conductivity>` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
* :doc:`ti/spring <fix_ti_spring>` -
* :doc:`tmd <fix_tmd>` - guide a group of atoms to a new configuration

4
doc/src/fix_adapt.rst
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@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | a,c,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

2
doc/src/fix_adapt_fep.rst
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@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

46
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@ -118,32 +118,38 @@ converge properly.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential "energy" inferred by the added force to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This is a fictitious quantity but is
needed so that the :doc:`minimize <minimize>` command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy inferred by the added force to
the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
energy is a fictitious quantity but is needed so that the
:doc:`minimize <minimize>` command can include the forces added by
this fix in a consistent manner. I.e. there is a decrease in
potential energy when atoms move in the direction of the added force.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial no*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is adding its forces. Default is the outermost
level.
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above. The vector is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The scalar and vector values calculated
by this fix are "extensive".
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above.
The vector is the total force on the group of atoms before the forces
on individual atoms are changed by the fix. The scalar and vector
values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

38
doc/src/fix_addtorque.rst
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@ -55,13 +55,15 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential "energy" inferred by the added forces to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This is a fictitious quantity but is
needed so that the :doc:`minimize <minimize>` command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added forces.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential "energy" inferred by the added torques
to the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
is a fictitious quantity but is needed so that the :doc:`minimize
<minimize>` command can include the forces added by this fix in a
consistent manner. I.e. there is a decrease in potential energy when
atoms move in the direction of the added forces.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by
this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
@ -78,16 +80,28 @@ No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
invoked by the :doc:`minimize <minimize>` command.
.. note::
If you want the fictitious potential energy associated with the
added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
.. note::
You should not specify force components with a variable that has
time-dependence for use with a minimizer, since the minimizer
increments the timestep as the iteration count during the
minimization.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""

69
doc/src/fix_atc.rst
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@ -122,10 +122,22 @@ Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. The :doc:`fix_modify <fix_modify>` options relevant to this
fix are listed below. No global scalar or vector or per-atom quantities
are stored by this fix for access by various :doc:`output commands
<Howto_output>`. No parameter of this fix can be used with the
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is not supported by
this fix, but this fix does add the kinetic energy imparted to atoms
by the momentum coupling mode of the AtC package to the global
potential energy of the system as part of :doc:`thermodynamic output
<thermo_style>`.
Additional :doc:`fix_modify <fix_modify>` options relevant to this
fix are listed below.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the energy
discussed in the previous paragraph. The scalar value is "extensive".
No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
invoked during :doc:`energy minimization <minimize>`.
@ -145,10 +157,10 @@ one, e.g. nve, nvt, etc. In addition, currently:
Related commands
""""""""""""""""
After specifying this fix in your input script, several other
:doc:`fix_modify <fix_modify>` commands are used to setup the problem,
e.g. define the finite element mesh and prescribe initial and boundary
conditions.
After specifying this fix in your input script, several
:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
problem, e.g. define the finite element mesh and prescribe initial and
boundary conditions. Each of these options has its own doc page.
*fix_modify* commands for setup:
@ -240,7 +252,8 @@ miscellaneous *fix_modify* commands:
* :doc:`fix_modify AtC remove_species <atc_remove_species>`
* :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders.
Note: a set of example input files with the attendant material files
are included in the ``examples/USER/atc`` folders.
Default
"""""""
@ -252,30 +265,52 @@ For detailed exposition of the theory and algorithms please see:
.. _Wagner:
**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An
atomistic-to-continuum coupling method for heat transfer in solids."
Special Issue of Computer Methods and Applied Mechanics (2008)
197:3351.
.. _Zimmeman2004:
**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE;
Klein, PA; Bammann, DJ, "Calculation of stress in atomistic
simulation." Special Issue of Modelling and Simulation in Materials
Science and Engineering (2004), 12:S319.
.. _Zimmerman2010:
**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A
material frame approach for evaluating continuum variables in
atomistic simulations." Journal of Computational Physics (2010),
229:2364.
.. _Templeton2010:
**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application
of a field-based method to spatially varying thermal transport
problems in molecular dynamics." Modelling and Simulation in
Materials Science and Engineering (2010), 18:085007.
.. _Jones:
**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine,
JA, "Electron transport enhanced molecular dynamics for metals and
semi-metals." International Journal for Numerical Methods in
Engineering (2010), 83:940.
.. _Templeton2011:
**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA;
Wong, BM, "A long-range electric field solver for molecular dynamics
based on atomistic-to-continuum modeling." Journal of Chemical Theory
and Computation (2011), 7:1736.
.. _Mandadapu:
**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization
as a field variable from molecular dynamics simulations." Journal of
Chemical Physics (2013), 139:054115.
Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
Please refer to the standard finite element (FE) texts, e.g. T.J.R
Hughes " The finite element method ", Dover 2003, for the basics of FE
simulation.

4
doc/src/fix_ave_chunk.rst
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@ -307,7 +307,9 @@ atoms in the chunk. The averaged output value for the chunk on the
average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep.
the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
kinetic energy are summed separately across the entire *Nfreq* timescale, and
the output value is calculated by dividing those two sums.
If the *norm* setting is *sample*\ , the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"

2
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@ -93,7 +93,7 @@ from a compute, fix, or variable, then see the :doc:`fix ave/chunk <fix_ave_chun
:doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to convert a
per-atom quantity into a single global value, see the :doc:`compute reduce <compute_reduce>` command.
The input values must either be all scalars. What kinds of
The input values must be all scalars. What kinds of
correlations between input values are calculated is determined by the
*type* keyword as discussed below.

4
doc/src/fix_ave_histo.rst
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@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one. E.g. these
.. code-block:: LAMMPS
compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
If the fix ave/histo/weight command is used, exactly two values must
be specified. If the values are vectors, they must be the same

2
doc/src/fix_balance.rst
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@ -216,7 +216,7 @@ above. It changes the positions of cutting planes between processors
in an iterative fashion, seeking to reduce the imbalance factor.
The *dimstr* argument is a string of characters, each of which must be
an "x" or "y" or "z". Eacn character can appear zero or one time,
an "x" or "y" or "z". Each character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once. You should normally only list dimensions where you expect there
to be a density variation in the particles.

33
doc/src/fix_bocs.rst
View File

@ -75,6 +75,39 @@ Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
are using *units real*\ , *V_avg* should be in cubic angstroms, and the
coefficients should all be in atmospheres \* cubic angstroms.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the cumulative global energy change to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the fix continues in an uninterrupted
fashion.
The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
fix. You can use it to assign a temperature :doc:`compute <compute>`
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The cumulative energy change in the system imposed by this fix is
included in the :doc:`thermodynamic output <thermo_style>` keywords
*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
doc page for details.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the same
cumulative energy change due to this fix described in the previous
paragraph. The scalar value calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
*start* and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

107
doc/src/fix_bond_react.rst
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@ -41,7 +41,7 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
.. parsed-literal::
@ -59,6 +59,12 @@ Syntax
off = allow both inter- and intramolecular reactions (default)
inter = search for reactions between molecules with different IDs
intra = search for reactions within the same molecule
*modify_create* keyword values
*fit* value = *all* or *fragmentID*
all = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*overlap* value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
Examples
""""""""
@ -89,7 +95,9 @@ documentation. Topology changes are defined in pre- and post-reaction
molecule templates and can include creation and deletion of bonds,
angles, dihedrals, impropers, bond types, angle types, dihedral types,
atom types, or atomic charges. In addition, reaction by-products or
other molecules can be identified and deleted.
other molecules can be identified and deleted. Finally, atoms can be
created and inserted at specific positions relative to the reaction
site.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@ -262,14 +270,14 @@ command page.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It
must contain the same number of atoms as the pre-reacted template. A
one-to-one correspondence between the atom IDs in the pre- and
post-reacted templates is specified in the map file as described
below. Note that during a reaction, an atom, bond, etc. type may
change to one that was previously not present in the simulation. These
new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
:doc:`molecule <molecule>` command page.
must contain the same number of atoms as the pre-reacted template
(unless there are created atoms). A one-to-one correspondence between
the atom IDs in the pre- and post-reacted templates is specified in
the map file as described below. Note that during a reaction, an atom,
bond, etc. type may change to one that was previously not present in
the simulation. These new types must also be defined during the setup
of a given simulation. A discussion of correctly handling this is also
provided on the :doc:`molecule <molecule>` command page.
.. note::
@ -283,7 +291,7 @@ A discussion of correctly handling this is also provided on the
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and four optional keywords. The
contains one mandatory keyword and five optional keywords. The
mandatory keyword is 'equivalences':
.. parsed-literal::
@ -296,11 +304,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
.. parsed-literal::
N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
N *deleteIDs* = # of atoms N that are specified for deletion
N *chiralIDs* = # of specified chiral centers N
N *constraints* = # of specified reaction constraints N
N *deleteIDs* = # of atoms N that are deleted
N *createIDs* = # of atoms N that are created
N *chiralIDs* = # of chiral centers N
N *constraints* = # of reaction constraints N
The body of the map file contains two mandatory sections and four
The body of the map file contains two mandatory sections and five
optional sections. The first mandatory section begins with the keyword
'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
in the pre-reacted molecule template. The second mandatory section
@ -313,8 +322,10 @@ the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
pre-reacted molecule template. The second optional section begins with
the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
template atoms to delete. The third optional section begins with the
keyword 'CreateIDs' and lists the atom IDs of the post-reaction
template atoms to create. The fourth optional section begins with the
keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fourth optional section begins with
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
@ -353,6 +364,38 @@ A sample map file is given below:
----------
A user-specified set of atoms can be deleted by listing their
pre-reaction template IDs in the DeleteIDs section. A deleted atom
must still be included in the post-reaction molecule template, in
which it cannot be bonded to an atom that is not deleted. In addition
to deleting unwanted reaction by-products, this feature can be used to
remove specific topologies, such as small rings, that may be otherwise
indistinguishable.
Atoms can be created by listing their post-reaction template IDs in
the CreateIDs section. A created atom should not be included in the
pre-reaction template. The inserted positions of created atoms are
determined by the coordinates of the post-reaction template, after
optimal translation and rotation of the post-reaction template to the
reaction site (using a fit with atoms that are neither created nor
deleted). The *modify_create* keyword can be used to modify the
default behavior when creating atoms. The *modify_create* keyword has
two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
may be used after the *modify_create* keyword. The *fit* sub-keyword
can be used to specify which post-reaction atoms are used for the
optimal translation and rotation of the post-reaction template. The
*fragmentID* value of the *fit* sub-keyword must be the name of a
molecule fragment defined in the post-reaction :doc:`molecule
<molecule>` template, and only atoms in this fragment are used for the
fit. Atoms are created only if no current atom in the simulation is
within a distance R of any created atom, including the effect of
periodic boundary conditions if applicable. R is defined by the
*overlap* sub-keyword. Note that the default value for R is 0.0, which
will allow atoms to strongly overlap if you are inserting where other
atoms are present. The velocity of each created atom is initialized in
a random direction with a magnitude calculated from the instantaneous
temperature of the reaction site.
The handedness of atoms that are chiral centers can be enforced by
listing their IDs in the ChiralIDs section. A chiral atom must be
bonded to four atoms with mutually different atom types. This feature
@ -457,6 +500,23 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
logical values using the logical AND operator "&&". More complex logic
can be achieved by explicitly adding the logical AND operator "&&" or
the logical OR operator "||" after a given constraint command. If a
logical operator is specified after a constraint, it must be placed
after all constraint parameters, on the same line as the constraint
(one per line). Similarly, parentheses can be used to group
constraints. The expression that results from concatenating all
constraints should be a valid logical expression that can be read by
the :doc:`variable <variable>` command after converting each
constraint to a logical value. Because exactly one constraint is
allowed per line, having a valid logical expression implies that left
parentheses "(" should only appear before a constraint, and right
parentheses ")" should only appear after a constraint and before any
logical operator.
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
@ -511,15 +571,6 @@ the same molecule ID are considered for the reaction.
A few other considerations:
Many reactions result in one or more atoms that are considered
unwanted by-products. Therefore, bond/react provides the option to
delete a user-specified set of atoms. These pre-reaction atoms are
identified in the map file. A deleted atom must still be included in
the post-reaction molecule template, in which it cannot be bonded to
an atom that is not deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable.
Optionally, you can enforce additional behaviors on reacting atoms.
For example, it may be beneficial to force reacting atoms to remain at
a certain temperature. For this, you can use the internally-created
@ -593,14 +644,14 @@ Default
"""""""
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
reset_mol_ids = yes, custom_charges = no, molecule = off
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
----------
.. _Gissinger:
**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
**(Gissinger2017)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
.. _Gissinger2020:
**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules (2020, in press).
**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).

276
doc/src/fix_charge_regulation.rst Normal file
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@ -0,0 +1,276 @@
.. index:: fix charge/regulation
fix charge/regulation command
=============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
* ID, group-ID are documented in fix command
* charge/regulation = style name of this fix command
* cation_type = atom type of free cations
* anion_type = atom type of free anions
* zero or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
*pH* value = pH of the solution
*pKa* value = acid dissociation constant
*pKb* value = base dissociation constant
*pIp* value = chemical potential of free cations
*pIm* value = chemical potential of free anions
*pKs* value = solution self-dissociation constant
*acid_type* = atom type of acid groups
*base_type* = atom type of base groups
*lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
*temp* value = temperature
*tempfixid* value = fix ID of temperature thermostat
*nevery* value = invoke this fix every nevery steps
*nmc* value = number of charge regulation MC moves to attempt every nevery steps
*xrd* value = cutoff distance for acid/base reaction
*seed* value = random # seed (positive integer)
*tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
*group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
*onlysalt* values = flag charge_cation charge_anion.
flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion)
charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes)
*pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI)
Examples
""""""""
.. code-block:: LAMMPS
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
Description
"""""""""""
This fix performs Monte Carlo (MC) sampling of charge regulation and
exchange of ions with a reservoir as discussed in :ref:`(Curk1) <Curk1>`
and :ref:`(Curk2) <Curk2>`. The implemented method is largely analogous
to the grand-reaction ensemble method in :ref:`(Landsgesell)
<Landsgesell>`. The implementation is parallelized, compatible with
existing LAMMPS functionalities, and applicable to any system utilizing
discrete, ionizable groups or surface sites.
Specifically, the fix implements the following three types of MC moves,
which discretely change the charge state of individual particles and
insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons
\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons
\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons
Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. In the former two types of
reactions, Monte Carlo moves alter the charge value of specific atoms
(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a
counterion to preserve the charge neutrality of the system, modeling the
dissociation/association process. The last type of reaction performs
grand canonical MC exchange of ion pairs with a (fictitious) reservoir.
In our implementation "acid" refers to particles that can attain charge
:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`,
whereas the MC exchange of free ions allows any integer charge values of
:math:`{Z^+}` and :math:`{Z^-}`.
Here we provide several practical examples for modeling charge
regulation effects in solvated systems. An acid ionization reaction
(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be
defined via a single line in the input file
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0
where the fix attempts to charge :math:`\mathrm{A}` (discharge
:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
insert (delete) a proton (atom type 2). Besides, the fix implements
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
both protons and hydroxyl ions is low, resulting in a relatively low
acceptance rate of MC moves.
A more efficient way is to allow salt ions to participate in ionization
reactions, which can be easily achieved via
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
where particles of atom type 4 and 5 are the salt cations and anions,
both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
:ref:`(Landsgesell) <Landsgesell>` for more details.
Similarly, we could have simultaneously added a base ionization reaction
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
.. code-block:: LAMMPS
fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
where the fix will attempt to charge :math:`\mathrm{B}` (discharge
:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If
neither the acid or the base type is specified, for example,
.. code-block:: LAMMPS
fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0
the fix simply inserts or deletes an ion pair of a free cation (atom
type 4) and a free anion (atom type 5) as done in a conventional
grand-canonical MC simulation.
The fix is compatible with LAMMPS sub-packages such as *molecule* or
*rigid*. That said, the acid and base particles can be part of larger
molecules or rigid bodies. Free ions that are inserted to or deleted
from the system must be defined as single particles (no bonded
interactions allowed) and cannot be part of larger molecules or rigid
bodies. If *molecule* package is used, all inserted ions have a molecule
ID equal to zero.
Note that LAMMPS implicitly assumes a constant number of particles
(degrees of freedom). Since using this fix alters the total number of
particles during the simulation, any thermostat used by LAMMPS, such as
NVT or Langevin, must use a dynamic calculation of system
temperature. This can be achieved by specifying a dynamic temperature
compute (e.g. dtemp) and using it with the desired thermostat, e.g. a
Langevin thermostat:
.. code-block:: LAMMPS
compute dtemp all temp
compute_modify dtemp dynamic yes
fix fT all langevin 1.0 1.0 1.0 123
fix_modify fT temp dtemp
The chemical potential units (e.g. pH) are in the standard log10
representation assuming reference concentration :math:`\rho_0 =
\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit
conversion, the length (in nanometers) of the LAMMPS unit length must be
specified via *lunit_nm* (default is set to the Bjerrum length in water
at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
ideal solution limit, the concentration of free ions will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
The temperature used in MC acceptance probability is set by *temp*. This
temperature should be the same as the temperature set by the molecular
dynamics thermostat. For most purposes, it is probably best to use
*tempfixid* keyword which dynamically sets the temperature equal to the
chosen MD thermostat temperature, in the example above we assumed the
thermostat fix-ID is *fT*. The inserted particles attain a random
velocity corresponding to the specified temperature. Using *tempfixid*
overrides any fixed temperature set by *temp*.
The *xrd* keyword can be used to restrict the inserted/deleted
counterions to a specific radial distance from an acid or base particle
that is currently participating in a reaction. This can be used to
simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
2, where *L* is the smallest box dimension, the radial restriction is
automatically turned off and free ion can be inserted or deleted
anywhere in the simulation box.
If the *tag yes* is used, every inserted atom gets a unique tag ID,
otherwise, the tag of every inserted atom is set to 0. *tag yes* might
cause an integer overflow in very long simulations since the tags are
unique to every particle and thus increase with every successful
particle insertion.
The *pmcmoves* keyword sets the relative probability of attempting the
three types of MC moves (reactions): acid charging, base charging, and
ion pair exchange. The fix only attempts to perform particle charging
MC moves if *acid_type* or *base_type* is defined. Otherwise fix only
performs free ion insertion/deletion. For example, if *acid_type* is not
defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is
automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33,
the vector would be normalized to [0,0.5,0.5].
The *only_salt* option can be used to perform multivalent
grand-canonical ion-exchange moves. If *only_salt yes* is used, no
charge exchange is performed, only ion insertion/deletion (*pmcmoves* is
set to [0,0,1]), but ions can be multivalent. In the example above, an
MC move would consist of three ion insertion/deletion to preserve the
charge neutrality of the system.
The *group* keyword can be used to add inserted particles to a specific
group-ID. All inserted particles are automatically added to group *all*.
Output
""""""
This fix computes a global vector of length 8, which can be accessed by
various output commands. The vector values are the following global
quantities:
* 1 = cumulative MC attempts
* 2 = cumulative MC successes
* 3 = current # of neutral acid atoms
* 4 = current # of -1 charged acid atoms
* 5 = current # of neutral base atoms
* 6 = current # of +1 charged base atoms
* 7 = current # of free cations
* 8 = current # of free anions
Restrictions
""""""""""""
This fix is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
The :doc:`atom_style <atom_style>`, used must contain the charge
property, for example, the style could be *charge* or *full*. Only
usable for 3D simulations. Atoms specified as free ions cannot be part
of rigid bodies or molecules and cannot have bonding interactions. The
scheme is limited to integer charges, any atoms with non-integer charges
will not be considered by the fix.
All interaction potentials used must be continuous, otherwise the MD
integration and the particle exchange MC moves do not correspond to the
same equilibrium ensemble. For example, if an lj/cut pair style is used,
the LJ potential must be shifted so that it vanishes at the cutoff. This
can be easily achieved using the :doc:`pair_modify <pair_modify>`
command, i.e., by using: *pair_modify shift yes*.
.. note::
Region restrictions are not yet implemented.
Related commands
""""""""""""""""
:doc:`fix gcmc <fix_gcmc>`,
:doc:`fix atom/swap <fix_atom_swap>`
Default
"""""""
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
[1/3, 1/3, 1/3], group-ID = all
----------
.. _Curk1:
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
.. _Curk2:
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
.. _Landsgesell:
**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).

37
doc/src/fix_client_md.rst
View File

@ -47,14 +47,15 @@ for running *ab initio* MD with quantum forces.
The group associated with this fix is ignored.
The protocol and :doc:`units <units>` for message format and content
that LAMMPS exchanges with the server code is defined on the :doc:`server md <server_md>` doc page.
that LAMMPS exchanges with the server code is defined on the
:doc:`server md <server_md>` doc page.
Note that when using LAMMPS as an MD client, your LAMMPS input script
should not normally contain force field commands, like a
:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`, or
:doc:`kspace_style <kspace_style>` command. However it is possible for
a server code to only compute a portion of the full force-field, while
LAMMPS computes the remaining part. Your LAMMPS script can also
:doc:`kspace_style <kspace_style>` command. However it is possible
for a server code to only compute a portion of the full force-field,
while LAMMPS computes the remaining part. Your LAMMPS script can also
specify boundary conditions or force constraints in the usual way,
which will be added to the per-atom forces returned by the server
code.
@ -69,16 +70,21 @@ LAMMPS and another code in tandem to perform a coupled simulation.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential energy computed by the server application to
the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy set by the server application to
the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the server application's contribution to the system's
virial as part of :doc:`thermodynamic output <thermo_style>`. The
default is *virial yes*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution computed by the server application to
the global pressure of the system via the :doc:`compute pressure
<compute_pressure>` command. This can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
@ -86,13 +92,16 @@ energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the MESSAGE package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
A script that uses this command must also use the
:doc:`message <message>` command to setup and shut down the messaging

44
doc/src/fix_cmap.rst
View File

@ -29,11 +29,12 @@ Description
This command enables CMAP cross-terms to be added to simulations which
use the CHARMM force field. These are relevant for any CHARMM model
of a peptide or protein sequences that is 3 or more amino-acid
residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>` for details,
including the analytic energy expressions for CMAP interactions. The
CMAP cross-terms add additional potential energy contributions to pairs
of overlapping phi-psi dihedrals of amino-acids, which are important
to properly represent their conformational behavior.
residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>`
for details, including the analytic energy expressions for CMAP
interactions. The CMAP cross-terms add additional potential energy
contributions to pairs of overlapping phi-psi dihedrals of
amino-acids, which are important to properly represent their
conformational behavior.
The examples/cmap directory has a sample input script and data file
for a small peptide, that illustrates use of the fix cmap command.
@ -93,19 +94,27 @@ the note below about how to include the CMAP energy when performing an
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the list of CMAP cross-terms to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command
This fix writes the list of CMAP cross-terms to :doc:`binary restart
files <restart>`. See the :doc:`read_restart <read_restart>` command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential "energy" of the CMAP interactions system's
potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy of the CMAP interactions to both
the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or
output by the :doc:`compute pe/atom <compute_pe_atom>` command. The
default setting for this fix is :doc:`fix_modify energy yes
<fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the interaction between atoms to
the system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial yes*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the CMAP interactions to both
the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
@ -118,11 +127,16 @@ the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
If you want the potential energy associated with the CMAP terms
forces to be included in the total potential energy of the system (the
quantity being minimized), you MUST enable the
forces to be included in the total potential energy of the system
(the quantity being minimized), you MUST not disable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
Restrictions

29
doc/src/fix_colvars.rst
View File

@ -35,12 +35,12 @@ Examples
Description
"""""""""""
This fix interfaces LAMMPS to the collective variables "Colvars"
library, which allows to calculate potentials of mean force
(PMFs) for any set of colvars, using different sampling methods:
currently implemented are the Adaptive Biasing Force (ABF) method,
metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias.
This fix interfaces LAMMPS to the collective variables (Colvars)
library, which allows to calculate potentials of mean force (PMFs) for
any set of colvars, using different sampling methods: currently
implemented are the Adaptive Biasing Force (ABF) method, metadynamics,
Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a
flexible harmonic restraint bias.
This documentation describes only the fix colvars command itself and
LAMMPS specific parts of the code. The full documentation of the
@ -98,9 +98,11 @@ This fix writes the current status of the colvars module into
mode status file that is written by the colvars module itself and the
kind of information in both files is identical.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy change from the biasing force added by the fix
to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the energy change from the biasing force added by
Colvars to the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`.
The *fix_modify configfile <config file>* option allows to add settings
from an additional config file to the colvars module. This option can
@ -113,15 +115,16 @@ in a pair of double quotes ("), or can span multiple lines when bracketed
by a pair of triple double quotes (""", like python embedded documentation).
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the cumulative
energy change due to this fix. The scalar value calculated by this
fix is "extensive".
:doc:`output commands <Howto_output>`. The scalar is the Colvars
energy mentioned above. The scalar value calculated by this fix is
"extensive".
Restrictions
""""""""""""
This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module

4
doc/src/fix_drude.rst
View File

@ -41,12 +41,12 @@ Restrictions
""""""""""""
This fix should be invoked before any other commands that implement
the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
Related commands
""""""""""""""""
:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
Default
"""""""

51
doc/src/fix_efield.rst
View File

@ -100,9 +100,9 @@ minimize the orientation of dipoles in an applied electric field.
The *energy* keyword specifies the name of an atom-style
:doc:`variable <variable>` which is used to compute the energy of each
atom as function of its position. Like variables used for *ex*\ , *ey*\ ,
*ez*\ , the energy variable is specified as v_name, where name is the
variable name.
atom as function of its position. Like variables used for *ex*\ ,
*ey*\ , *ez*\ , the energy variable is specified as v_name, where name
is the variable name.
Note that when the *energy* keyword is used during an energy
minimization, you must insure that the formula defined for the
@ -117,31 +117,38 @@ minimization will not converge properly.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential "energy" inferred by the added force due to
the electric field to the system's potential energy as part of
:doc:`thermodynamic output <thermo_style>`. This is a fictitious
quantity but is needed so that the :doc:`minimize <minimize>` command
can include the forces added by this fix in a consistent manner.
I.e. there is a decrease in potential energy when atoms move in the
direction of the added force due to the electric field.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy inferred by the added force due
to the electric field to the global potential energy of the system as
part of :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
Note that this energy is a fictitious quantity but is needed so that
the :doc:`minimize <minimize>` command can include the forces added by
this fix in a consistent manner. I.e. there is a decrease in
potential energy when atoms move in the direction of the added force
due to the electric field.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial no*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix adding its forces. Default is the outermost level.
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix adding its forces. Default is the
outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above. The vector is the
total force added to the group of atoms. The scalar and vector values
calculated by this fix are "extensive".
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above.
The vector is the total force added to the group of atoms. The scalar
and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

35
doc/src/fix_external.rst
View File

@ -84,7 +84,8 @@ code `Quest <quest_>`_.
If mode is *pf/array* then the fix simply stores force values in an
array. The fix adds these forces to each atom in the group, once
every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.
every *Napply* steps, similar to the way the :doc:`fix addforce
<fix_addforce>` command works.
The name of the public force array provided by the FixExternal
class is
@ -150,19 +151,27 @@ of properties that the caller code may want to communicate to LAMMPS
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential "energy" set by the external driver to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`. This is a fictitious quantity but is
needed so that the :doc:`minimize <minimize>` command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy set by the external driver to
both the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or output
by the :doc:`compute pe/atom <compute_pe_atom>` command. The default
setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
Note that this energy may be a fictitious quantity but it is needed so
that the :doc:`minimize <minimize>` command can include the forces
added by this fix in a consistent manner. I.e. there is a decrease in
potential energy when atoms move in the direction of the added force.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the interactions computed by the
external program to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial yes*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution computed by the external program to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
@ -178,7 +187,7 @@ invoked by the :doc:`minimize <minimize>` command.
If you want the fictitious potential energy associated with the
added forces to be included in the total potential energy of the
system (the quantity being minimized), you MUST enable the
system (the quantity being minimized), you MUST not disable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
Restrictions

35
doc/src/fix_ffl.rst
View File

@ -76,28 +76,31 @@ Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The instantaneous values of the extended variables are written to
:doc:`binary restart files <restart>`. Because the state of the random
number generator is not saved in restart files, this means you cannot
do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
:doc:`binary restart files <restart>`. Because the state of the
random number generator is not saved in restart files, this means you
cannot do "exact" restarts with this fix, where the simulation
continues on the same as if no restart had taken place. However, in a
statistical sense, a restarted simulation should produce the same
behavior. Note however that you should use a different seed each time
you restart, otherwise the same sequence of random numbers will be
used each time, which might lead to stochastic synchronization and
subtle artifacts in the sampling.
The cumulative energy change in the system imposed by this fix is
included in the :doc:`thermodynamic output <thermo_style>` keywords
*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
doc page for details.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the same
cumulative energy change due to this fix described in the previous
paragraph. The scalar value calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
*start* and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the cumulative
energy change due to this fix. The scalar value calculated by this
fix is "extensive".
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

79
doc/src/fix_flow_gauss.rst
View File

@ -55,17 +55,22 @@ momentum.
GD applies an external fluctuating gravitational field that acts as a
driving force to keep the system away from equilibrium. To maintain
steady state, a profile-unbiased thermostat must be implemented to
dissipate the heat that is added by the driving force. :doc:`Compute temp/profile <compute_temp_profile>` can be used to implement a
dissipate the heat that is added by the driving force. :doc:`Compute
temp/profile <compute_temp_profile>` can be used to implement a
profile-unbiased thermostat.
A common use of this fix is to compute a pressure drop across a pipe,
pore, or membrane. The pressure profile can be computed in LAMMPS with
:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc <fix_atc>`. Note that the simple :doc:`compute stress/atom <compute_stress_atom>` method is only accurate away
from inhomogeneities in the fluid, such as fixed wall atoms. Further,
the computed pressure profile must be corrected for the acceleration
:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix
ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc
<fix_atc>`. Note that the simple :doc:`compute stress/atom
<compute_stress_atom>` method is only accurate away from
inhomogeneities in the fluid, such as fixed wall atoms. Further, the
computed pressure profile must be corrected for the acceleration
applied by GD before computing a pressure drop or comparing it to
other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The pressure
correction is discussed and described in :ref:`(Strong) <Strong>`.
other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The
pressure correction is discussed and described in :ref:`(Strong)
<Strong>`.
For a complete example including the considerations discussed
above, see the examples/USER/flow_gauss directory.
@ -102,14 +107,15 @@ computed by the fix will return zero.
of wall atoms fixed, such as :doc:`fix spring/self <fix_spring_self>`.
If this fix is used in a simulation with the :doc:`rRESPA <run_style>`
integrator, the applied acceleration must be computed and applied at the same
rRESPA level as the interactions between the flowing fluid and the obstacle.
The rRESPA level at which the acceleration is applied can be changed using
the :doc:`fix_modify <fix_modify>` *respa* option discussed below. If the
flowing fluid and the obstacle interact through multiple interactions that are
computed at different rRESPA levels, then there must be a separate flow/gauss
fix for each level. For example, if the flowing fluid and obstacle interact
through pairwise and long-range Coulomb interactions, which are computed at
integrator, the applied acceleration must be computed and applied at
the same rRESPA level as the interactions between the flowing fluid
and the obstacle. The rRESPA level at which the acceleration is
applied can be changed using the :doc:`fix_modify <fix_modify>`
*respa* option discussed below. If the flowing fluid and the obstacle
interact through multiple interactions that are computed at different
rRESPA levels, then there must be a separate flow/gauss fix for each
level. For example, if the flowing fluid and obstacle interact through
pairwise and long-range Coulomb interactions, which are computed at
rRESPA levels 3 and 4, respectively, then there must be two separate
flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
*fix_modify respa 4*.
@ -119,38 +125,49 @@ flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
No information about this fix is written to :doc:`binary restart files
<restart>`.
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to subtract the work done from the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy added by the fix to the global
potential energy of the system as part of :doc:`thermodynamic output
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows the user to set at which level of the :doc:`rRESPA <run_style>`
integrator the fix computes and adds the external acceleration. Default is the
outermost level.
fix. This allows the user to set at which level of the :doc:`rRESPA
<run_style>` integrator the fix computes and adds the external
acceleration. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the negative of the work done on the system, see above
discussion. The vector is the total force that this fix applied to
the group of atoms on the current timestep. The scalar and vector
values calculated by this fix are "extensive".
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the negative of the work done on the
system, see the discussion above. It is only calculated if the
*energy* keyword is enabled or :doc:`fix_modify energy yes
<fix_modify>` is set.
The vector is the total force that this fix applied to the group of
atoms on the current timestep. The scalar and vector values
calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
none
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`fix addforce <fix_addforce>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`velocity <velocity>`
:doc:`fix addforce <fix_addforce>`,
:doc:`compute temp/profile <compute_temp_profile>`,
:doc:`velocity <velocity>`
Default
"""""""

20
doc/src/fix_gcmc.rst
View File

@ -398,12 +398,13 @@ adds all inserted atoms of the specified type to the
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the fix to :doc:`binary restart files <restart>`. This includes information about the random
number generator seed, the next timestep for MC exchanges, the number
of MC step attempts and successes etc. See
the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of MC
step attempts and successes etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
.. note::
@ -411,8 +412,8 @@ the operation of the fix continues in an uninterrupted fashion.
after reading the restart with :doc:`reset_timestep <reset_timestep>`.
The fix will try to detect it and stop with an error.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.
None of the :doc:`fix_modify <fix_modify>` options are relevant to
this fix.
This fix computes a global vector of length 8, which can be accessed
by various :doc:`output commands <Howto_output>`. The vector values are
@ -430,7 +431,8 @@ the following global cumulative quantities:
The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

35
doc/src/fix_gle.rst
View File

@ -103,28 +103,31 @@ Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The instantaneous values of the extended variables are written to
:doc:`binary restart files <restart>`. Because the state of the random
number generator is not saved in restart files, this means you cannot
do "exact" restarts with this fix, where the simulation continues on
the same as if no restart had taken place. However, in a statistical
sense, a restarted simulation should produce the same behavior.
Note however that you should use a different seed each time you
restart, otherwise the same sequence of random numbers will be used
each time, which might lead to stochastic synchronization and
:doc:`binary restart files <restart>`. Because the state of the
random number generator is not saved in restart files, this means you
cannot do "exact" restarts with this fix, where the simulation
continues on the same as if no restart had taken place. However, in a
statistical sense, a restarted simulation should produce the same
behavior. Note however that you should use a different seed each time
you restart, otherwise the same sequence of random numbers will be
used each time, which might lead to stochastic synchronization and
subtle artifacts in the sampling.
The cumulative energy change in the system imposed by this fix is
included in the :doc:`thermodynamic output <thermo_style>` keywords
*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
doc page for details.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the same
cumulative energy change due to this fix described in the previous
paragraph. The scalar value calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
*start* and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the cumulative
energy change due to this fix. The scalar value calculated by this
fix is "extensive".
This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

26
doc/src/fix_gravity.rst
View File

@ -103,23 +103,27 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the gravitational potential energy of the system to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the gravitational potential energy of the system to
the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is adding its forces. Default is the outermost level.
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. This scalar is the gravitational
potential energy of the particles in the defined field, namely mass \*
(g dot x) for each particles, where x and mass are the particles
position and mass, and g is the gravitational field. The scalar value
calculated by this fix is "extensive".
:doc:`output commands <Howto_output>`. This scalar is the
gravitational potential energy of the particles in the defined field,
namely mass \* (g dot x) for each particles, where x and mass are the
particles position and mass, and g is the gravitational field. The
scalar value calculated by this fix is "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

12
doc/src/fix_halt.rst
View File

@ -115,6 +115,18 @@ The version with "bondmax" will just run somewhat faster, due to less
overhead in computing bond lengths and not storing them in a separate
compute.
A variable can be used to implement a large variety of conditions,
including to stop when a specific file exists. Example:
.. code-block:: LAMMPS
variable exit equal is_file(EXIT)
fix 10 all halt 100 v_exit != 0 error soft
Will stop the current run command when a file ``EXIT`` is created
in the current working directory. The condition can be cleared
by removing the file through the :doc:`shell <shell>` command.
The choice of operators listed above are the usual comparison
operators. The XOR operation (exclusive or) is also included as "\|\^".
In this context, XOR means that if either the attribute or avalue is

23
doc/src/fix_hyper_global.rst
View File

@ -200,16 +200,20 @@ algorithm.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy of the bias potential to the system's
potential energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the energy of the bias potential to the global
potential energy of the system as part of :doc:`thermodynamic output
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
energy no <fix_modify>`.
This fix computes a global scalar and global vector of length 12, which
can be accessed by various :doc:`output commands <Howto_output>`. The
scalar is the magnitude of the bias potential (energy units) applied on
the current timestep. The vector stores the following quantities:
This fix computes a global scalar and global vector of length 12,
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the magnitude of the bias potential
(energy units) applied on the current timestep. The vector stores the
following quantities:
* 1 = boost factor on this step (unitless)
* 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
@ -253,7 +257,8 @@ The scalar and vector values calculated by this fix are all
"intensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

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