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tomswinburne
2020-08-24 16:54:16 +02:00
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6
doc/Makefile
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@ -83,7 +83,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
@rm -rf html/JPG
@cp -r src/PDF html/PDF
@mkdir -p html/JPG
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@rm -rf html/PDF/.[sg]*
@mkdir -p html/_static/mathjax
@cp -r $(MATHJAX)/es5 html/_static/mathjax/
@ -194,9 +194,7 @@ $(VENV):
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install --upgrade pip; \
pip install Sphinx; \
pip install sphinxcontrib-spelling ;\
pip install breathe; \
pip install --use-feature=2020-resolver -r requirements.txt; \
deactivate;\
)

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doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "15 April 2020" "2020-04-15"
.TH LAMMPS "21 August 2020" "2020-08-21"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

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doc/requirements.txt Normal file
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@ -0,0 +1,4 @@
Sphinx
sphinxcontrib-spelling
breathe
Pygments

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doc/src/Build_basics.rst
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@ -193,14 +193,17 @@ compiler and any :doc:`accelerator packages <Speed_packages>` you have
included in the build.
You can tell CMake to look for a specific compiler with setting CMake
variable during configuration. For a few common choices, there are also
presets in the ``cmake/presets`` folder. For convenience, there is a
``CMAKE_TUNE_FLAGS`` variable that can be set to apply global compiler
options. More on that below, but you can also specify the corresponding
``CMAKE_*_FLAGS`` variables individually if you want to experiment with
alternate optimization flags. You should specify all 3 compilers, so
that the (few) LAMMPS source files written in C or Fortran are built
with a compiler consistent with the one used for the C++ files:
variables (listed below) during configuration. For a few common
choices, there are also presets in the ``cmake/presets`` folder. For
convenience, there is a ``CMAKE_TUNE_FLAGS`` variable that can be set to
apply global compiler options (applied to compilation only), to be used
for adding compiler or host specific optimization flags in addition to
the "flags" variables listed below. You may also specify the
corresponding ``CMAKE_*_FLAGS`` variables individually, if you want to
experiment with alternate optimization flags. You should specify all 3
compilers, so that the (few) LAMMPS source files written in C or Fortran
are built with a compiler consistent with the one used for the C++
files:
.. code-block:: bash
@ -229,11 +232,7 @@ can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly,
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By
default these are initialized to some compiler specific flags, to
optimize the LAMMPS executable with optimizations and instructions
available on the host where LAMMPS is compiled. For example, for Intel
compilers this would be ``-xHost`` and for GNU compilers this would be
``-march=native``. To turn these flags off, do ``-D CMAKE_TUNE_FLAGS=``.
default this variable is empty.
.. note::
@ -372,7 +371,8 @@ it. The build step will also create generic soft links, named
``liblammps.a`` and ``liblammps.so``\ , which point to the specific
``liblammps_machine.a/so`` files.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Note that for creating a shared library, all the libraries it depends on
must be compiled to be compatible with shared libraries. This should be
@ -462,7 +462,8 @@ tool. The actual translation is then done via make commands.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://sphinx-doc.org
**Documentation make option**\ :
Documentation make option
^^^^^^^^^^^^^^^^^^^^^^^^^
The following make commands can be issued in the doc folder of the
LAMMPS source distribution.
@ -489,7 +490,8 @@ your system.
current LAMMPS version (HTML and PDF files), from the website
`download page <https://lammps.sandia.gov/download.html>`_.
**CMake build option**\ :
CMake build option
^^^^^^^^^^^^^^^^^^
It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this
@ -512,7 +514,8 @@ Build LAMMPS tools
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
using CMake or Make.
**CMake build3**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -521,7 +524,8 @@ using CMake or Make.
The generated binaries will also become part of the LAMMPS installation
(see below).
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash
@ -545,7 +549,8 @@ a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
**CMake build**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -553,7 +558,8 @@ you want to copy files to is protected.
make # perform make after CMake command
make install # perform the installation into prefix
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
There is no "install" option in the ``src/Makefile`` for LAMMPS. If
you wish to do this you will need to first build LAMMPS, then manually

2
doc/src/Build_cmake.rst
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@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
``cmake .`` and then compile again. The included dependency tracking
should make certain that only the necessary subset of files are
re-compiled. You can also delete compiled objects, libraries and
executables with ``cmake --build . clean`` (or ``make clean``).
executables with ``cmake --build . --target clean`` (or ``make clean``).
After compilation, you may optionally install the LAMMPS executable into
your system with:

393
doc/src/Build_development.rst
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@ -8,8 +8,8 @@ useful during development, testing or debugging.
.. _compilation:
Verify compilation flags
------------------------
Monitor compilation flags
-------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
@ -19,7 +19,8 @@ compilation you can use the following option.
-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
Another way of doing this without reconfiguration is calling make with
variable VERBOSE set to 1:
.. code-block:: bash
@ -33,77 +34,385 @@ Address, Undefined Behavior, and Thread Sanitizer Support
---------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in code
which use different sanitizer libraries to detect problems in the code
during run-time. They can detect issues like:
- `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
- `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
- `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
Please note that this kind of instrumentation usually comes with a small
performance hit (much less than using tools like `Valgrind
<https://valgrind.org>`_). The to enable these features additional
compiler flags need to be added to the compilation and linking stages.
This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
variable during configuration. Examples:
Please note that this kind of instrumentation usually comes with a
performance hit (but much less than using tools like `Valgrind
<https://valgrind.org>`_ with a more low level approach). The to enable
these features additional compiler flags need to be added to the
compilation and linking stages. This is done through setting the
``ENABLE_SANITIZER`` variable during configuration. Examples:
.. code-block:: bash
-D CMAKE_TUNE_FLAGS=-fsanitize=address # enable address sanitizer / memory leak checker
-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behavior sanitizer
-D CMAKE_TUNE_FLAGS=-fsanitize=thread # enable thread sanitizer
-D ENABLE_SANITIZER=none # no sanitizer active (default)
-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
-D ENABLE_SANITIZER=leak # enable memory leak checker (only)
-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
-D ENABLE_SANITIZER=thread # enable thread sanitizer
----------
.. _testing:
Code Coverage and Testing
---------------------------------------
Code Coverage and Unit Testing
------------------------------
We do extensive regression testing of the LAMMPS code base on a continuous
basis. Some of the logic to do this has been added to the CMake build so
developers can run the tests directly on their workstation.
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
on various platforms and with a variety of settings), unit testing
(i.e. whether certain individual parts of the code produce the expected
results for given inputs), run testing (whether selected complete input
decks run without crashing for multiple configurations), and regression
testing (i.e. whether selected input examples reproduce the same
results over a given number of steps and operations within a given
error margin). The status of this automated testing can be viewed on
`https://ci.lammps.org <https://ci.lammps.org>`_.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development
headers to compile and will download and compile a recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
After compilation is complete, the unit testing is started in the build
folder using the ``ctest`` command, which is part of the CMake software.
The output of this command will be looking something like this::
[...]$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: MolPairStyle:hybrid-overlay
1/109 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
Start 2: MolPairStyle:hybrid
2/109 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
Start 3: MolPairStyle:lj_class2
[...]
Start 107: PotentialFileReader
107/109 Test #107: PotentialFileReader ................ Passed 0.04 sec
Start 108: EIMPotentialFileReader
108/109 Test #108: EIMPotentialFileReader ............. Passed 0.03 sec
Start 109: TestSimpleCommands
109/109 Test #109: TestSimpleCommands ................. Passed 0.02 sec
100% tests passed, 0 tests failed out of 26
Total Test time (real) = 25.57 sec
The ``ctest`` command has many options, the most important ones are:
.. list-table::
* - Option
- Function
* - -V
- verbose output: display output of individual test runs
* - -j <num>
- parallel run: run <num> tests in parallel
* - -R <regex>
- run subset of tests matching the regular expression <regex>
* - -E <regex>
- exclude subset of tests matching the regular expression <regex>
* - -N
- dry-run: display list of tests without running them
* - -T memcheck
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
kinds of tests implemented in different programming languages (C++, C, Python,
Fortran) and testing different aspects of the LAMMPS software and its features.
At the moment only tests for "force styles" are implemented. More on those
in the next section.
.. note::
this is incomplete and only represents a small subset of tests that we run
The unit test framework is new and still under development.
The coverage is only minimal and will be expanded over time.
Tests styles of the same kind of style (e.g. pair styles or
bond styles) are performed with the same executable using
different input files in YAML format. So to add a test for
another pair style can be done by copying the YAML file and
editing the style settings and then running the individual test
program with a flag to update the computed reference data.
Detailed documentation about how to add new test program and
the contents of the YAML files for existing test programs
will be provided in time as well.
Unit tests for force styles
^^^^^^^^^^^^^^^^^^^^^^^^^^^
A large part of LAMMPS are different "styles" for computing non-bonded
and bonded interactions selected through the :doc:`pair_style`,
:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
:doc:`improper_style`, and :doc:`kspace_style`. Since these all share
common interfaces, it is possible to write generic test programs that
will call those common interfaces for small test systems with less than
100 atoms and compare the results with pre-recorded reference results.
A test run is then a a collection multiple individual test runs each
with many comparisons to reference results based on template input
files, individual command settings, relative error margins, and
reference data stored in a YAML format file with ``.yaml``
suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
``test_angle_style`` are implemented. They will compare forces, energies and
(global) stress for all atoms after a ``run 0`` calculation and after a
few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
with different settings and also for multiple accelerated styles. If a
prerequisite style or package is missing, the individual tests are
skipped. All tests will be executed on a single MPI process, so using
the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
since this will skip the MPI initialization for each test run.
Below is an example command and output:
.. parsed-literal::
[tests]$ test_pair_style mol-pair-lj_cut.yaml
[==========] Running 6 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 6 tests from PairStyle
[ RUN ] PairStyle.plain
[ OK ] PairStyle.plain (24 ms)
[ RUN ] PairStyle.omp
[ OK ] PairStyle.omp (18 ms)
[ RUN ] PairStyle.intel
[ OK ] PairStyle.intel (6 ms)
[ RUN ] PairStyle.opt
[ SKIPPED ] PairStyle.opt (0 ms)
[ RUN ] PairStyle.single
[ OK ] PairStyle.single (7 ms)
[ RUN ] PairStyle.extract
[ OK ] PairStyle.extract (6 ms)
[----------] 6 tests from PairStyle (62 ms total)
[----------] Global test environment tear-down
[==========] 6 tests from 1 test suite ran. (63 ms total)
[ PASSED ] 5 tests.
[ SKIPPED ] 1 test, listed below:
[ SKIPPED ] PairStyle.opt
In this particular case, 5 out of 6 sets of tests were conducted, the
tests for the ``lj/cut/opt`` pair style was skipped, since the tests
executable did not include it. To learn what individual tests are performed,
you (currently) need to read the source code. You can use code coverage
recording (see next section) to confirm how well the tests cover the code
paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
* - Option
- Function
* - -g <newfile>
- regenerate reference data in new YAML file
* - -u
- update reference data in the original YAML file
* - -s
- print error statistics for each group of comparisons
* - -v
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
test programs, but a workaround has been implemented where these flags can be
set in an environment variable ``TEST_ARGS``. Example:
.. code-block:: bash
-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
env TEST_ARGS=-s ctest -V -R BondStyle
If you enable testing in the CMake build it will create an additional
target called "test". You can run them with:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
and working.
.. admonition:: Recommendations and notes for YAML files
:class: note
- The reference results should be recorded without any code
optimization or related compiler flags enabled.
- The ``epsilon`` parameter defines the relative precision with which
the reference results must be met. The test geometries often have
high and low energy parts and thus a significant impact from
floating-point math truncation errors is to be expected. Some
functional forms and potentials are more noisy than others, so this
parameter needs to be adjusted. Typically a value around 1.0e-13
can be used, but it may need to be as large as 1.0e-8 in some
cases.
- The tests for pair styles from OPT, USER-OMP and USER-INTEL are
performed with automatically rescaled epsilon to account for
additional loss of precision from code optimizations and different
summation orders.
- When compiling with (aggressive) compiler optimization, some tests
are likely to fail. It is recommended to inspect the individual
tests in detail to decide, whether the specific error for a specific
property is acceptable (it often is), or this may be an indication
of mis-compiled code (or an undesired large loss of precision due
to significant reordering of operations and thus less error cancellation).
Unit tests for timestepping related fixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A substantial subset of :doc:`fix styles <fix>` are invoked regularly
during MD timestepping and manipulate per-atom properties like
positions, velocities, and forces. For those fix styles, testing can be
done in a very similar fashion as for force fields and thus there is a
test program `test_fix_timestep` that shares a lot of code, properties,
and command line flags with the force field style testers described in
the previous section.
This tester will set up a small molecular system run with verlet run
style for 4 MD steps, then write a binary restart and continue for
another 4 MD steps. At this point coordinates and velocities are
recorded and compared to reference data. Then the system is cleared,
restarted and running the second 4 MD steps again and the data is
compared to the same reference. That is followed by another restart
after which per atom type masses are replaced with per-atom masses and
the second 4 MD steps are repeated again and compared to the same
reference. Also global scalar and vector data of the fix is recorded
and compared. If the fix is a thermostat and thus the internal property
``t_target`` can be extracted, then this is compared to the reference
data. The tests are repeated with the respa run style.
If the fix has a multi-threaded version in the USER-OMP package, then
the entire set of tests is repeated for that version as well.
For this to work, some additional conditions have to be met by the
YAML format test inputs.
- The fix to be tested (and only this fix), should be listed in the
``prerequisites:`` section
- The fix to be tested must be specified in the ``post_commands:``
section with the fix-ID ``test``. This section may contain other
commands and other fixes (e.g. an instance of fix nve for testing
a thermostat or force manipulation fix)
- For fixes that can tally contributions to the global virial, the
line ``fix_modify test virial yes`` should be included in the
``post_commands:`` section of the test input.
- For thermostat fixes the target temperature should be ramped from
an arbitrary value (e.g. 50K) to a pre-defined target temperature
entered as ``${t_target}``.
- For fixes that have thermostatting support included, but do not
have it enabled in the input (e.g. fix rigid with default settings),
the ``post_commands:`` section should contain the line
``variable t_target delete`` to disable the target temperature ramp
check to avoid false positives.
Use custom linker for faster link times when ENABLE_TESTING is active
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When compiling LAMMPS with enabled tests, most test executables will
need to be linked against the LAMMPS library. Since this can be a very
large library with many C++ objects when many packages are enabled, link
times can become very long on machines that use the GNU BFD linker (e.g.
Linux systems). Alternatives like the ``lld`` linker of the LLVM project
or the ``gold`` linker available with GNU binutils can speed up this step
substantially. CMake will by default test if any of the two can be
enabled and use it when ``ENABLE_TESTING`` is active. It can also be
selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``. The
``default`` option will use the system default linker otherwise, the
linker is chosen explicitly. This option is only available for the
GNU or Clang C++ compiler.
Tests for other components and utility functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Additional tests that validate utility functions or specific components
of LAMMPS are implemented as standalone executable which may, or may not
require creating a suitable LAMMPS instance. These tests are more specific
and do not require YAML format input files. To add a test, either an
existing source file needs to be extended or a new file added, which in turn
requires additions to the ``CMakeLists.txt`` file in the source folder.
Collect and visualize code coverage metrics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can also collect code coverage metrics while running LAMMPS or the
tests by enabling code coverage support during the CMake configuration:
.. code-block:: bash
cmake --build . test
-D ENABLE_COVERAGE=on # enable coverage measurements (off by default)
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the
run faster.
This will instrument all object files to write information about which
lines of code were accessed during execution in files next to the
corresponding object files. These can be post-processed to visually
show the degree of coverage and which code paths are accessed and which
are not taken. When working on unit tests (see above), this can be
extremely helpful to determine which parts of the code are not executed
and thus what kind of tests are still missing. The coverage data is
cumulative, i.e. new data is added with each new run.
You can also collect code coverage metrics while running the tests by
enabling coverage support during building.
Enabling code coverage will also add the following build targets to
generate coverage reports after running the LAMMPS executable or the
unit tests:
.. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
make clean_coverage_html # delete folder with HTML format coverage report
make reset_coverage # delete all collected coverage data and HTML output
This will also add the following targets to generate coverage reports
after running the LAMMPS executable:
.. code-block:: bash
make test # run tests first!
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
These reports require GCOVR to be installed. The easiest way to do this
to install it via pip:
These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
to do this to install it via pip:
.. code-block:: bash
pip install git+https://github.com/gcovr/gcovr.git
After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
* - .. figure:: JPG/coverage-overview-top.png
:target: JPG/coverage-overview-top.png
Top of the overview page
- .. figure:: JPG/coverage-overview-manybody.png
:target: JPG/coverage-overview-manybody.png
Styles with good coverage
- .. figure:: JPG/coverage-file-top.png
:target: JPG/coverage-file-top.png
Top of individual source page
- .. figure:: JPG/coverage-file-branches.png
:target: JPG/coverage-file-branches.png
Source page with branches
Coding style utilities
----------------------
To aid with enforcing some of the coding style conventions in LAMMPS
some additional build targets have been added. These require Python 3.5
or later and will only work on Unix-like operating and file systems.
The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.

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@ -1,12 +1,12 @@
Link LAMMPS as a library to another code
========================================
LAMMPS is designed as a library of C++ objects and can thus be
LAMMPS is designed as a library of C++ objects that can be
integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the :doc:`Howto
library <Howto_library>` doc page for a description of the interface
and how to extend it for your needs.
library <Howto_library>` page for a description of the interface
and how to use it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in a file
@ -31,18 +31,18 @@ the suffix ``.so.0`` (or some other number).
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
----------
**Link with LAMMPS as a static library**\ :
Link with LAMMPS as a static library
------------------------------------
The calling application can link to LAMMPS as a static library with
compilation and link commands as in the examples shown below. These
are examples for a code written in C in the file *caller.c*.
are examples for a code written in C in the file ``caller.c``.
The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required
executable code from the library is copied into the calling executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
@ -55,7 +55,8 @@ The commands to compile and link a coupled executable are then:
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
This assumes that LAMMPS has been compiled in the folder
``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
@ -83,20 +84,20 @@ LAMMPS library without any optional packages that depend on libraries
need to include all flags, libraries, and paths for the coupled
executable, that are also required to link the LAMMPS executable.
*CMake build*\ :
CMake build
^^^^^^^^^^^
When using CMake, additional libraries with sources in the lib folder
are built, but not included in ``liblammps.a`` and (currently) not
installed with "make install" and not included in the *pkgconfig*
installed with ``make install`` and not included in the ``pkgconfig``
configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is
therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared
library instead.
.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=static serial". And you also
@ -110,10 +111,10 @@ change to:
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since the
LAMMPS library is C++ code. You can display the currently applied
settings for building LAMMPS for the "serial" machine target by using
the command:
Note, that you need to link with ``g++`` instead of ``gcc`` even if you have
written your code in C, since LAMMPS itself is C++ code. You can display the
currently applied settings for building LAMMPS for the "serial" machine target
by using the command:
.. code-block:: bash
@ -136,12 +137,11 @@ Which should output something like:
From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the
equivalent and replace "serial" with the corresponding *machine* name
equivalent and replace "serial" with the corresponding "machine" name
of the makefile.
----------
**Link with LAMMPS as a shared library**\ :
Link with LAMMPS as a shared library
------------------------------------
When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
@ -151,7 +151,8 @@ linking the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library with
the POEMS package installed becomes:
*CMake build*\ :
CMake build
^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the CMake
build process are the same as for the static library.
@ -161,10 +162,11 @@ build process are the same as for the static library.
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
*Traditional make*\ :
Traditional make
^^^^^^^^^^^^^^^^
The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shared serial" becomes:
traditional make build using ``make mode=shared serial`` becomes:
.. code-block:: bash
@ -231,29 +233,3 @@ If a required library is missing, you would get a 'not found' entry:
libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
/lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
----------
**Calling the LAMMPS library**\ :
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface from a shared library through the `ctypes python module <ctypes_>`_.
See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _ctypes: https://docs.python.org/3/library/ctypes.html

29
doc/src/Build_package.rst
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@ -45,7 +45,8 @@ packages:
The mechanism for including packages is simple but different for CMake
versus make.
**CMake build**\ :
CMake build
^^^^^^^^^^^
.. code-block:: csh
@ -72,7 +73,8 @@ once with CMake.
invoke cmake. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
**Traditional make**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: bash
@ -108,7 +110,8 @@ once with make.
within the same command. You can include or exclude multiple packages
in a single make command, e.g. make yes-colloid no-manybody.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Any package can be included or excluded in a LAMMPS build, independent
of all other packages. However, some packages include files derived
@ -132,7 +135,7 @@ src directory.
.. _cmake_presets:
**CMake shortcuts for installing many packages**\ :
CMake presets for installing many packages
Instead of specifying all the CMake options via the command-line,
CMake allows initializing its settings cache using script files.
@ -148,13 +151,14 @@ one of them as a starting point and customize it to your needs.
.. code-block:: bash
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel 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
cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel 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
.. note::
@ -184,7 +188,8 @@ one of them as a starting point and customize it to your needs.
----------
**Make shortcuts for installing many packages**\ :
Make shortcuts for installing many packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.

82
doc/src/Build_settings.rst
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@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
LAMMPS can use them if they are available on your system.
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -74,7 +75,12 @@ to assist:
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARIES=path
**Makefile.machine settings**\ :
Traditional make
^^^^^^^^^^^^^^^^
To change the FFT library to be used and its options, you have to edit
your machine Makefile. Below are examples how the makefile variables
could be changed.
.. code-block:: make
@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
the compiler can find the FFT header and library files in its default search path.
You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
**CMake and make info**\ :
CMake build
^^^^^^^^^^^
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``\ . The install command typically requires root privileges
make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see
various options.
@ -169,20 +176,25 @@ ARRAY mode.
.. _size:
Size of LAMMPS data types
Size of LAMMPS integer types
------------------------------------
LAMMPS has a few integer data types which can be defined as 4-byte or
8-byte integers. The default setting of "smallbig" is almost always
adequate.
LAMMPS has a few integer data types which can be defined as either
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
The default setting of "smallbig" is almost always adequate.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
**Makefile.machine setting**\ :
Traditional build
^^^^^^^^^^^^^^^^^
If you want a setting different from the default, you need to edit your
machine Makefile.
.. code-block:: make
@ -190,7 +202,8 @@ adequate.
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
The default "smallbig" setting allows for simulations with:
@ -251,7 +264,8 @@ PNG image files. Likewise the :doc:`dump movie <dump_image>` command
outputs movie files in MPEG format. Using these options requires the
following settings:
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -276,7 +290,8 @@ variables:
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
**Makefile.machine settings**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link. You must
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
that is a directory in your PATH environment variable.
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
Using ``ffmpeg`` to output movie files requires that your machine
supports the "popen" function in the standard runtime library.
@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
gzip compression by several LAMMPS commands, including
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
**CMake variables**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
**CMake and make info**\ :
CMake and make info
^^^^^^^^^^^^^^^^^^^
This option requires that your machine supports the "popen()" function
in the standard runtime library and that a gzip executable can be
@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being
aligned on 64-byte boundaries.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead. When
compiling LAMMPS for Windows systems, malloc() will always be used
and this setting ignored.
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -398,13 +419,15 @@ types, the following setting will be needed. It converts "long long"
to a "long" data type, which should be the desired 8-byte integer on
those systems:
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
@ -420,17 +443,26 @@ Exception handling when using LAMMPS as a library
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course the calling code has to be set up to
*catch* exceptions from within LAMMPS.
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions thrown from within LAMMPS.
**CMake variable**\ :
CMake build
^^^^^^^^^^^
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
**Makefile.machine setting**\ :
Traditional make
^^^^^^^^^^^^^^^^
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
.. note::
When LAMMPS is running in parallel, it is not always possible to
cleanly recover from an exception since not all parallel ranks may
throw an exception and thus other MPI ranks may get stuck waiting for
messages from the ones with errors.

2
doc/src/Build_windows.rst
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@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu
from within Windows and from there on, you can pretty much use that
shell like you are running on an Ubuntu Linux machine (e.g. installing
software via apt-get and more). For more details on that, please
see :doc:`this tutorial <Howto_bash>`
see :doc:`this tutorial <Howto_wsl>`
.. _gnu:

11
doc/src/Commands_all.rst
View File

@ -46,13 +46,6 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump atom/adios <dump_adios>`
* :doc:`dump custom/adios <dump_adios>`
* :doc:`dump image <dump_image>`
* :doc:`dump movie <dump_image>`
* :doc:`dump netcdf <dump_netcdf>`
* :doc:`dump netcdf/mpiio <dump_netcdf>`
* :doc:`dump vtk <dump_vtk>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`echo <echo>`
@ -94,6 +87,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`package <package>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_style <pair_style>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`
@ -107,7 +101,8 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`

1
doc/src/Commands_bond.rst
View File

@ -46,6 +46,7 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`
.. _angle:

12
doc/src/Commands_compute.rst
View File

@ -42,7 +42,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`com <compute_com>`
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom <compute_coord_atom>`
* :doc:`coord/atom (k) <compute_coord_atom>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
@ -79,9 +79,8 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`meso/e/atom <compute_meso_e_atom>`
* :doc:`meso/rho/atom <compute_meso_rho_atom>`
* :doc:`meso/t/atom <compute_meso_t_atom>`
* :doc:`mesont <compute_mesont>`
* :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
* :doc:`msd/chunk <compute_msd_chunk>`
@ -124,6 +123,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>`
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>`
* :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>`
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>`
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`
@ -133,6 +133,9 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`
* :doc:`sph/rho/atom <compute_sph_rho_atom>`
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/mop <compute_stress_mop>`
@ -161,5 +164,6 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`viscosity/cos <compute_viscosity_cos>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`

9
doc/src/Commands_fix.rst
View File

@ -22,6 +22,7 @@ OPT.
.. table_from_list::
:columns: 5
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
@ -41,6 +42,7 @@ OPT.
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
* :doc:`bond/create/angle <fix_bond_create>`
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`
@ -94,10 +96,9 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`meso <fix_meso>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`meso/stationary <fix_meso_stationary>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
* :doc:`msst <fix_msst>`
@ -148,6 +149,7 @@ OPT.
* :doc:`oneway <fix_oneway>`
* :doc:`orient/bcc <fix_orient>`
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
@ -202,6 +204,8 @@ OPT.
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
* :doc:`sph <fix_sph>`
* :doc:`sph/stationary <fix_sph_stationary>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`
@ -242,3 +246,4 @@ OPT.
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
* :doc:`widom <fix_widom>`

6
doc/src/Commands_input.rst
View File

@ -31,9 +31,9 @@ does something different than this sequence:
run 100
In the first case, the specified timestep (0.5 fs) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
timestep is used for the 2nd one.
simulations of 100 timesteps each. In the second case, the default
timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
timestep is used for the second one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms

23
doc/src/Commands_pair.rst
View File

@ -92,8 +92,8 @@ OPT.
* :doc:`drip <pair_drip>`
* :doc:`eam (gikot) <pair_eam>`
* :doc:`eam/alloy (gikot) <pair_eam>`
* :doc:`eam/cd (o) <pair_eam>`
* :doc:`eam/cd/old (o) <pair_eam>`
* :doc:`eam/cd <pair_eam>`
* :doc:`eam/cd/old <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
@ -136,22 +136,22 @@ OPT.
* :doc:`lj/class2/soft <pair_fep_soft>`
* :doc:`lj/cubic (go) <pair_lj_cubic>`
* :doc:`lj/cut (gikot) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/msm (go) <pair_lj>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj>`
* :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/thole/long (o) <pair_thole>`
* :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
* :doc:`lj/cut/tip4p/long (got) <pair_lj>`
* :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
* :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`lj/expand (gko) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@ -180,8 +180,10 @@ OPT.
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :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:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
@ -227,7 +229,6 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (k) <pair_snap>`
* :doc:`snap (k) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`

2
doc/src/Developer/developer.tex
View File

@ -142,7 +142,7 @@ follows:
minimize.
\item The Special class walks the bond topology of a molecular system
to find 1st, 2nd, 3rd neighbors of each atom. It is invoked by
to find first, second, third neighbors of each atom. It is invoked by
several commands, like read\_data, read\_restart, and replicate.
\item The Atom class stores all per-atom arrays. More precisely, they

42
doc/src/Errors_messages.rst
View File

@ -381,7 +381,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are defined.
*Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -391,7 +391,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
the atoms are too far apart to make a valid bond.
*Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor.
The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
@ -401,12 +401,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are too far apart to make a valid bond.
*Bond atoms %d %d missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond atoms missing on proc %d at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -1374,7 +1374,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
template does not qualify.
*Cannot use fix box/relax on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two
When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1388,7 +1388,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
also keyword tri or xy, this is wrong.
*Cannot use fix box/relax with tilt factor scaling on a 2nd non-periodic dimension*
When specifying scaling on a tilt factor component, the 2nd of the two
When specifying scaling on a tilt factor component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1429,7 +1429,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
This would be changing the same box dimension twice.
*Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension*
When specifying an off-diagonal pressure component, the 2nd of the two
When specifying an off-diagonal pressure component, the second of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
@ -1447,13 +1447,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory.
*Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension*
The 2nd dimension in the barostatted tilt factor must be periodic.
The second dimension in the barostatted tilt factor must be periodic.
*Cannot use fix pour rigid and not molecule*
Self-explanatory.
@ -1909,18 +1909,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Compute for fix pafi must have 9 fields per atom*
Self-explanatory.
*Compute gyration ID does not exist for compute gyration/shape*
Self-explanatory. Provide a valid compute ID.
*Compute gyration/shape compute ID does not point to a gyration compute*
Self-explanatory. Provide and ID of a compute gyration command.
*Compute ID for compute chunk /atom does not exist*
Self-explanatory.
*Compute ID for compute chunk/atom does not exist*
Self-explanatory.
*Compute gyration ID does not exist for compute gyration/shape*
Self-explanatory. Provide a valid compute ID.
*Compute gyration/shape compute ID does not point to a gyration compute*
Self-explanatory. Provide and ID of a compute gyration command.
*Compute ID for compute reduce does not exist*
Self-explanatory.
@ -1945,9 +1945,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Compute ID for fix numdiff does not exist*
Self-explanatory.
*Compute ID for fix pafi does not exist*
Self-explanatory.
*Compute ID for fix store/state does not exist*
Self-explanatory.
@ -2123,8 +2120,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Compute hexorder/atom requires a pair style be defined*
Self-explanatory.
*Compute improper/local used when impropers are not allowed*
The atom style does not support impropers.
@ -3881,9 +3876,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
error occurs, it is likely a bug, so send an email to the
`developers <https://lammps.sandia.gov/authors.html>`_.
*Fix pafi requires a damped dynamics minimizer*
Use a different minimization style.
*Fix peri neigh does not exist*
Somehow a fix that the pair style defines has been deleted.
@ -7206,7 +7198,7 @@ keyword to allow for additional bonds to be formed
does not exist.
*Replacing a fix, but new style != old style*
A fix ID can be used a 2nd time, but only if the style matches the
A fix ID can be used a second time, but only if the style matches the
previous fix. In this case it is assumed you with to reset a fix's
parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to.

26
doc/src/Errors_warnings.rst
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@ -43,17 +43,17 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Self-explanatory.
*Bond atom missing in box size check*
The 2nd atoms needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond atom missing in image check*
The 2nd atom in a particular bond is missing on this processor.
The second atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
*Bond atoms missing at step %ld*
The 2nd atom needed to compute a particular bond is missing on this
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
incorrect periodic images of atoms in interaction lists. To avoid, either use
:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
Since LAMMPS stores topology data with individual atoms, all atoms
comprising a bond, angle, dihedral or improper must be present on any
sub-domain that "owns" the atom with the information, either as a
local or a ghost atom. The communication cutoff is what determines up
to what distance from a sub-domain boundary ghost atoms are created.
The communication cutoff is by default the largest non-bonded cutoff
plus the neighbor skin distance, but for short or non-bonded cutoffs
and/or long bonds, this may not be sufficient. This warning indicates
that there is an increased risk of a simulation stopping unexpectedly
because of Bond/Angle/Dihedral/Improper atoms missing. It can be
silenced by manually setting the communication cutoff via
:doc:`comm_modify cutoff <comm_modify>`. However, since the
heuristic used to determine the estimate is not always accurate, it
is not changed automatically and the warning may be ignored depending
on the specific system being simulated.
*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
Self-explanatory.
@ -486,7 +504,7 @@ This will most likely cause errors in kinetic fluctuations.
a new style.
*No Kspace calculation with verlet/split*
The 2nd partition performs a kspace calculation so the kspace_style
The second partition performs a kspace calculation so the kspace_style
command must be used.
*No automatic unit conversion to XTC file format conventions possible for units lj*

2
doc/src/Examples.rst
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@ -163,7 +163,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site.

2
doc/src/Howto.rst
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@ -19,7 +19,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_pylammps
Howto_bash
Howto_wsl
General howto
=============

4
doc/src/Howto_bioFF.rst
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@ -102,8 +102,8 @@ documentation for the formula it computes.
* :doc:`pair_style <pair_buck>` buck/coul/cut
* :doc:`pair_style <pair_buck>` buck/coul/long
* :doc:`pair_style <pair_lj>` lj/cut
* :doc:`pair_style <pair_lj>` lj/cut/coul/cut
* :doc:`pair_style <pair_lj>` lj/cut/coul/long
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/lj
* :doc:`pair_style <pair_hbond_dreiding>` hbond/dreiding/morse

171
doc/src/Howto_body.rst
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@ -9,13 +9,15 @@ surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
simpler entities that body particles. See the :doc:`Howto spherical <Howto_spherical>` doc page for a general overview of all
these particle types.
simpler entities than body particles. See the :doc:`Howto spherical
<Howto_spherical>` doc page for a general overview of all these
particle types.
Body particles are used via the :doc:`atom_style body <atom_style>`
command. It takes a body style as an argument. The current body
styles supported by LAMMPS are as follows. The name in the first
column is used as the *bstyle* argument for the :doc:`atom_style body <atom_style>` command.
column is used as the *bstyle* argument for the :doc:`atom_style body
<atom_style>` command.
+----------------------+---------------------------------------------------+
| *nparticle* | rigid body with N sub-particles |
@ -30,8 +32,9 @@ thus how they can be used to compute pairwise body/body or
bond/non-body (point particle) interactions. More details of each
style are described below.
More styles may be added in the future. See the :doc:`Modify body <Modify_body>` doc page for details on how to add a new body
style to the code.
More styles may be added in the future. See the :doc:`Modify body
<Modify_body>` doc page for details on how to add a new body style to
the code.
----------
@ -55,10 +58,10 @@ interactions, building neighbor lists, migrating particles between
processors, output of particles to a dump file, etc. This means that
interactions between pairs of bodies or between a body and non-body
(point) particle need to be encoded in an appropriate pair style. If
such a pair style were to mimic the :doc:`fix rigid <fix_rigid>` model,
it would need to loop over the entire collection of interactions
between pairs of simple particles within the two bodies, each time a
single body/body interaction was computed.
such a pair style were to mimic the :doc:`fix rigid <fix_rigid>`
model, it would need to loop over the entire collection of
interactions between pairs of simple particles within the two bodies,
each time a single body/body interaction was computed.
Thus it only makes sense to use body particles and develop such a pair
style, when particle/particle interactions are more complex than what
@ -160,27 +163,6 @@ of the body particle.
The :doc:`pair_style body/nparticle <pair_body_nparticle>` command can be used
with this body style to compute body/body and body/non-body interactions.
For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of sub-particle
2 = y position of sub-particle
3 = z position of sub-particle
These values are the current position of the sub-particle within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientation of the body particle.
For images created by the :doc:`dump image <dump_image>` command, if the
*body* keyword is set, then each body particle is drawn as a
collection of spheres, one for each sub-particle. The size of each
sphere is determined by the *bflag1* parameter for the *body* keyword.
The *bflag2* argument is ignored.
----------
**Specifics of body style rounded/polygon:**
@ -208,7 +190,7 @@ The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.
When the :doc:`read_data <read_data>` command reads a data file for this
body style, the following information must be provided for each entry
body style, the following information must be provided for each body
in the *Bodies* section of the data file:
.. parsed-literal::
@ -219,21 +201,25 @@ in the *Bodies* section of the data file:
x1 y1 z1
...
xN yN zN
i j j k k ...
diameter
where M = 6 + 3\*N + 2\*N + 1, and N is the number of vertices in the
body particle.
where M = 6 + 3\*N + 1, and N is the number of vertices in the body
particle.
The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
list 6 moments of inertia, followed by the coordinates of the N
vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by
2N vertex indices corresponding to the end points of the N edges,
followed by a single diameter value = the rounded diameter of the
circle that surrounds each vertex. The diameter value can be different
for each body particle. These floating-point values can be listed on
as many lines as you wish; see the :doc:`read_data <read_data>` command
for more details.
a diameter value = the rounded diameter of the circle that surrounds
each vertex. The diameter value can be different for each body
particle. These floating-point values can be listed on as many lines
as you wish; see the :doc:`read_data <read_data>` command for more
details.
.. note::
It is important that the vertices for each polygonal body particle be
listed in order around its perimeter, so that edges can be inferred.
LAMMPS does not check that this is the case.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
@ -260,10 +246,6 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
-0.7071 0.7071 0
0.7071 0.7071 0
0.7071 -0.7071 0
0 1
1 2
2 3
3 0
1.0
A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
@ -345,8 +327,10 @@ in the *Bodies* section of the data file:
1 2 3 4
diameter
where M = 6 + 3\*N + 2\*E + 4\*F + 1, and N is the number of vertices in
the body particle, E = number of edges, F = number of faces.
where M = 6 + 3\*N + 2\*E + 4\*F + 1, and N is the number of vertices
in the body particle, E = number of edges, F = number of faces. For N
= 1 or 2, the format is simpler. E and F are ignored and no edges or
faces are listed, so that M = 6 + 3\*N + 1.
The integer line has three values: number of vertices (N), number of
edges (E) and number of faces (F). The floating point line(s) list 6
@ -356,16 +340,26 @@ the end points of the E edges, then 4\*F vertex indices defining F
faces. The last value is the diameter value = the rounded diameter of
the sphere that surrounds each vertex. The diameter value can be
different for each body particle. These floating-point values can be
listed on as many lines as you wish; see the
:doc:`read_data <read_data>` command for more details. Because the
maximum number of vertices per face is hard-coded to be 4
(i.e. quadrilaterals), faces with more than 4 vertices need to be
split into triangles or quadrilaterals. For triangular faces, the
last vertex index should be set to -1.
listed on as many lines as you wish; see the :doc:`read_data
<read_data>` command for more details.
The ordering of the 4 vertices within a face should follow
the right-hand rule so that the normal vector of the face points
outwards from the center of mass.
Note that vertices are numbered from 0 to N-1 inclusive. The order of
the 2 vertices in each edge does not matter. Faces can be triangles
or quadrilaterals. In both cases 4 vertices must be specified. For a
triangle the 4th vertex is -1. The 4 vertices within each triangle or
quadrilateral face should be ordered by the right-hand rule so that
the normal vector of the face points outwards from the center of mass.
For polyhedron with faces with more than 4 vertices, you should split
the complex face into multiple simple faces, each of which is a
triangle or quadrilateral.
.. note::
If a face is a quadrilateral then its 4 vertices must be co-planar.
LAMMPS does not check that this is the case. If you have a quad-face
of a polyhedron that is not planar (e.g. a cube whose vertices have
been randomly displaced), then you should represent the single quad
face as two triangle faces instead.
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
@ -421,8 +415,8 @@ by circles of diameter 0.5, is specified as follows:
.. parsed-literal::
1 1 13
2
1 3 13
2 1 1
0 1.33333 1.33333 0 0 0
-2 0 0
2 0 0
@ -432,27 +426,34 @@ A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
.. parsed-literal::
1 1 10
1
1 3 10
1 1 1
0.9 0.9 0.9 0 0 0
0 0 0
3.0
The :doc:`pair_style body/rounded/polhedron <pair_body_rounded_polyhedron>` command can
be used with this body style to compute body/body interactions. The
:doc:`fix wall/body/polyhedron <fix_wall_body_polygon>` command can be
used with this body style to compute the interaction of body particles
with a wall.
The number of edges and faces for a rod or sphere must be listed,
but is ignored.
The :doc:`pair_style body/rounded/polhedron
<pair_body_rounded_polyhedron>` command can be used with this body
style to compute body/body interactions. The :doc:`fix
wall/body/polyhedron <fix_wall_body_polygon>` command can be used with
this body style to compute the interaction of body particles with a
wall.
----------
For output purposes via the :doc:`compute body/local <compute_body_local>` and :doc:`dump local <dump>`
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
**Output specifics for all body styles:**
For the :doc:`compute body/local <compute_body_local>` and :doc:`dump
local <dump>` commands, all 3 of the body styles described on his page
produces one datum for each of the N vertices (of sub-particles) in a
body particle. The datum has 3 values:
.. parsed-literal::
1 = x position of vertex
1 = x position of vertex (or sub-particle)
2 = y position of vertex
3 = z position of vertex
@ -461,15 +462,29 @@ simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientation of the body particle.
For images created by the :doc:`dump image <dump_image>` command, if the
*body* keyword is set, then each body particle is drawn as a polygon
consisting of N line segments. Note that the line segments are drawn
between the N vertices, which does not correspond exactly to the
physical extent of the body (because the :doc:`pair_style rounded/polygon <pair_body_rounded_polygon>` defines finite-size
spheres at those point and the line segments between the spheres are
tangent to the spheres). The drawn diameter of each line segment is
determined by the *bflag1* parameter for the *body* keyword. The
*bflag2* argument is ignored.
The :doc:`dump image <dump_image>` command and its *body* keyword can
be used to render body particles.
For the *nparticle* body style, each body is drawn as a
collection of spheres, one for each sub-particle. The size of each
sphere is determined by the *bflag1* parameter for the *body* keyword.
The *bflag2* argument is ignored.
For the *rounded/polygon* body style, each body is drawn as a polygon
with N line segments. For the *rounded/polyhedron* body style, each
face of each body is drawn as a polygon with N line segments. The
drawn diameter of each line segment is determined by the *bflag1*
parameter for the *body* keyword. The *bflag2* argument is ignored.
Note that for both the *rounded/polygon* and *rounded/polyhedron*
styles, line segments are drawn between the pairs of vertices.
Depending on the diameters of the line segments this may be slightly
different than the physical extent of the body as calculated by the
:doc:`pair_style rounded/polygon <pair_body_rounded_polygon>` or
:doc:`pair_style rounded/polyhedron <pair_body_rounded_polyhedron>`
commands. Conceptually, the pair styles define the surface of a 2d or
3d body by lines or planes that are tangent to the finite-size spheres
of specified diameter which are placed on each vertex position.
----------

2
doc/src/Howto_chunk.rst
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@ -197,7 +197,7 @@ compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule
chunks, to create a 2nd set of micelle-scale chunks (clustered
chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment

12
doc/src/Howto_cmake.rst
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@ -47,7 +47,7 @@ using a shell like Bash.
- Linux: any Terminal window will work
- MacOS X: launch the Terminal application.
- Windows 10: install and run the :doc:`Windows subsystem for Linux <Howto_bash>`
- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
We also assume that you have downloaded and unpacked a recent LAMMPS source code package
or used Git to create a clone of the LAMMPS sources on your compilation machine.
@ -331,7 +331,7 @@ Some common LAMMPS specific variables
* - ``BUILD_DOC``
- include building the HTML format documentation for packaging/installing (default: ``off``)
* - ``CMAKE_TUNE_FLAGS``
- common compiler flags, for optimization or instrumentation (default: compiler specific)
- common compiler flags, for optimization or instrumentation (default:)
* - ``LAMMPS_MACHINE``
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``LAMMPS_EXCEPTIONS``
@ -415,8 +415,10 @@ This is particularly convenient, if you have set a custom build command
via the ``CMAKE_MAKE_PROGRAM`` variable.
When calling the build program, you can also select which "target" is to
be build through appending the name of the target to the build command.
Example: ``cmake --build . all``. The following abstract targets are available:
be build through appending the ``--target`` flag and the name of the target
to the build command. When using ``make`` as build tool, you can just append
the target name to the command. Example: ``cmake --build . --target all`` or
``make all``. The following abstract targets are available:
.. list-table::
:header-rows: 1
@ -432,7 +434,7 @@ Example: ``cmake --build . all``. The following abstract targets are available:
* - ``install``
- install all target files into folders in ``CMAKE_INSTALL_PREFIX``
* - ``test``
- run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
- run some tests (if configured with ``-D ENABLE_TESTING=on``)
* - ``clean``
- remove all generated files

2
doc/src/Howto_coreshell.rst
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@ -119,7 +119,7 @@ non-polarized ions (ions without an attached satellite particle). The
groups, one for the core atoms, another for the shell atoms.
Non-polarized ions which might also be included in the treated system
should not be included into either of these groups, they are taken
into account by the *group-ID* (2nd argument) of the compute. The
into account by the *group-ID* (second argument) of the compute. The
groups can be defined using the :doc:`group *type*\ <group>` command.
Note that to perform thermostatting using this definition of
temperature, the :doc:`fix modify temp <fix_modify>` command should be

2
doc/src/Howto_multiple.rst
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@ -91,4 +91,4 @@ With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
the fourth simulation, and so forth, until all 8 were completed.

51
doc/src/Howto_output.rst
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@ -3,13 +3,15 @@ Output from LAMMPS (thermo, dumps, computes, fixes, variables)
There are four basic kinds of LAMMPS output:
* :doc:`Thermodynamic output <thermo_style>`, which is a list
of quantities printed every few timesteps to the screen and logfile.
* :doc:`Thermodynamic output <thermo_style>`, which is a list of
quantities printed every few timesteps to the screen and logfile.
* :doc:`Dump files <dump>`, which contain snapshots of atoms and various
per-atom values and are written at a specified frequency.
* Certain fixes can output user-specified quantities to files: :doc:`fix ave/time <fix_ave_time>` for time averaging, :doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and :doc:`fix print <fix_print>` for single-line output of
:doc:`variables <variable>`. Fix print can also output to the
screen.
* Certain fixes can output user-specified quantities to files:
:doc:`fix ave/time <fix_ave_time>` for time averaging,
:doc:`fix ave/chunk <fix_ave_chunk>` for spatial or other averaging, and
:doc:`fix print <fix_print>` for single-line output of
:doc:`variables <variable>`. Fix print can also output to the screen.
* :doc:`Restart files <restart>`.
A simulation prints one set of thermodynamic output and (optionally)
@ -41,7 +43,7 @@ to output and the kind of data they operate on and produce:
.. _global:
Global/per-atom/local data
---------------------------------------
--------------------------
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
@ -54,7 +56,7 @@ bond distances.
.. _scalar:
Scalar/vector/array data
-------------------------------------
------------------------
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
@ -81,10 +83,27 @@ the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
.. _disambiguation:
Disambiguation
--------------
Some computes and fixes produce data in multiple styles, e.g. a global
scalar and a per-atom vector. Usually the context in which the input
script references the data determines which style is meant. Example: if
a compute provides both a global scalar and a per-atom vector, the
former will be accessed by using ``c_ID`` in an equal-style variable,
while the latter will be accessed by using ``c_ID`` in an atom-style
variable. Note that atom-style variable formulas can also access global
scalars, but in this case it is not possible to do directly because of
the ambiguity. Instead, an equal-style variable can be defined which
accesses the global scalar, and that variable used in the atom-style
variable formula in place of ``c_ID``.
.. _thermo:
Thermodynamic output
---------------------------------
--------------------
The frequency and format of thermodynamic output is set by the
:doc:`thermo <thermo>`, :doc:`thermo_style <thermo_style>`, and
@ -112,7 +131,7 @@ intensive result.
.. _dump:
Dump file output
---------------------------
----------------
Dump file output is specified by the :doc:`dump <dump>` and
:doc:`dump_modify <dump_modify>` commands. There are several
@ -138,7 +157,7 @@ command.
.. _fixoutput:
Fixes that write output files
---------------------------------------------
-----------------------------
Several fixes take various quantities as input and can write output
files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
@ -192,7 +211,7 @@ from normal thermodynamic or dump file output.
.. _computeoutput:
Computes that process output quantities
-----------------------------------------------------------
---------------------------------------
The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
or local vector quantities as inputs and "reduce" them (sum, min, max,
@ -219,7 +238,7 @@ output commands.
.. _fixprocoutput:
Fixes that process output quantities
--------------------------------------------------------
------------------------------------
The :doc:`fix vector <fix_vector>` command can create global vectors as
output from global scalars as input, accumulating them one element at
@ -244,7 +263,7 @@ The output of this fix can be used as input to other output commands.
.. _compute:
Computes that generate values to output
-----------------------------------------------------
---------------------------------------
Every :doc:`compute <compute>` in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
@ -257,7 +276,7 @@ without the word "atom" or "local" produce global values.
.. _fix:
Fixes that generate values to output
----------------------------------------------
------------------------------------
Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
@ -269,7 +288,7 @@ describes them.
.. _variable:
Variables that generate values to output
-------------------------------------------------------
----------------------------------------
:doc:`Variables <variable>` defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
@ -284,7 +303,7 @@ commands described in this section.
.. _table:
Summary table of output options and data flow between commands
--------------------------------------------------------------------------
--------------------------------------------------------------
This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of

2
doc/src/Howto_restart.rst
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@ -28,7 +28,7 @@ scripts are based on. If that script had the line
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
This script could be used to read the first restart file and re-run the
last 50 timesteps:
.. code-block:: LAMMPS

6
doc/src/Howto_tip4p.rst
View File

@ -11,11 +11,11 @@ angle style of *harmonic* or *charmm* should also be used.
A TIP4P model is run with LAMMPS using either this command
for a cutoff model:
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these two commands for a long-range model:
* :doc:`pair_style lj/cut/tip4p/long <pair_lj>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
* :doc:`kspace_style pppm/tip4p <kspace_style>`
For both models, the bond lengths and bond angles should be held fixed
@ -95,7 +95,7 @@ typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj>` command.
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.

6
doc/src/Howto_triclinic.rst
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@ -85,7 +85,7 @@ where *V* is the volume of the box, **X** is the original vector quantity and
**x** is the vector in the LAMMPS basis.
There is no requirement that a triclinic box be periodic in any
dimension, though it typically should be in at least the 2nd dimension
dimension, though it typically should be in at least the second dimension
of the tilt (y in xy) if you want to enforce a shift in periodic
boundary conditions across that boundary. Some commands that work
with triclinic boxes, e.g. the :doc:`fix deform <fix_deform>` and :doc:`fix npt <fix_nh>` commands, require periodicity or non-shrink-wrap
@ -120,7 +120,7 @@ The 9 parameters, as well as lx,ly,lz, can be output via the
To avoid extremely tilted boxes (which would be computationally
inefficient), LAMMPS normally requires that no tilt factor can skew
the box more than half the distance of the parallel box length, which
is the 1st dimension in the tilt factor (x for xz). This is required
is the first dimension in the tilt factor (x for xz). This is required
both when the simulation box is created, e.g. via the
:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands,
as well as when the box shape changes dynamically during a simulation,
@ -137,7 +137,7 @@ limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
command), then the box is "flipped" to an equivalent shape with a tilt
factor within the bounds, so the run can continue. See the :doc:`fix deform <fix_deform>` doc page for further details.
One exception to this rule is if the 1st dimension in the tilt
One exception to this rule is if the first dimension in the tilt
factor (x for xy) is non-periodic. In that case, the limits on the
tilt factor are not enforced, since flipping the box in that dimension
does not change the atom positions due to non-periodicity. In this

21
doc/src/Howto_viscosity.rst
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@ -1,10 +1,11 @@
Calculate viscosity
===================
The shear viscosity eta of a fluid can be measured in at least 5 ways
The shear viscosity eta of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model. Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
Lennard-Jones fluid model and 1 method for SPC/E water model.
Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
@ -130,9 +131,25 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
However, instead of measure the momentum flux in response of applied velocity gradient,
it measures the velocity profile in response of applied stress.
A cosine-shaped periodic acceleration is added to the system via the
:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the
generated velocity profile and remove the velocity bias before thermostatting.
.. note::
An article by :ref:`(Hess) <Hess3>` discussed the accuracy and efficiency of these methods.
----------
.. _Daivis-viscosity:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _Hess3:
**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

359
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@ -0,0 +1,359 @@
Using LAMMPS on Windows 10 with WSL
###################################
**written by Richard Berger**
----------
It's always been tricky for us to have LAMMPS users and developers work on
Windows. We primarily develop LAMMPS to run on Linux clusters. To teach
LAMMPS in workshop settings, we had to redirect Windows users to
Linux Virtual Machines such as VirtualBox or Unix-like compilation with
Cygwin.
With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),
Microsoft has added a new way to work on Linux-based code. The Windows
Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual
Machine that transparently integrates into Windows. All you need is to ensure
you have the latest Windows updates installed and enable this new feature.
Linux VMs are then easily installed using the Microsoft Store.
In this tutorial, I'll show you how to set up and compile LAMMPS for both serial
and MPI usage in WSL2.
Installation
============
Upgrade to the latest Windows 10
--------------------------------
Type "Updates" in Windows Start and select "Check for Updates".
.. image:: img/wsl_tutorial/updates.png
:scale: 50%
Install all pending updates and reboot your system as many times as
necessary. Continue until your Windows installation is updated.
.. image:: img/wsl_tutorial/windows_update.png
:scale: 50%
Verify your system has at least **version 2004 and build 19041 or later**. You
can find this information by clicking on "OS build info".
.. image:: img/wsl_tutorial/osinfo.png
:scale: 50%
Enable WSL
----------
Next, we must install two additional Windows features to enable WSL support.
Open a PowerShell window as an administrator. Type "PowerShell" in Windows
Start and select "Run as Administrator".
.. image:: img/wsl_tutorial/powershell.png
:scale: 50%
Windows will ask you for administrator access. After you accept a new command
line window will appear. Type in the following command to install WSL:
.. code-block::
dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
.. image:: img/wsl_tutorial/wsl_install1.png
Next, enable the VirtualMachinePlatform feature using the following command:
.. code-block::
dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
.. image:: img/wsl_tutorial/wsl_install2.png
Finally, reboot your system.
Update WSL kernel component
---------------------------
Download and install the :download:`WSL Kernel Component Update <https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi>`.
Afterwards, reboot your system.
Set WSL2 as default
-------------------
Again, open PowerShell as administrator and run the following command:
.. code-block:: powershell
wsl --set-default-version 2
This command ensures that all future Linux installations will use WSL version 2.
.. image:: img/wsl_tutorial/wsl_install3.png
Install a Linux Distribution
----------------------------
Next, we need to install a Linux distribution via the Microsoft Store.
Install `Ubuntu 20.04 LTS <ms-windows-store://pdp/?ProductId=9n6svws3rx71>`_.
Once installed, you can launch it like any other application from the Start
Menu.
.. image:: img/wsl_tutorial/ubuntu_in_store.png
:scale: 50%
Initial Setup
^^^^^^^^^^^^^
The first time you launch the Ubuntu Linux console, it will prompt you for a
UNIX username and password. You will need this password to perform :code:`sudo`
commands later. Once completed, your Linux shell is ready for use. All your
actions and commands will run as the Linux user you specified.
.. image:: img/wsl_tutorial/first_login.png
:scale: 50%
Windows Explorer / WSL integration
==================================
Your Linux installation will have its own Linux filesystem, which contains
the Ubuntu files. Your Linux user will have a regular Linux home directory in
:code:`/home/<USERNAME>`. This directory is different from your Windows User
directory. Windows and Linux filesystems are connected through WSL.
All hard drives in Windows are accessible in the :code:`/mnt` directory in Linux.
E.g., WSL maps the :code:`C` hard drive to the :code:`/mnt/c` directory. That means you
can access your Windows User directory in :code:`/mnt/c/Users/<WINDOWS_USERNAME>`.
The Windows Explorer can also access the Linux filesystem. To illustrate this
integration, open an Ubuntu console and navigate to a directory of your
choice. To view this location in Windows Explorer, use the :code:`explorer.exe .`
command (do not forget the final dot!).
.. image:: img/wsl_tutorial/wsl_integration.png
:scale: 50%
--------
Compiling LAMMPS
================
You now have a fully functioning Ubuntu installation and can follow most
guides to install LAMMPS on a Linux system. Here are some of the essential
steps to follow:
Install prerequisite packages
-----------------------------
Before we can begin, we need to download the necessary compiler toolchain and
libraries to compile LAMMPS. In our Ubuntu-based Linux installation, we will
use the :code:`apt` package manager to install additional packages.
First, upgrade all existing packages using :code:`apt update` and :code:`apt upgrade`.
.. code-block:: bash
sudo apt update
sudo apt upgrade -y
Next, install the following packages with :code:`apt install`:
.. code-block:: bash
sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev \
libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip \
python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev \
hdf5-tools
Download LAMMPS
---------------
Obtain a copy of the LAMMPS source code and go into it using the :code:`cd` command.
Option 1: Download a LAMMPS tarball using wget
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. code-block:: bash
wget https://github.com/lammps/lammps/archive/stable_3Mar2020.tar.gz
tar xvzf stable_3Mar2020.tar.gz
cd lammps
Option 2: Download a LAMMPS development version from GitHub
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. code-block:: bash
git clone --depth=1 https://github.com/lammps/lammps.git
cd lammps
Configure and Compile LAMMPS with CMake
---------------------------------------
A beginner-friendly way to compile LAMMPS is to use CMake. Create a :code:`build`
directory to compile LAMMPS and move into it. This directory will store the
build configuration and any binaries generated during compilation.
.. code-block:: bash
mkdir build
cd build
There are countless ways to compile LAMMPS. It is beyond the scope of this
tutorial. If you want to find out more about what can be enabled, please
consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
To compile a minimal version of LAMMPS, we're going to use a preset.
Presets are a way to specify a collection of CMake options using a file.
.. code-block:: bash
cmake ../cmake/presets/minimal.cmake ../cmake
This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command.
.. code-block:: bash
make -j 4
The :code:`-j` option specifies how many parallel processes will perform the
compilation. This option can significantly speed up compilation times. Use a
number that corresponds to the number of processors in your system.
After the compilation completes successfully, you will have an executable
called :code:`lmp` in the :code:`build` directory.
.. image:: img/wsl_tutorial/compilation_result.png
:scale: 50%
Please take note of the absolute path of your :code:`build` directory. You will
need to know the location to execute the LAMMPS binary later.
One way of getting the absolute path of the current directory is through the
:code:`$PWD` variable:
.. code-block:: bash
# prints out the current value of the PWD variable
echo $PWD
Let us save this value in a temporary variable :code:`LAMMPS_BUILD_DIR` for future use:
.. code-block:: bash
LAMMPS_BUILD_DIR=$PWD
The full path of the LAMMPS binary then is :code:`$LAMMPS_BUILD_DIR/lmp`.
------------
Running an example script
=========================
Now that we have a LAMMPS binary, we will run a script from the examples folder.
Switch into the :code:`examples/melt` folder:
.. code-block::
cd ../examples/melt
To run this example in serial, use the following command line:
.. code-block::
$LAMMPS_BUILD_DIR/lmp -in in.melt
To run the same script in parallel using MPI with 4 processes, do the following:
.. code-block:: bash
mpirun -np 4 $LAMMPS_BUILD_DIR/lmp -in in.melt
If you run LAMMPS for the first time, the Windows Firewall might prompt you
to confirm access. LAMMPS is accessing the network stack to enable parallel
computation. Allow the access.
.. image:: img/wsl_tutorial/windows_firewall.png
:scale: 75%
In either serial or MPI case, LAMMPS executes and will output something similar to this:
.. code-block::
LAMMPS (30 Jun 2020)
...
...
...
Total # of neighbors = 151513
Ave neighs/atom = 37.878250
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00
**Congratulations! You've successfully compiled and executed LAMMPS on WSL!**
Final steps
===========
It is cumbersome to always specify the path of your LAMMPS binary. You can
avoid this by adding the absolute path of your :code:`build` directory to your PATH
environment variable.
.. code-block:: bash
export PATH=$LAMMPS_BUILD_DIR:$PATH
You can then run LAMMPS input scripts like this:
.. code-block:: bash
lmp -in in.melt
or
.. code-block:: bash
mpirun -np 4 lmp -in in.melt
.. note::
The value of this :code:`PATH` variable will disappear once you close your
console window. To persist this setting edit the :code:`$HOME/.bashrc` file using your
favorite text editor and add this line:
.. code-block:: bash
export PATH=/full/path/to/your/lammps/build:$PATH
**Example:**
If the LAMMPS executable `lmp` has the following absolute path:
.. code-block:: bash
/home/<USERNAME>/lammps/build/lmp
the :code:`PATH` variable should be:
.. code-block:: bash
export PATH=/home/<USERNAME>/lammps/build:$PATH
Once set up, all your Ubuntu consoles will always have access to your :code:`lmp`
binary without having to specify its location.
Conclusion
==========
I hope this gives you good overview on how to start compiling and running LAMMPS on
Windows. WSL makes preparing and running scripts on Windows a much better
experience.
If you are completely new to Linux, I highly recommend investing some time in
studying Linux online tutorials. E.g., tutorials about Bash Shell and Basic
Unix commands (e.g., `Linux Journey <https://linuxjourney.com/>`_). Acquiring
these skills will make you much more productive in this environment.
.. seealso::
* `Windows Subsystem for Linux Documentation <https://docs.microsoft.com/en-us/windows/wsl/>`_

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@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables
A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This
allows you to install LAMMPS with a single command, and stay
up-to-date with the current version of LAMMPS by simply updating your
operating system.
up-to-date with the current stable version of LAMMPS by simply updating
your operating system. Please note, that the repository below offers
two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The
LAMMPS developers recommend to use the ``lammps-stable`` package for
any production simulations. The ``lammps-daily`` package is built
from the LAMMPS development sources, and those versions may have known
issues and bugs when new features are added and the software has not
undergone full release testing.
To install the appropriate personal-package archives (PPAs), do the
following once:
@ -37,16 +43,16 @@ To install LAMMPS do the following once:
.. code-block:: bash
$ sudo apt-get install lammps-daily
$ sudo apt-get install lammps-stable
This downloads an executable named ``lmp_daily`` to your box, which
This downloads an executable named ``lmp_stable`` to your box, which
can then be used in the usual way to run input scripts:
.. code-block:: bash
$ lmp_daily -in in.lj
$ lmp_stable -in in.lj
To update LAMMPS to the most current version, do the following:
To update LAMMPS to the most current stable version, do the following:
.. code-block:: bash
@ -58,25 +64,25 @@ To get a copy of the current documentation and examples:
.. code-block:: bash
$ sudo apt-get install lammps-daily-doc
$ sudo apt-get install lammps-stable-doc
which will download the doc files in
``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
``/usr/share/doc/lammps-doc/examples``.
To get a copy of the current potentials files:
.. code-block:: bash
$ sudo apt-get install lammps-daily-data
$ sudo apt-get install lammps-stable-data
which will download the potentials files to
``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
hard-coded to look for potential files in this directory (it does not
use the `LAMMPS_POTENTIALS` environment variable, as described
in :doc:`pair_coeff <pair_coeff>` command).
The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
results in the above command also installing the `kim-api` binaries when LAMMPS
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
can install the `openkim-models` package
@ -89,9 +95,9 @@ To un-install LAMMPS, do the following:
.. code-block:: bash
$ sudo apt-get remove lammps-daily
$ sudo apt-get remove lammps-stable
Please use ``lmp_daily -help`` to see which compilation options, packages,
Please use ``lmp_stable -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this

2
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@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
describes a variety of 3rd party tools for this task. Furthermore,
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems.

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@ -32,11 +32,12 @@ a brief description of the basic code structure of LAMMPS.
----------
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands_all>` since it gives quick access to a doc page for
every LAMMPS command.
.. _lws: https://lammps.sandia.gov
.. _user_documentation:
.. toctree::
:maxdepth: 2
:numbered: 3

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@ -1,60 +1,62 @@
Building the LAMMPS manual
**************************
Depending on how you obtained LAMMPS, the doc directory has up
to 6 sub-directories, 2 Nroff files, and optionally 2 PDF files
plus 2 e-book format files:
Depending on how you obtained LAMMPS and whether you have built the
manual yourself, this directory has a number of sub-directories and
files. Here is a list with descriptions:
.. code-block:: bash
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
docenv # virtualenv for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
README # brief info about the documentation
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
utils # tools and settings for building the documentation
lammps.1 # man page for the lammps command
msi2lmp.1 # man page for the msi2lmp command
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
LAMMPS.epub # Manual in ePUB e-book format
LAMMPS.mobi # Manual in MOBI e-book format
docenv # virtualenv folder for processing the manual sources
doctrees # temporary data from processing the manual
mathjax # code and fonts for rendering math in html
doxygen # doxygen configuration and output
.gitignore # list of files and folders to be ignored by git
doxygen-warn.log # logfile with warnings from running doxygen
github-development-workflow.md # notes on the LAMMPS development workflow
include-file-conventions.md # notes on LAMMPS' include file conventions
If you downloaded LAMMPS as a tarball from the web site, the html folder
and the PDF files should be included.
If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one
of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should download a html_www
site. Just type ``make fetch``. This should download a html_www
directory and Manual_www.pdf/Developer_www.pdf files. Note that if
new LAMMPS features have been added more recently than the date of
your LAMMPS version, the fetched documentation will include those
changes (but your source code will not, unless you update your local
repository).
b. You can build the HTML or PDF files yourself, by typing "make html"
or "make pdf". This requires various tools including Sphinx, git,
and the MathJax javascript library, which the build process will attempt
to download automatically into a virtual environment in the folder
doc/docenv and the folder mathjax, respectively, if not already available.
This download is required only once, unless you type "make clean-all".
After that, viewing and processing of the documentation can be done
without internet access. To generate the PDF version of the manual,
the PDFLaTeX software and several LaTeX packages are required as well.
However, those cannot be installed automatically at the moment.
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf``. This requires various tools and files. Some of them
have to be installed (more on that below). For the rest the build
process will attempt to download and install them into a python
virtual environment and local folders. This download is required
only once, unless you type ``make clean-all``. After that, viewing and
processing of the documentation can be done without internet access.
----------
The generation of all documentation is managed by the Makefile in
the doc directory.
The generation of all documentation is managed by the Makefile in the
doc directory. The following documentation related make commands are
available:
.. code-block:: bash
Documentation Build Options:
make html # generate HTML in html dir using Sphinx
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
# in doc dir via htmldoc and pdflatex
@ -62,8 +64,10 @@ the doc directory.
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
make anchor_check # check for duplicate anchor labels
make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
@ -74,29 +78,30 @@ the doc directory.
Installing prerequisites for HTML build
=======================================
To run the HTML documentation build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
To run the HTML documentation build toolchain, python 3, git, doxygen,
and virtualenv have to be installed locally. Here are instructions for
common setups:
Ubuntu
------
.. code-block:: bash
sudo apt-get install python-virtualenv
sudo apt-get install python-virtualenv git doxygen
Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x)
------------------------------------------------------------------------------------
.. code-block:: bash
sudo yum install python3-virtualenv
sudo yum install python3-virtualenv git doxygen
Fedora (since version 22)
-------------------------
.. code-block:: bash
sudo dnf install python3-virtualenv
sudo dnf install python3-virtualenv git doxygen
MacOS X
-------
@ -120,22 +125,92 @@ Once Python 3 is installed, open a Terminal and type
This will install virtualenv from the Python Package Index.
----------
Installing prerequisites for PDF build
======================================
Installing prerequisites for epub build
=======================================
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with support for PDFLaTeX and a selection
of LaTeX styles/packages are required.
ePUB
----
Installing prerequisites for e-book reader builds
=================================================
Same as for HTML. This uses mostly the same tools and configuration
files as the HTML tree. In addition it uses LaTeX to convert embedded
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with a few add-on LaTeX packages
as well as the ``dvipng`` tool are required to convert embedded
math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file
(for e-book readers, like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
On the Kindle readers in particular, you also have support for
PDF files, so you could download and view the PDF version as an alternative.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
files, so you could download and view the PDF version as an alternative.
Instructions for Developers
===========================
When adding new styles or options to the LAMMPS code, corresponding
documentation is required and either existing files in the ``src``
folder need to be updated or new files added. These files are written
in `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
Before contributing any documentation, please check that both the HTML
and the PDF format documentation can translate without errors. Please also
check the output to the console for any warnings or problems. There will
be multiple tests run automatically:
- A test for correctness of all anchor labels and their references
- A test that all LAMMPS packages (= folders with sources in
``lammps/src``) are documented and listed. A typical warning shows
the name of the folder with the suspected new package code and the
documentation files where they need to be listed:
.. parsed-literal::
Found 33 standard and 41 user packages
Standard package NEWPACKAGE missing in Packages_standard.rst
Standard package NEWPACKAGE missing in Packages_details.rst
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:
.. parsed-literal::
Parsed style names w/o suffixes from C++ tree in ../src:
Angle styles: 21 Atom styles: 24
Body styles: 3 Bond styles: 17
Command styles: 41 Compute styles: 143
Dihedral styles: 16 Dump styles: 26
Fix styles: 223 Improper styles: 13
Integrate styles: 4 Kspace styles: 15
Minimize styles: 9 Pair styles: 234
Reader styles: 4 Region styles: 8
Compute style entry newcomp is missing or incomplete in Commands_compute.rst
Compute style entry newcomp is missing or incomplete in compute.rst
Fix style entry newfix is missing or incomplete in Commands_fix.rst
Fix style entry newfix is missing or incomplete in fix.rst
Pair style entry new is missing or incomplete in Commands_pair.rst
Pair style entry new is missing or incomplete in pair_style.rst
Found 6 issue(s) with style lists
In addition, there is the option to run a spellcheck on the entire
manual with ``make spelling``. This requires `a library called enchant
<https://github.com/AbiWord/enchant>`_. To avoid printing out *false
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov

252
doc/src/Modify_atom.rst
View File

@ -3,115 +3,169 @@ Atom styles
Classes that define an :doc:`atom style <atom_style>` are derived from
the AtomVec class and managed by the Atom class. The atom style
determines what attributes are associated with an atom. A new atom
style can be created if one of the existing atom styles does not
define all the attributes you need to store and communicate with
atoms.
determines what attributes are associated with an atom and
communicated when it is a ghost atom or migrates to a new processor.
A new atom style can be created if one of the existing atom styles
does not define all the attributes you need to store and communicate
with atoms.
Atom_vec_atomic.cpp is a simple example of an atom style.
Atom_vec_atomic.cpp is the simplest example of an atom style.
Examining the code for others will make these instructions more clear.
Here is a brief description of methods you define in your new derived
class. See atom_vec.h for details.
Note that the :doc:`atom style hybrid <atom_style>` command can be
used to define atoms or particles which have the union of properties
of individual styles. Also the :doc:`fix property/atom <fix_property_atom>`
command can be used to add a single property (e.g. charge
or a molecule ID) to a style that does not have it. It can also be
used to add custom properties to an atom, with options to communicate
them with ghost atoms or read them from a data file. Other LAMMPS
commands can access these custom properties, as can new pair, fix,
compute styles that are written to work with these properties. For
example, the :doc:`set <set>` command can be used to set the values of
custom per-atom properties from an input script. All of these methods
are less work than writing code for a new atom style.
+-------------------------+--------------------------------------------------------------------------------+
| init | one time setup (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| grow | re-allocate atom arrays to longer lengths (required) |
+-------------------------+--------------------------------------------------------------------------------+
| grow_reset | make array pointers in Atom and AtomVec classes consistent (required) |
+-------------------------+--------------------------------------------------------------------------------+
| copy | copy info for one atom to another atom's array locations (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_comm | store an atom's info in a buffer communicated every timestep (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_comm_vel | add velocity info to communication buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_comm_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_comm | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_comm_vel | also retrieve velocity info (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_comm_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_reverse | store an atom's info in a buffer communicating partial forces (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_reverse_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_reverse | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_reverse_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_border | store an atom's info in a buffer communicated on neighbor re-builds (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_border_vel | add velocity info to buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_border_hybrid | store extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_border | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_border_vel | also retrieve velocity info (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_border_hybrid | retrieve extra info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_exchange | store all an atom's info to migrate to another processor (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_exchange | retrieve an atom's info from the buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| size_restart | number of restart quantities associated with proc's atoms (required) |
+-------------------------+--------------------------------------------------------------------------------+
| pack_restart | pack atom quantities into a buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| unpack_restart | unpack atom quantities from a buffer (required) |
+-------------------------+--------------------------------------------------------------------------------+
| create_atom | create an individual atom of this style (required) |
+-------------------------+--------------------------------------------------------------------------------+
| data_atom | parse an atom line from the data file (required) |
+-------------------------+--------------------------------------------------------------------------------+
| data_atom_hybrid | parse additional atom info unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| data_vel | parse one line of velocity information from data file (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| data_vel_hybrid | parse additional velocity data unique to this atom style (optional) |
+-------------------------+--------------------------------------------------------------------------------+
| memory_usage | tally memory allocated by atom arrays (required) |
+-------------------------+--------------------------------------------------------------------------------+
If you follow these directions your new style will automatically work
in tandem with others via the :doc:`atom_style hybrid <atom_style>`
command.
The constructor of the derived class sets values for several variables
that you must set when defining a new atom style, which are documented
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word "customize" and you will find locations you will need to
modify.
The first step is to define a set of strings in the constructor of the
new derived class. Each string will have zero or more space-separated
variable names which are identical to those used in the atom.h header
file for per-atom properties. Note that some represent per-atom
vectors (q, molecule) while other are per-atom arrays (x,v). For all
but the last 2 strings you do not need to specify any of
(id,type,x,v,f). Those are included automatically as needed in the
other strings.
.. note::
.. list-table::
It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the :doc:`fix property/atom <fix_property_atom>` doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
* - fields_grow
- full list of properties which is allocated and stored
* - fields_copy
- list of properties to copy atoms are rearranged on-processor
* - fields_comm
- list of properties communicated to ghost atoms every step
* - fields_comm_vel
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
* - fields_reverse
- list of properties summed from ghost atoms every step
* - fields_border
- list of properties communicated with ghost atoms every reneighboring step
* - fields_border_vel
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
* - fields_exchange
- list of properties communicated when an atom migrates to another processor
* - fields_restart
- list of properties written/read to/from a restart file
* - fields_create
- list of properties defined when an atom is created by :doc:`create_atoms <create_atoms>`
* - fields_data_atom
- list of properties (in order) in the Atoms section of a data file, as read by :doc:`read_data <read_data>`
* - fields_data_vel
- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
New :doc:`pair styles <pair_style>`, :doc:`fixes <fix>`, or
:doc:`computes <compute>` can be added to LAMMPS, as discussed below.
The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find_custom() method that is
useful in this context:
In these strings you can list variable names which LAMMPS already
defines (in some other atom style), or you can create new variable
names. You should not re-use a LAMMPS variable for something with
different meaning in your atom style. If the meaning is related, but
interpreted differently by your atom style, then using the same
variable name means a user should not use your style and the other
style together in a :doc:`atom_style hybrid <atom_style>` command.
Because there will only be one value of the variable and different
parts of LAMMPS will then likely use it differently. LAMMPS has
no way of checking for this.
.. code-block:: c++
If you are defining new variable names then make them descriptive and
unique to your new atom style. For example choosing "e" for energy is
a bad choice; it is too generic. A better choice would be "e_foo",
where "foo" is specific to your style.
int index = atom->find_custom(char *name, int &flag);
If any of the variable names in your new atom style do not exist in
LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
The "name" of a custom attribute, as specified in the :doc:`fix property/atom <fix_property_atom>` command, is checked to verify
that it exists and its index is returned. The method also sets flag =
0/1 depending on whether it is an integer or floating-point attribute.
The vector of values associated with the attribute can then be
accessed using the returned index as
Search for the word "customize" or "customization" in these 2 files to
see where to add your variable. Adding a flag to the 2nd
customization section in atom.h is only necessary if your code (e.g. a
pair style) needs to check that a per-atom property is defined. These
flags should also be set in the constructor of the atom style child
class.
.. code-block:: c++
In atom.cpp, aside from the constructor and destructor, there are 3
methods that a new variable name or flag needs to be added to.
int *ivector = atom->ivector[index];
double *dvector = atom->dvector[index];
In Atom::peratom_create() when using the add_peratom() method, a
final length argument of 0 is for per-atom vectors, a length > 1 is
for per-atom arrays. Note the use of an extra per-thread flag and the
add_peratom_vary() method when last dimension of the array is
variable-length.
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.
Adding the variable name to Atom::extract() enable the per-atom data
to be accessed through the :doc:`LAMMPS library interface
<Howto_library>` by a calling code, including from :doc:`Python
<Python_head>`.
The constructor of the new atom style will also typically set a few
flags which are defined at the top of atom_vec.h. If these are
unclear, see how other atom styles use them.
The grow_pointers() method is also required to make
a copy of peratom data pointers, as explained in the code.
There are a number of other optional methods which your atom style can
implement. These are only needed if you need to do something
out-of-the-ordinary which the default operation of the AtomVec parent
class does not take care of. The best way to figure out why they are
sometimes useful is to look at how other atom styles use them.
* process_args = use if the atom style has arguments
* init = called before each run
* force_clear = called before force computations each timestep
A few atom styles define "bonus" data associated with some or all of
their particles, such as :doc:`atom_style ellipsoid or tri
<atom_style>`. These methods work with that data:
* copy_bonus
* clear_bonus
* pack_comm_bonus
* unpack_comm_bonus
* pack_border_bonus
* unpack_border_bonus
* pack_exchange_bonus
* unpack_exchange_bonus
* size_restart_bonus
* pack_restart_bonus
* unpack_restart_bonus
* data_atom_bonus
* memory_usage_bonus
The :doc:`atom_style body <atom_style>` command can define a particle
geometry with an arbitrary number of values. This method reads it
from a data file:
* data_body
These methods are called before or after operations handled by the
parent AtomVec class. They allow an atom style to do customized
operations on the per-atom values. For example :doc:`atom_style
sphere <atom_style>` reads a diameter and density of each particle
from a data file. But these need to be converted internally to a
radius and mass. That operation is done in the data_atom_post()
method.
* pack_restart_pre
* pack_restart_post
* unpack_restart_init
* create_atom_post
* data_atom_post
* pack_data_pre
* pack_data_post
These methods enable the :doc:`compute property/atom <compute_property_atom>`
command to access per-atom variables it does not
already define as arguments, so that they can be written to a dump
file or used by other LAMMPS commands.
* property_atom
* pack_property_atom

72
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@ -1,37 +1,51 @@
Submitting new features for inclusion in LAMMPS
===============================================
We encourage users to submit new features or modifications for LAMMPS
to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage
and coordinate this is as of Fall 2016 via the LAMMPS project on
`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
contact the LAMMPS developers or the indicated developer of a package
or feature directly and send in your contribution via e-mail.
We encourage users to submit new features or modifications for LAMMPS to
`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage and
coordinate this is via the LAMMPS project on `GitHub
<https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub
Tutorial <Howto_github>` for a demonstration on how to do that. An
alternative is to contact the LAMMPS developers or the indicated
developer of a package or feature directly and send in your contribution
via e-mail, but that can add a significant delay on getting your
contribution included, depending on how busy the developer is you
contact, how complex a task it would be to integrate that code, and how
many - if any - changes are required before the code can be included.
For any larger modifications or programming project, you are
encouraged to contact the LAMMPS developers ahead of time, in order to
discuss implementation strategies and coding guidelines, that will
make it easier to integrate your contribution and result in less work
for everybody involved. You are also encouraged to search through the
list of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_ and submit a new issue
for a planned feature, so you would not duplicate the work of others
(and possibly get scooped by them) or have your work duplicated by
others.
For any larger modifications or programming project, you are encouraged
to contact the LAMMPS developers ahead of time, in order to discuss
implementation strategies and coding guidelines, that will make it
easier to integrate your contribution and result in less work for
everybody involved. You are also encouraged to search through the list
of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
and submit a new issue for a planned feature, so you would not duplicate
the work of others (and possibly get scooped by them) or have your work
duplicated by others.
How quickly your contribution will be integrated depends largely on
how much effort it will cause to integrate and test it, how much it
requires changes to the core codebase, and of how much interest it is
to the larger LAMMPS community. Please see below for a checklist of
typical requirements. Once you have prepared everything, see the
:doc:`Using GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on how to
submit your changes or new files through a GitHub pull request. If you
prefer to submit patches or full files, you should first make certain,
that your code works correctly with the latest patch-level version of
LAMMPS and contains all bug fixes from it. Then create a gzipped tar
file of all changed or added files or a corresponding patch file using
'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
compression, as this works well on all platforms.
For informal communication with (some of) the LAMMPS developers you may
ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
This slack work space is by invitation only. Thus for access, please
send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how much it requires
changes to the core codebase, and of how much interest it is to the
larger LAMMPS community. Please see below for a checklist of typical
requirements. Once you have prepared everything, see the :doc:`Using
GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on
how to submit your changes or new files through a GitHub pull
request. If you prefer to submit patches or full files, you should first
make certain, that your code works correctly with the latest patch-level
version of LAMMPS and contains all bug fixes from it. Then create a
gzipped tar file of all changed or added files or a corresponding patch
file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
use gzip compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`. Else we will add them as a

2
doc/src/Modify_fix.rst
View File

@ -27,7 +27,7 @@ derived class. See fix.h for details.
+---------------------------+--------------------------------------------------------------------------------------------+
| setup_pre_force | called before force computation in setup (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+
| setup | called immediately before the 1st timestep and after forces are computed (optional) |
| setup | called immediately before the first timestep and after forces are computed (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+
| min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) |
+---------------------------+--------------------------------------------------------------------------------------------+

18
doc/src/Modify_kspace.rst
View File

@ -10,12 +10,12 @@ Ewald.cpp is an example of computing K-space interactions.
Here is a brief description of methods you define in your new derived
class. See kspace.h for details.
+---------------+----------------------------------------------+
| init | initialize the calculation before a run |
+---------------+----------------------------------------------+
| setup | computation before the 1st timestep of a run |
+---------------+----------------------------------------------+
| compute | every-timestep computation |
+---------------+----------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+----------------------------------------------+
+---------------+------------------------------------------------+
| init | initialize the calculation before a run |
+---------------+------------------------------------------------+
| setup | computation before the first timestep of a run |
+---------------+------------------------------------------------+
| compute | every-timestep computation |
+---------------+------------------------------------------------+
| memory_usage | tally of memory usage |
+---------------+------------------------------------------------+

82
doc/src/Packages_details.rst
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@ -44,6 +44,7 @@ page gives those details.
* :ref:`MC <PKG-MC>`
* :ref:`MESSAGE <PKG-MESSAGE>`
* :ref:`MISC <PKG-MISC>`
* :ref:`MLIAP <PKG-MLIAP>`
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MPIIO <PKG-MPIIO>`
* :ref:`MSCG <PKG-MSCG>`
@ -81,6 +82,7 @@ page gives those details.
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
* :ref:`USER-MGPT <PKG-USER-MGPT>`
* :ref:`USER-MISC <PKG-USER-MISC>`
* :ref:`USER-MOFFF <PKG-USER-MOFFF>`
@ -304,7 +306,8 @@ gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`. See
also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
**Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
(Northwestern U) while at ORNL and later. AMD HIP support by Evgeny
Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
**Install:**
@ -489,7 +492,7 @@ interactions. These include Ewald, particle-particle particle-mesh
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a
library provided with LAMMPS, third party libraries like FFTW, or a
vendor-supplied FFT library. See the :doc:`Build settings <Build_settings>` doc page for details on how to select
different FFT options for your LAMPMS build.
@ -651,6 +654,29 @@ listing, "ls src/MISC", to see the list of commands.
----------
.. _PKG-MLIAP:
MLIAP package
-------------
**Contents:**
A general interface for machine-learning interatomic potentials.
**Install:**
To use this package, also the :ref:`SNAP package<PKG-SNAP>` needs to be installed.
**Author:** Aidan Thompson (Sandia).
**Supporting info:**
* src/MLIAP: filenames -> commands
* :doc:`pair_style mliap <pair_mliap>`
* examples/mliap
----------
.. _PKG-MOLECULE:
MOLECULE package
@ -1712,6 +1738,56 @@ algorithm.
* examples/USER/mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd
* examples/USER/meso
* http://lammps.sandia.gov/movies.html#mesodpd
----------
.. _PKG-USER-MESONT:
USER-MESONT package
-------------------
**Contents:**
USER-MESONT is a LAMMPS package for simulation of nanomechanics of
nanotubes (NTs). The model is based on a coarse-grained representation
of NTs as "flexible cylinders" consisting of a variable number of
segments. Internal interactions within a NT and the van der Waals
interaction between the tubes are described by a mesoscopic force field
designed and parameterized based on the results of atomic-level
molecular dynamics simulations. The description of the force field is
provided in the papers listed below. This package contains two
independent implementations of this model: :doc:`pair_style mesocnt
<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
implementation based on a Fortran library in the ``lib/mesont`` folder.
**Download of potential files:**
The potential files for these pair styles are *very* large and thus
are not included in the regular downloaded packages of LAMMPS or the
git repositories. Instead, they will be automatically downloaded
from a web server when the package is installed for the first time.
**Authors of the *mesont* styles:**
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
**Author of the *mesocnt* pair style:**
Philipp Kloza (U Cambridge)
**Supporting info:**
* src/USER-MESONT: filenames -> commands
* src/USER-MESONT/README
* :doc:`atom_style mesont <atom_style>`
* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
* :doc:`compute mesont <compute_mesont>`
* :doc:`pair_style mesocnt <pair_mesocnt>`
* examples/USER/mesont
* tools/mesont
----------
.. _PKG-USER-MOFFF:
@ -2064,7 +2140,7 @@ molecules, and chiral-sensitive reactions.
* examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* disarmmd.org
* reacter.org
----------

2
doc/src/Packages_standard.rst
View File

@ -59,6 +59,8 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MISC <PKG-MISC>` | miscellaneous single-file commands | n/a | no | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MLIAP <PKG-MLIAP>` | multiple machine learning potentials | :doc:`pair_style mliap <pair_mliap>` | mliap | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MOLECULE <PKG-MOLECULE>` | molecular system force fields | :doc:`Howto bioFF <Howto_bioFF>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MPIIO <PKG-MPIIO>` | MPI parallel I/O dump and restart | :doc:`dump <dump>` | n/a | no |

2
doc/src/Packages_user.rst
View File

@ -67,6 +67,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESONT <PKG-USER-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont | int |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |

25
doc/src/Python_examples.rst
View File

@ -80,16 +80,23 @@ See the python/README file for instructions on how to run them and the
source code for individual scripts for comments about what they do.
Here are screenshots of the vizplotgui_tool.py script in action for
different visualization package options. Click to see larger images:
different visualization package options:
.. image:: JPG/screenshot_gl_small.jpg
:target: JPG/screenshot_gl.jpg
.. |pyex1| image:: img/screenshot_gl.jpg
:width: 24%
.. image:: JPG/screenshot_atomeye_small.jpg
:target: JPG/screenshot_atomeye.jpg
.. |pyex2| image:: img/screenshot_atomeye.jpg
:width: 24%
.. image:: JPG/screenshot_pymol_small.jpg
:target: JPG/screenshot_pymol.jpg
.. |pyex3| image:: img/screenshot_pymol.jpg
:width: 24%
.. |pyex4| image:: img/screenshot_vmd.jpg
:width: 24%
|pyex1| |pyex2| |pyex3| |pyex4|
.. raw:: html
Click to see larger versions of the images.
.. image:: JPG/screenshot_vmd_small.jpg
:target: JPG/screenshot_vmd.jpg

9
doc/src/Python_library.rst
View File

@ -254,12 +254,3 @@ following steps:
* You should now be able to invoke the new interface function from a
Python script.
----------
.. autoclass:: lammps.lammps
:members:
:no-undoc-members:
.. autoclass:: lammps.NeighList
:members:
:no-undoc-members:

4
doc/src/Python_test.rst
View File

@ -10,7 +10,7 @@ and type:
>>> lmp = lammps()
If you get no errors, you're ready to use LAMMPS from Python. If the
2nd command fails, the most common error to see is
second command fails, the most common error to see is
.. parsed-literal::
@ -78,7 +78,7 @@ above, create a test.py file containing these lines:
pypar.finalize()
To run LAMMPS in parallel, assuming you have installed the
`mpi4py <https://bitbucket.org/mpi4py/mpi4py>`_ package as discussed
`mpi4py <https://mpi4py.readthedocs.io>`_ package as discussed
above, create a test.py file containing these lines:
.. code-block:: python

8
doc/src/Run_options.rst
View File

@ -324,17 +324,17 @@ physical processors is done by MPI before LAMMPS begins. It may be
useful in some cases to alter the rank order. E.g. to insure that
cores within each node are ranked in a desired order. Or when using
the :doc:`run_style verlet/split <run_style>` command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
to insure that a specific Kspace processor (in the second partition) is
matched up with a specific set of processors in the first partition.
See the :doc:`Speed tips <Speed_tips>` doc page for more details.
If the keyword *nth* is used with a setting *N*\ , then it means every
Nth processor will be moved to the end of the ranking. This is useful
when using the :doc:`run_style verlet/split <run_style>` command with 2
partitions via the -partition command-line switch. The first set of
processors will be in the first partition, the 2nd set in the 2nd
processors will be in the first partition, the second set in the second
partition. The -reorder command-line switch can alter this so that
the 1st N procs in the 1st partition and one proc in the 2nd partition
the first N procs in the first partition and one proc in the second partition
will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4"
and "-partition 9 3" and you are running on 12 processors, the

6
doc/src/Speed_gpu.rst
View File

@ -50,6 +50,10 @@ but this can be overridden using the device 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
software installed. Versions of ROCm older than 3.5 are currently deprecated
by AMD.
**Building LAMMPS with the GPU package:**
See the :ref:`Build extras <gpu>` doc page for
@ -88,7 +92,7 @@ GPUs/node to 1.
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
same as the "package gpu" command. See the :doc:`package <package>`
the "package gpu" command. See the :doc:`package <package>`
command doc page for details, including the default values used for
all its options if it is not specified.

6
doc/src/Speed_intel.rst
View File

@ -138,10 +138,10 @@ For Intel Xeon Phi co-processors (Offload):
**Required hardware/software:**
When using Intel compilers version 16.0 or later is required.
In order to use offload to co-processors, an Intel Xeon Phi
co-processor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
co-processor and an Intel compiler are required.
Although any compiler can be used with the USER-INTEL package,
currently, vectorization directives are disabled by default when

17
doc/src/accel_styles.rst Normal file
View File

@ -0,0 +1,17 @@
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.

9
doc/src/angle_charmm.rst
View File

@ -37,7 +37,7 @@ The *charmm* angle style uses the potential
E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2
with an additional Urey_Bradley term based on the distance :math:`r` between
the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`,
the first and third atoms in the angle. :math:`K`, :math:`\theta_0`,
:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle
type.
@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
* :math:`K_{ub}` (energy/distance\^2)
* :math:`r_{ub}` (distance)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------

60
doc/src/angle_class2.rst
View File

@ -41,27 +41,29 @@ The *class2* angle style uses the potential
E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a
bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are
the equilibrium bond lengths.
where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond
term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is
the equilibrium angle and :math:`r_1` and :math:`r_2` are the
equilibrium bond lengths.
See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field.
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas 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>` or :doc:`read_restart <read_restart>`
commands.
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}`
formulas 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>` or
:doc:`read_restart <read_restart>` commands.
These are the 4 coefficients for the :math:`E_a` formula:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various :math:`K` are in per-radian.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 4 coefficients, the first of which
@ -93,23 +95,7 @@ since it is the same value from the :math:`E_a` formula.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------
@ -122,11 +108,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order:
In this expanded term 6 coefficients for the :math:`E_a` formula need to be set:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_5` (energy/radian\^5)
* :math:`K_6` (energy/radian\^6)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
* :math:`K_5` (energy)
* :math:`K_6` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6.
The bond-bond and bond-angle terms remain unchanged.

4
doc/src/angle_coeff.rst
View File

@ -31,7 +31,7 @@ Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple angle types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types,
then an asterisk with no numeric values means all types from 1 to N. A
@ -53,7 +53,7 @@ same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Angle Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

18
doc/src/angle_cosine.rst
View File

@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_cosine_delta.rst
View File

@ -46,23 +46,7 @@ internally.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_cosine_periodic.rst
View File

@ -54,23 +54,7 @@ geometry.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_cosine_shift.rst
View File

@ -45,23 +45,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_cosine_shift_exp.rst
View File

@ -56,23 +56,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_cosine_squared.rst
View File

@ -46,23 +46,7 @@ internally.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

9
doc/src/angle_cross.rst
View File

@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K_{SS}` (energy/distance\^2)
* :math:`K_{BS0}` (energy/distance/rad)
* :math:`K_{BS1}` (energy/distance/rad)
* :math:`K_{BS0}` (energy/distance)
* :math:`K_{BS1}` (energy/distance)
* :math:`r_{12,0}` (distance)
* :math:`r_{32,0}` (distance)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are
effectively energy/distance per radian.
Restrictions
""""""""""""

18
doc/src/angle_dipole.rst
View File

@ -82,23 +82,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
Restrictions
""""""""""""

18
doc/src/angle_fourier.rst
View File

@ -42,23 +42,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/angle_fourier_simple.rst
View File

@ -41,23 +41,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

25
doc/src/angle_harmonic.rst
View File

@ -44,31 +44,16 @@ The following coefficients must be defined for each angle type via the
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

14
doc/src/angle_mm3.rst
View File

@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example
:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ...
where :math:`\theta_0` is the equilibrium value of the angle, and
:math:`K` is a prefactor. The anharmonic prefactors have units
:math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6
\cdot 10^{-5} \deg^{-2}`, ...
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>`
or :doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
Restrictions
""""""""""""

29
doc/src/angle_quartic.rst
View File

@ -39,32 +39,17 @@ the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy/radian\^2)
* :math:`K_3` (energy/radian\^3)
* :math:`K_4` (energy/radian\^4)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

30
doc/src/angle_sdk.rst
View File

@ -44,33 +44,19 @@ is included in :math:`K`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above:
* :math:`K` (energy/radian\^2)
* :math:`K` (energy)
* :math:`\theta_0` (degrees)
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of :math:`K` are in energy/radian\^2.
The also required *lj/sdk* parameters will be extracted automatically
from the pair_style.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
pair_style.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

28
doc/src/angle_table.rst
View File

@ -75,7 +75,7 @@ parenthesized comments):
...
181 180.0 0.0 0.0
A section begins with a non-blank line whose 1st character is not a
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
@ -99,7 +99,7 @@ is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and
fplo and fphi, which are the second derivatives at the innermost and
outermost angle settings. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two
@ -110,9 +110,9 @@ equilibrium angle value, which is used, for example, by the :doc:`fix shake <fix
set to 180.0.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
On each line, the first value is the index from 1 to N, the second value is
the angle value (in degrees), the third value is the energy (in energy
units), and the fourth is -dE/d(theta) (also in energy units). The third
term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term
@ -126,23 +126,7 @@ one that matches the specified keyword.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

2
doc/src/atc_control_momentum.rst
View File

@ -52,7 +52,7 @@ the finite element temperature. *flux* is a similar mode, but rather
adds energy to the atoms based on conservation of energy.
*correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the
compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the
controller's matrix solver.

2
doc/src/atc_control_thermal.rst
View File

@ -56,7 +56,7 @@ adds energy to the atoms based on conservation of energy. *hoover* and
atoms.
*correction_max_iterations* sets the maximum number of iterations to
compute the 2nd order in time correction term for lambda with the
compute the second order in time correction term for lambda with the
fractional step method. The method uses the same tolerance as the
controller's matrix solver.

4
doc/src/atc_hardy_fields.rst
View File

@ -25,8 +25,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume

4
doc/src/atc_hardy_gradients.rst
View File

@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume

4
doc/src/atc_hardy_rates.rst
View File

@ -23,8 +23,8 @@ Syntax
- temperature : temperature derived from the relative atomic kinetic energy
- kinetic_temperature : temperature derived from the full kinetic energy
- number_density : simple kernel estimation of number of atoms per unit volume
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or first Piola-Kirchhoff stress tensor for lagrangian analysis
- transformed_stress : first Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
- potential_energy : potential energy per unit volume
- kinetic_energy : kinetic energy per unit volume

18
doc/src/atc_time_integration.rst
View File

@ -33,11 +33,11 @@ Command to select the thermal or momentum time integration.
Options for thermal time integration:
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, thermostats based on controlling power
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, thermostats based on controlling power
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal temperature
atomic velocity update with second order Verlet, mixed nodal temperature
update, 3/4 Gear for continuum and 2 Verlet for atomic contributions,
thermostats based on controlling discrete energy changes
@ -46,18 +46,18 @@ Options for thermal time integration:
Options for momentum time integration:
*verlet*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 2nd order Verlet, kinetostats based on controlling force
atomic velocity update with second order Verlet, nodal temperature update
with second order Verlet, kinetostats based on controlling force
*fractional_step*
atomic velocity update with 2nd order Verlet, mixed nodal momentum
update, 2nd order Verlet for continuum and exact 2nd order Verlet for
atomic velocity update with second order Verlet, mixed nodal momentum
update, second order Verlet for continuum and exact second order Verlet for
atomic contributions, kinetostats based on controlling discrete
momentum changes
*gear*
atomic velocity update with 2nd order Verlet, nodal temperature update
with 3rd or 4th order Gear, kinetostats based on controlling power.
atomic velocity update with second order Verlet, nodal temperature update
with third or fourth order Gear, kinetostats based on controlling power.
---------

42
doc/src/atom_style.rst
View File

@ -10,7 +10,7 @@ Syntax
atom_style style args
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *spin* or *tri* or *template* or *hybrid*
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
.. parsed-literal::
@ -18,7 +18,9 @@ Syntax
*body* args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the :doc:`Howto body <Howto_body>` doc page for details
see the :doc:`Howto body <Howto_body>` doc
page for details
*sphere* arg = 0/1 (optional) for static/dynamic particle radii
*tdpd* arg = Nspecies
Nspecies = # of chemical species
*template* arg = template-ID
@ -91,10 +93,6 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *edpd* | temperature and heat capacity | eDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tdpd* | chemical concentration | tDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+--------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
@ -103,7 +101,9 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *line* | end points, angular velocity | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *meso* | rho, e, cv | SPH particles |
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mesont* | mass, radius, length, buckling, connections, tube id| mesoscopic nanotubes |
+--------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
@ -111,10 +111,14 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sph* | rho, esph, cv | SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sphere* | diameter, mass, angular velocity | granular models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *spin* | magnetic moment | system with magnetic particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tdpd* | chemical concentration | tDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *template* | template index, template atom | small molecules with fixed topology |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tri* | corner points, angular momentum | rigid bodies |
@ -144,9 +148,16 @@ basis.
For the *sphere* style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle. Note that by use of the *disc* keyword with the :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>` commands, spheres can be effectively
treated as 2d discs for a 2d simulation if desired. See also the :doc:`set density/disc <set>` command.
particle. Note that by use of the *disc* keyword with the :doc:`fix
nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
<fix_npt_sphere>` commands, spheres can be effectively treated as 2d
discs for a 2d simulation if desired. See also the :doc:`set
density/disc <set>` command. The *sphere* style takes an optional 0
or 1 argument. A value of 0 means the radius of each sphere is
constant for the duration of the simulation. A value of 1 means the
radii may vary dynamically during the simulation, e.g. due to use of
the :doc:`fix adapt <fix_adapt>` command.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
@ -189,8 +200,8 @@ particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The *meso* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
The *sph* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (esph), and heat capacity
(cv).
The *smd* style is for a general formulation of Smooth Particle
@ -335,9 +346,11 @@ for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *meso* style is part of the USER-SPH package for smoothed particle
The *sph* style is part of the USER-SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *mesont* style is part of the USER-MESONT package.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the USER-AWPMD package for the
@ -351,7 +364,8 @@ Related commands
Default
"""""""
atom_style atomic
The default atom style is atomic. If atom_style sphere is used its
default argument is 0.
----------

14
doc/src/balance.rst
View File

@ -177,16 +177,16 @@ volume (area in 2d) assigned to each processor, as in the following 2d
diagram where processor sub-domains are shown and particles are
colored by the processor that owns them.
.. list-table::
.. |balance1| image:: img/balance_uniform.jpg
:width: 32%
* - .. figure:: JPG/balance_uniform_small.jpg
:target: JPG/balance_uniform.jpg
.. |balance2| image:: img/balance_nonuniform.jpg
:width: 32%
- .. figure:: JPG/balance_nonuniform_small.jpg
:target: JPG/balance_nonuniform.jpg
.. |balance3| image:: img/balance_rcb.jpg
:width: 32%
- .. figure:: JPG/balance_rcb_small.jpg
:target: JPG/balance_rcb.jpg
|balance1| |balance2| |balance3|
The leftmost diagram is the default partitioning of the simulation box
across processors (one sub-box for each of 16 processors); the middle

18
doc/src/bond_class2.rst
View File

@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

4
doc/src/bond_coeff.rst
View File

@ -32,7 +32,7 @@ Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
be used, as in the first example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
@ -54,7 +54,7 @@ same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
corresponds to the first example above would be listed as
.. parsed-literal::

22
doc/src/bond_fene.rst
View File

@ -38,8 +38,8 @@ The *fene* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
@ -54,23 +54,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

22
doc/src/bond_fene_expand.rst
View File

@ -32,12 +32,12 @@ The *fene/expand* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
term is attractive, the second Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
now extends to :math:`R_0 + \Delta` and the second term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@ -52,23 +52,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_gromos.rst
View File

@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_harmonic.rst
View File

@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_harmonic_shift.rst
View File

@ -48,23 +48,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_harmonic_shift_cut.rst
View File

@ -46,23 +46,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_morse.rst
View File

@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

2
doc/src/bond_none.rst
View File

@ -13,7 +13,7 @@ Syntax
Examples
""""""""
.. code-blocK:: LAMMPS
.. code-block:: LAMMPS
bond_style none

18
doc/src/bond_nonlinear.rst
View File

@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

18
doc/src/bond_quartic.rst
View File

@ -88,23 +88,7 @@ status of broken bonds or permanently delete them, e.g.:
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

106
doc/src/bond_special.rst Normal file
View File

@ -0,0 +1,106 @@
.. index:: bond_style special
bond_style special command
=================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style special
Examples
""""""""
.. code-block:: LAMMPS
bond_style special
bond_coeff 0.5 0.5
Description
"""""""""""
The *special* bond style can be used to create conceptual bonds which
effectively impose weightings on the pairwise Lennard Jones and/or
Coulombic interactions between selected pairs of particles in the
system. The form of the pairwise interaction will be whatever is
computed by the :doc:`pair_style <pair_style>` command defined for the
system; this command defines the weightings for its two terms.
This command can thus be useful to apply weightings that cannot be
handled by the :doc:`special_bonds <special_bonds>` command, such as
on 1-5 or 1-6 interactions. Or it can be used to add pairwise forces
between one or more pairs of atoms that otherwise would not be include
in the :doc:`pair_style <pair_style>` computation.
The potential for this bond style has the form
.. math::
E = w_{LJ} E_{LJ} + w_{Coul} E_{Coul}
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`w_{LJ}` weight (0.0 to 1.0) on pairwise Lennard-Jones interactions
* :math:`w_{Coul}` weight (0.0 to 1.0) on pairwise Coulombic interactions
----------
Normally this bond style should be used in conjunction with one (or
more) other bond styles which compute forces between atoms directly
bonded to each other in a molecule. This means the :doc:`bond_style
hybrid <bond_hybrid>` command should be used with bond_style special
as one of its sub-styles.
Note that the same as for any other bond style, pairs of bonded atoms
must be enumerated in the data file read by the :doc:`read_data
<read_data>` command. Thus if this command is used to weight all 1-5
interactions in the system, all the 1-5 pairs of atoms must be listed
in the "Bonds" section of the data file.
This bond style imposes strict requirements on settings made with the
:doc:`special_bonds <special_bonds>` command. These requirements
ensure that the new bonds created by this style do not create spurious
1-2, 1-3, or 1-4 interactions within the molecular topology.
Specifically 1-2 interactions must have weights of zero, 1-3
interactions must either have weights of unity or :doc:`special_bonds
angle yes <special_bonds>` must be used, and 1-4 interactions must
have weights of unity or :doc:`special_bonds dihedral yes <special_bonds>`
must be used.
If this command is used to create bonded interactions between
particles that are further apart than usual (e.g. 1-5 or 1-6
interactions), this style may require an increase in the communication
cutoff via the :doc:`comm_modify cutoff <comm_modify>` command. If
LAMMPS cannot find a partner atom in a bond, an error will be issued.
Restrictions
""""""""""""
This bond 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.
This bond style requires the use of a :doc:`pair_style <pair_style>` which
computes a pairwise additive interaction and provides the ability to
compute interactions for individual pairs of atoms. Manybody potentials
are not compatible in general, but also some other pair styles are missing
the required functionality and thus will cause an error.
This command is not compatible with long-range Coulombic interactions. If a
`kspace_style <kspace_style>` is declared, an error will be issued.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
**Default:** none

1
doc/src/bond_style.rst
View File

@ -98,6 +98,7 @@ accelerated styles exist.
* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
* :doc:`quartic <bond_quartic>` - breakable quartic bond
* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond
* :doc:`table <bond_table>` - tabulated by bond length
----------

26
doc/src/bond_table.rst
View File

@ -74,7 +74,7 @@ parenthesized comments):
...
101 1.00 338.0000 -1352.0000
A section begins with a non-blank line whose 1st character is not a
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
@ -109,9 +109,9 @@ equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix
length is to the distance in the table with the lowest potential energy.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
On each line, the first value is the index from 1 to N, the second value is
the bond length r (in distance units), the third value is the energy (in
energy units), and the fourth is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the calculation is
@ -124,23 +124,7 @@ one that matches the specified keyword.
----------
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
:doc:`suffix <suffix>` command in your input script.
See the :doc:`Speed packages <Speed_packages>` doc page for more
instructions on how to use the accelerated styles effectively.
.. include:: accel_styles.rst
----------

8
doc/src/bond_write.rst
View File

@ -47,7 +47,13 @@ The file is written in the format used as input for the
:doc:`bond_style <bond_style>` *table* option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).
and a force (in force units). In case a new file is created, the first
line will be a comment with a "DATE:" and "UNITS:" tag with the current
date and :doc:`units <units>` settings. For subsequent invocations of
the bond_write command for the same file, data will be appended and the
current units settings will be compared to the data from the header, if
present, and bond_write will refuse to add a table if the units are not
the same.
Restrictions
""""""""""""

4
doc/src/boundary.rst
View File

@ -76,9 +76,9 @@ atoms becomes less than 50.0. This can be useful if you start a
simulation with an empty box or if you wish to leave room on one side
of the box, e.g. for atoms to evaporate from a surface.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension
For triclinic (non-orthogonal) simulation boxes, if the second dimension
of a tilt factor (e.g. y for xy) is periodic, then the periodicity is
enforced with the tilt factor offset. If the 1st dimension is
enforced with the tilt factor offset. If the first dimension is
shrink-wrapped, then the shrink wrapping is applied to the tilted box
face, to encompass the atoms. E.g. for a positive xy tilt, the xlo
and xhi faces of the box are planes tilting in the +y direction as y

2
doc/src/box.rst
View File

@ -38,7 +38,7 @@ skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` do
boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the 1st
than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to
*small*\ , which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*

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