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Merge remote-tracking branch 'lammps/develop' into merge-develop

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This commit is contained in:
Ludwig Ahrens
2024-01-31 14:41:36 +01:00
parent d61c379b0c 52de76d97b
commit 35215606e8
770 changed files with 9722 additions and 6446 deletions
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4
.github/workflows/codeql-analysis.yml vendored
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@ -35,7 +35,7 @@ jobs:
python-version: '3.x'
- name: Initialize CodeQL
uses: github/codeql-action/init@v2
uses: github/codeql-action/init@v3
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
@ -55,4 +55,4 @@ jobs:
cmake --build . --parallel 2
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
uses: github/codeql-action/analyze@v3

2
.github/workflows/coverity.yml vendored
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@ -25,7 +25,7 @@ jobs:
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

2
.github/workflows/unittest-macos.yml vendored
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@ -32,7 +32,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}

7
cmake/Modules/Packages/GPU.cmake
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@ -1,3 +1,10 @@
# Silence CMake warnings about FindCUDA being obsolete.
# We may need to eventually rewrite this section to use enable_language(CUDA)
if(POLICY CMP0146)
cmake_policy(SET CMP0146 OLD)
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

5
cmake/Modules/Packages/KOKKOS.cmake
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@ -16,11 +16,6 @@ endif()
if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
# NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
########################################################################

4
cmake/Modules/Packages/MDI.cmake
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@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)

6
cmake/presets/oneapi.cmake
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@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)

3
doc/Makefile
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@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -231,6 +233,7 @@ role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\

8
doc/github-development-workflow.md
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@ -36,10 +36,10 @@ requests.
MUST be submitted as a pull request to GitHub. All changes to the
"develop" branch must be made exclusively through merging pull requests.
The "release" and "stable" branches, respectively, are only to be
updated upon feature or stable releases based on the associated
tags. Updates to the stable release in between stable releases
updated upon "feature releases" or "stable releases" based on the
associated tags. Updates to the stable release in between stable releases
(for example, back-ported bug fixes) are first merged into the "maintenance"
branch and then into the "stable" branch as update releases.
branch and then into the "stable" branch as "stable update releases".
Pull requests may also be submitted to (long-running) feature branches
created by LAMMPS developers inside the LAMMPS project, if needed. Those
@ -131,7 +131,7 @@ testing -- that the code in the branch "develop" does not get easily
broken. These tests are run after every update to a pull request. More
extensive and time-consuming tests (including regression testing) are
performed after code is merged to the "develop" branch. There are feature
releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
developers feel, that a sufficient number of changes have been included
and all post-merge testing has been successful. These feature releases are
marked with a `patch_<version date>` tag and the "release" branch

5
doc/graphviz/Makefile
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@ -16,8 +16,11 @@ clean:
rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
ifeq ($(HAS_DOT),YES)
$(IMGDIR)/%.png: %.dot
$(IMGDIR)/lammps-classes.png : lammps-classes.dot
dot -Tpng -Kneato -o $@ $<
$(IMGDIR)/%.png: %.dot
dot -Tpng -Kdot -o $@ $<
endif
ifeq ($(HAS_DOT),NO)

34
doc/graphviz/lammps-releases.dot Normal file
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@ -0,0 +1,34 @@
// LAMMPS branches and releases
digraph releases {
rankdir="LR";
github [shape="box" label="Pull Requests\non GitHub" height=0.75];
github -> develop [label="Merge commits"];
{
rank = "same";
work [shape="none" label="Development branches:"]
develop [label="'develop' branch" height=0.75];
maintenance [label="'maintenance' branch" height=0.75];
};
{
rank = "same";
upload [shape="none" label="Release branches:"]
release [label="'release' branch" height=0.75];
stable [label="'stable' branch" height=0.75];
};
develop -> release [label="Feature release\n(every 4-8 weeks)"];
release -> stable [label="Stable release\n(once per year)"];
stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
develop -> maintenance [label="Backports of bugfixes" style="dashed"];
maintenance -> stable [label="Updates to stable release"];
{
rank = "same";
tag [shape="none" label="Applied tags:"];
patchtag [shape="box" label="patch_<date>"];
stabletag [shape="box" label="stable_<date>"];
updatetag [shape="box" label="stable_<date>_update<num>"];
};
release -> patchtag [label="feature release" style="dotted"];
stable -> stabletag [label="stable release" style="dotted"];
stable -> updatetag [label="update release" style="dotted"];
}

41
doc/src/Build_development.rst
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@ -255,16 +255,18 @@ 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:
suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
``test_angle_style``, ``test_dihedral_style``, and
``test_improper_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 force style 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:
.. code-block:: console
@ -416,15 +418,16 @@ 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.
Linux systems). Alternatives like the ``mold`` linker, the ``lld``
linker of the LLVM project, or the ``gold`` linker available with GNU
binutils can speed up this step substantially (in this order). CMake
will by default test if any of the three 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
``mold``, ``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++ compilers.
Tests for other components and utility functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

2
doc/src/Commands_bond.rst
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@ -124,7 +124,7 @@ OPT.
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`

2
doc/src/Commands_pair.rst
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@ -146,7 +146,7 @@ OPT.
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

3
doc/src/Developer_platform.rst
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@ -70,6 +70,9 @@ File and path functions and global constants
.. doxygenfunction:: is_console
:project: progguide
.. doxygenfunction:: disk_free
:project: progguide
.. doxygenfunction:: path_is_directory
:project: progguide

101
doc/src/Developer_unittest.rst
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@ -121,7 +121,7 @@ will be suppressed and only a summary printed, but adding
the '-V' option will then produce output from the tests
above like the following:
.. code-block::
.. code-block:: console
[...]
1: [ RUN ] Tokenizer.empty_string
@ -526,3 +526,102 @@ The ``unittest/tools`` folder contains tests for programs in the
shell, which are implemented as a python scripts using the ``unittest``
Python module and launching the tool commands through the ``subprocess``
Python module.
Troubleshooting failed unit tests
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The are by default no unit tests for newly added features (e.g. pair, fix,
or compute styles) unless your pull request also includes tests for the
added features. If you are modifying some features, you may see failures
for existing tests, if your modifications have some unexpected side effects
or your changes render the existing text invalid. If you are adding an
accelerated version of an existing style, then only tests for INTEL,
KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
Tests for the GPU package are time consuming and thus are only run
*after* a merge, or when a special label, ``gpu_unit_tests`` is added
to the pull request. After the test has started, it is often best to
remove the label since every PR activity will re-trigger the test (that
is a limitation of triggering a test with a label). Support for unit
tests with using KOKKOS with GPU acceleration is currently not supported.
When you see a failed build on GitHub, click on ``Details`` to be taken
to the corresponding LAMMPS Jenkins CI web page. Click on the "Exit"
symbol near the ``Logout`` button on the top right of that page to go to
the "classic view". In the classic view, there is a list of the
individual runs that make up this test run (they are shown but cannot be
inspected in the default view). You can click on any of those.
Clicking on ``Test Result`` will display the list of failed tests. Click
on the "Status" column to sort the tests based on their Failed or Passed
status. Then click on the failed test to expand its output.
For example, the following output snippet shows the failed unit test
.. code-block:: console
[ RUN ] PairStyle.gpu
/home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:63: Failure
Expected: (err) <= (epsilon)
Actual: 0.00018957912910606503 vs 0.0001
Google Test trace:
/home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:56: EXPECT_FORCES: init_forces (newton off)
/home/builder/workspace/dev/pull_requests/ubuntu_gpu/unit_tests/cmake_gpu_opencl_mixed_smallbig_clang_static/unittest/force-styles/test_main.cpp:64: Failure
Expected: (err) <= (epsilon)
Actual: 0.00022892713393549854 vs 0.0001
The failed assertions provide line numbers in the test source
(e.g. ``test_main.cpp:56``), from which one can understand what
specific assertion failed.
Note that the force style engine runs one of a small number of systems
in a rather off-equilibrium configuration with a few atoms for a few
steps, writes data and restart files, uses :doc:`the clear command
<clear>` to reset LAMMPS, and then runs from those files with different
settings (e.g. newton on/off) and integrators (e.g. verlet vs. respa).
Beyond potential issues/bugs in the source code, the mismatch between
the expected and actual values could be that force arrays are not
properly cleared between multiple run commands or that class members are
not correctly initialized or written to or read from a data or restart
file.
While the epsilon (relative precision) for a single, `IEEE 754 compliant
<https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
point operation is at about 2.2e-16, the achievable precision for the
tests is lower due to most numbers being sums over intermediate results
and the non-associativity of floating point math leading to larger
errors. In some cases specific properties of the tested style. As a
rule of thumb, the test epsilon can often be in the range 5.0e-14 to
1.0e-13. But for "noisy" force kernels, e.g. those a larger amount of
arithmetic operations involving `exp()`, `log()` or `sin()` functions,
and also due to the effect of compiler optimization or differences
between compilers or platforms, epsilon may need to be further relaxed,
sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
tables are used, epsilon may need to be set to 1.0e-10 or even higher.
For tests of accelerated styles, the per-test epsilon is multiplied
by empirical factors that take into account the differences in the order
of floating point operations or that some or most intermediate operations
may be done using approximations or with single precision floating point
math.
To rerun the failed unit test individually, change to the ``build`` directory
and run the test with verbose output. For example,
.. code-block:: bash
env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
``ctest`` with the ``-V`` flag also shows the exact command line
of the test. One can then use ``gdb --args`` to further debug and
catch exceptions with the test command, for example,
.. code-block:: bash
gdb --args /path/to/lammps/build/test_pair_style /path/to/lammps/unittest/force-styles/tests/mol-pair-lj_cut_coul_long.yaml
It is recommended to configure the build with ``-D
BUILD_SHARED_LIBS=on`` and use a custom linker to shorten the build time
during recompilation. Installing `ccache` in your development
environment helps speed up recompilation by caching previous
compilations and detecting when the same compilation is being done
again. Please see :doc:`Build_development` for further details.

66
doc/src/Developer_updating.rst
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@ -20,6 +20,7 @@ Available topics in mostly chronological order are:
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
@ -196,6 +197,71 @@ New:
fp = utils::open_potential(filename, lmp);
Use symbolic Atom and AtomVec constants instead of numerical values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
Properties in LAMMPS that were represented by integer values (0, 1,
2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
classes derived from it) (and its derived classes) have been converted
to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
Old:
.. code-block:: c++
molecular = 0;
mass_type = 1;
if (atom->molecular == 2)
if (atom->map_style == 2)
atom->add_callback(0);
atom->delete_callback(id,1);
New:
.. code-block:: c++
molecular = Atom::ATOMIC;
mass_type = AtomVec::PER_TYPE;
if (atom->molecular == Atom::TEMPLATE)
if (atom->map_style == Atom::MAP_HASH)
atom->add_callback(Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

45
doc/src/Fortran.rst
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@ -315,6 +315,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_variable: function
:f set_variable: :f:subr:`set_variable`
:ftype set_variable: subroutine
:f set_string_variable: :f:subr:`set_set_string_variable`
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -1398,7 +1402,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Set the value of a string-style variable.
.. versionadded:: 3Nov2022
.. deprecated:: TBD
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
variable, an error is generated.
.. warning::
This subroutine is deprecated and :f:subr:`set_string_variable`
should be used instead.
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
--------
.. f:subroutine:: set_string_variable(name, str)
Set the value of a string-style variable.
.. versionadded:: TBD
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
@ -1406,7 +1431,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
:to: :cpp:func:`lammps_set_string_variable`
--------
.. f:subroutine:: set_internal_variable(name, val)
Set the value of a internal-style variable.
.. versionadded:: TBD
This function assigns a new value from the floating-point number *val* to
the internal-style variable *name*\ . If *name* does not exist or is not
an internal-style variable, an error is generated.
:p character(len=*) name: name of the variable
:p read(c_double) val: new value to assign to the variable
:to: :cpp:func:`lammps_set_internal_variable`
--------

10
doc/src/Howto_github.rst
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@ -480,11 +480,11 @@ Some recent changes to the workflow are not captured in this tutorial.
For example, in addition to the *develop* branch, to which all new
features should be submitted, there is also a *release*, a *stable*, and
a *maintenance* branch; the *release* branch is updated from the
*develop* as part of a feature release, and *stable* (together with
*release*) are updated from *develop* when a stable release is made. In
between stable releases, selected bug fixes and infrastructure updates
are back-ported from the *develop* branch to the *maintenance* branch
and occasionally merged to *stable* as an update release.
*develop* branch as part of a "feature release", and *stable* (together
with *release*) are updated from *develop* when a "stable release" is
made. In between stable releases, selected bug fixes and infrastructure
updates are back-ported from the *develop* branch to the *maintenance*
branch and occasionally merged to *stable* as an update release.
Furthermore, the naming of the release tags now follow the pattern
"patch_<Day><Month><Year>" to simplify comparisons between releases.

20
doc/src/Install_git.rst
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@ -28,16 +28,16 @@ provides `limited support for subversion clients <svn_>`_.
You can follow the LAMMPS development on 4 different git branches:
* **release** : this branch is updated with every patch or feature release;
updates are always "fast-forward" merges from *develop*
* **develop** : this branch follows the ongoing development and
is updated with every merge commit of a pull request
* **stable** : this branch is updated from the *release* branch with
every stable release version and also has selected bug fixes with every
update release when the *maintenance* branch is merged into it
* **maintenance** : this branch collects back-ported bug fixes from the
*develop* branch to the *stable* branch. It is used to update *stable*
for update releases and it synchronized with *stable* at each stable release.
* **develop** : this branch follows the ongoing development and is
updated with every merge commit of a pull request
* **release** : this branch is updated with every "feature release";
updates are always "fast-forward" merges from *develop*
* **maintenance** : this branch collects back-ported bug fixes from the
*develop* branch to the *stable* branch. It is used to update the
*stable* branch for "stable update releases".
* **stable** : this branch is updated from the *release* branch with
every "stable release" version and also has selected bug fixes with
every "update release" when the *maintenance* branch is merged into it
To access the git repositories on your box, use the clone command to
create a local copy of the LAMMPS repository with a command like:

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12
doc/src/Library_objects.rst
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@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
-----------------------
@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_set_string_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_set_internal_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_variable_info
:project: progguide

99
doc/src/Manual_version.rst
View File

@ -3,45 +3,25 @@ What does a LAMMPS version mean
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously, and we aim to keep it working
correctly and reliably at all times. You can follow its development
in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
Modifications of the LAMMPS source code (like bug fixes, code refactors,
updates to existing features, or addition of new features) are organized
into pull requests. Pull requests will be merged into the *develop*
branch of the git repository after they pass automated testing and code
review by the LAMMPS developers. When a sufficient number of changes
have accumulated *and* the *develop* branch version passes an extended
set of automated tests, we release it as a *feature release*, which are
currently made every 4 to 8 weeks. The *release* branch of the git
repository is updated with every such release. A summary of the most
important changes of the patch releases are on `this website page
<https://www.lammps.org/bug.html>`_. More detailed release notes are
`available on GitHub <https://github.com/lammps/lammps/releases/>`_.
Once or twice a year, we have a "stabilization period" where we apply
only bug fixes and small, non-intrusive changes to the *develop*
branch. At the same time, the code is subjected to more detailed and
thorough manual testing than the default automated testing. Also,
several variants of static code analysis are run to improve the overall
code quality, consistency, and compliance with programming standards,
best practices and style conventions.
The release after such a stabilization period is called a *stable*
version and both, the *release* and the *stable* branches are updated
with it. Between stable releases, we collect back-ported bug fixes and
updates from the *develop* branch in the *maintenance* branch. From the
*maintenance* branch we make occasional update releases and update the
*stable* branch accordingly.
correctly and reliably at all times. Also, several variants of static
code analysis are run regularly to maintain or improve the overall code
quality, consistency, and compliance with programming standards, best
practices and style conventions. You can follow its development in a
public `git repository on GitHub <https://github.com/lammps/lammps>`_.
Each version of LAMMPS contains all the documented *features* up to and
including its version date. For recently added features, we add markers
to the documentation at which specific LAMMPS version a feature or
keyword was added or significantly changed.
The version date is printed to the screen and log file every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball. And it is on the
Identifying the Version
^^^^^^^^^^^^^^^^^^^^^^^
The version date is printed to the screen and log file every time you
run LAMMPS. There also is an indication, if a LAMMPS binary was
compiled from version with modifications **after** a release.
It is also visible in the file src/version.h and in the LAMMPS directory
name created when you unpack a downloaded tarball. And it is on the
first page of the :doc:`manual <Manual>`.
* If you browse the HTML pages of the online version of the LAMMPS
@ -53,3 +33,56 @@ first page of the :doc:`manual <Manual>`.
* If you browse the HTML pages included in your downloaded tarball, they
describe the version you have, which may be older than the online
version.
LAMMPS releases, branches, and tags
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. figure:: JPG/lammps-releases.png
:figclass: align-center
Relations between releases, main branches, and tags in the LAMMPS git repository
Development
"""""""""""
Modifications of the LAMMPS source code (like bug fixes, code
refactoring, updates to existing features, or addition of new features)
are organized into pull requests. Pull requests will be merged into the
*develop* branch of the git repository after they pass automated testing
and code review by the LAMMPS developers.
Feature Releases
""""""""""""""""
When a sufficient number of new features and updates have accumulated
*and* the LAMMPS version on the *develop* branch passes an extended set
of automated tests, we release it as a *feature release*, which are
currently made every 4 to 8 weeks. The *release* branch of the git
repository is updated with every such *feature release* and a tag in the
format ``patch_1May2014`` is added. A summary of the most important
changes of these releases for the current year are posted on `this
website page <https://www.lammps.org/bug.html>`_. More detailed release
notes are `available on GitHub
<https://github.com/lammps/lammps/releases/>`_.
Stable Releases
"""""""""""""""
About once a year, we release a *stable release* version of LAMMPS.
This is done after a "stabilization period" where we apply only bug
fixes and small, non-intrusive changes to the *develop* branch but no
new features. At the same time, the code is subjected to more detailed
and thorough manual testing than the default automated testing.
After such a *stable release*, both the *release* and the *stable*
branches are updated and two tags are applied, a ``patch_1May2014`` format
and a ``stable_1May2014`` format tag.
Stable Release Updates
""""""""""""""""""""""
Between *stable releases*, we collect bug fixes and updates back-ported
from the *develop* branch in a branch called *maintenance*. From the
*maintenance* branch we make occasional *stable update releases* and
update the *stable* branch accordingly. The first update to the
``stable_1May2014`` release would be tagged as
``stable_1May2014_update1``. These updates contain no new features.

4
doc/src/angle_charmm.rst
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@ -70,7 +70,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

19
doc/src/angle_lepton.rst
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@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
angle_style lepton
angle_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
angle_style lepton
angle_style lepton no_offset
angle_coeff 1 120.0 "k*theta^2; k=250.0"
angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@ -41,6 +51,13 @@ angle coefficient. For example `"200.0*theta^2"` represents a
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that the value U is 0.0
for $theta = theta_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an

614
doc/src/atom_style.rst
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@ -49,248 +49,221 @@ Examples
Description
"""""""""""
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
command.
The *atom_style* command selects which per-atom attributes are
associated with atoms in a LAMMPS simulation and thus stored and
communicated with those atoms as well as read from and stored in data
and restart files. Different models (e.g. :doc:`pair styles
<pair_style>`) require access to specific per-atom attributes and thus
require a specific atom style. For example, to compute Coulomb
interactions, the atom must have a "charge" (aka "q") attribute.
A number of distinct atom styles exist that combine attributes. Some
atom styles are a superset of other atom styles. Further attributes
may be added to atoms either via using a hybrid style which provides a
union of the attributes of the sub-styles, or via the :doc:`fix
property/atom <fix_property_atom>` command. The *atom_style* command
must be used before a simulation is setup via a :doc:`read_data
<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
<create_box>` command.
.. note::
Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Many of the atom styles discussed here are only enabled if LAMMPS was
built with a specific package, as listed below in the Restrictions
section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style *bond*, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
Once a style is selected and the simulation box defined, it cannot be
changed but only augmented with the :doc:`fix property/atom
<fix_property_atom>` command. So one should select an atom style
general enough to encompass all attributes required. E.g. with atom
style *bond*, it is not possible to define angles and use angle styles.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the :doc:`read_data <read_data>` command.
It is OK to use a style more general than needed, though it may be
slightly inefficient because it will allocate and communicate
additional unused data.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
Atom style attributes
"""""""""""""""""""""
The atom style *atomic* has the minimum subset of per-atom attributes
and is also the default setting. It encompasses the following per-atom
attributes (name of the vector or array in the :doc:`Atom class
<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
position (x), velocities (v), forces (f), image flags (image), group
membership (mask). Since all atom styles are a superset of atom style
*atomic*\ , they all include these attributes.
This table lists all the available atom styles, which attributes they
provide, which :doc:`package <Packages>` is required to use them, and
what the typical applications are that use them. See the
:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
:doc:`set <set>` commands for info on how to set these various
quantities.
:doc:`set <set>` commands for details on how to set these various
quantities. More information about many of the styles is provided in
the Additional Information section below.
+--------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+--------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+--------------+-----------------------------------------------------+--------------------------------------+
| *atomic* | only the default values | coarse-grain liquids, solids, metals |
+--------------+-----------------------------------------------------+--------------------------------------+
| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bond* | bonds | bead-spring polymers |
+--------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dpd* | internal temperature and internal energies | DPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *edpd* | temperature and heat capacity | eDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+--------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *full* | molecular + charge | bio-molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *line* | end points, angular velocity | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *peri* | mass, volume | mesoscopic Peridynamic models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *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 |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
+--------------+-----------------------------------------------------+--------------------------------------+
| *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 |
+--------------+-----------------------------------------------------+--------------------------------------+
| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
+--------------+-----------------------------------------------------+--------------------------------------+
.. list-table::
:header-rows: 1
:widths: auto
* - Atom style
- Attributes
- Required package
- Applications
* - *amoeba*
- *full* + "1-5 special neighbor data"
- :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA/HIPPO force fields
* - *angle*
- *bond* + "angle data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers with stiffness
* - *atomic*
- tag, type, x, v, f, image, mask
-
- atomic liquids, solids, metals
* - *body*
- *atomic* + radius, rmass, angmom, torque, body
- :ref:`BODY <PKG-BODY>`
- arbitrary bodies, see :doc:`body howto <Howto_body>`
* - *bond*
- *atomic* + molecule, nspecial, special + "bond data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers
* - *bpm/sphere*
- *bond* + radius, rmass, omega, torque, quat
- :ref:`BPM <PKG-BPM>`
- granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
* - *charge*
- *atomic* + q
-
- atomic systems with charges
* - *dielectric*
- *full* + mu, area, ed, em, epsilon, curvature, q_scaled
- :ref:`DIELECTRIC <PKG-DIELECTRIC>`
- systems with surface polarization
* - *dipole*
- *charge* + mu
- :ref:`DIPOLE <PKG-DIPOLE>`
- atomic systems with charges and point dipoles
* - *dpd*
- *atomic* + rho + "reactive DPD data"
- :ref:`DPD-REACT <PKG-DPD-REACT>`
- reactive DPD
* - *edpd*
- *atomic* + "eDPD data"
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Energy conservative DPD (eDPD)
* - *electron*
- *charge* + espin, eradius, ervel, erforce
- :ref:`EFF <PKG-EFF>`
- Electron force field systems
* - *ellipsoid*
- *atomic* + rmass, angmom, torque, ellipsoid
-
- aspherical particles
* - *full*
- *molecular* + q
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular force fields
* - *line*
- *atomic* + molecule, radius, rmass, omega, torque, line
-
- 2-d rigid body particles
* - *mdpd*
- *atomic* + rho, drho, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Many-body DPD (mDPD)
* - *molecular*
- *angle* + "dihedral and improper data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- apolar and uncharged molecules
* - *oxdna*
- *atomic* + id5p
- :ref:`CG-DNA <PKG-CG-DNA>`
- coarse-grained DNA and RNA models
* - *peri*
- *atomic* + rmass, vfrac, s0, x0
- :ref:`PERI <PKG-PERI>`
- mesoscopic Peridynamics models
* - *smd*
- *atomic* + molecule, radius, rmass + "smd data"
- :ref:`MACHDYN <PKG-MACHDYN>`
- Smooth Mach Dynamics models
* - *sph*
- *atomic* + "sph data"
- :ref:`SPH <PKG-SPH>`
- Smoothed particle hydrodynamics models
* - *sphere*
- *atomic* + radius, rmass, omega, torque
-
- finite size spherical particles, e.g. granular models
* - *spin*
- *atomic* + "magnetic moment data"
- :ref:`SPIN <PKG-SPIN>`
- magnetic particles
* - *tdpd*
- *atomic* + cc, cc_flux, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Transport DPD (tDPD)
* - *template*
- *atomic* + molecule, molindex, molatom
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular systems where attributes are taken from :doc:`molecule files <molecule>`
* - *tri*
- *sphere* + molecule, angmom, tri
-
- 3-d triangulated rigid body LJ particles
* - *wavepacket*
- *charge* + "wavepacket data"
- :ref:`AWPMD <PKG-AWPMD>`
- Antisymmetrized wave packet MD
.. note::
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>` page for examples of cases where this is
useful and details on how to initialize, access, and output the
custom values.
It is possible to add some attributes, such as a molecule ID and
charge, to atom styles that do not have them built in using the
:doc:`fix property/atom <fix_property_atom>` command. This command
also allows new custom-named attributes consisting of extra integer
or floating-point values or vectors to be added to atoms. See the
:doc:`fix property/atom <fix_property_atom>` page for examples of
cases where this is useful and details on how to initialize,
access, and output these custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
*tri*, and *body* styles, which define finite-size particles. See the
:doc:`Howto spherical <Howto_spherical>` page for an overview of using
finite-size particle models with LAMMPS.
----------
All of the point-particle styles assign mass to particles on a
per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
Particle size and mass
""""""""""""""""""""""
For the *sphere* and *bpm/sphere* styles, 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 for the *sphere* style,
spheres can be effectively treated as 2d discs for a 2d simulation if
desired. See also the :doc:`set density/disc <set>` command. These
styles take 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.
All of the atom styles define point particles unless they (1) define
finite-size spherical particles via the *radius* attribute, or (2)
define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
*line*, and *tri* styles). Most of these styles can also be used with
mixtures of point and finite-size particles.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
Note that the *radius* property may need to be provided as a
*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
files <read_data>`). See the :doc:`Howto spherical <Howto_spherical>`
page for an overview of using finite-size spherical and aspherical
particle models with LAMMPS.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
Unless an atom style defines the per-atom *rmass* attribute, particle
masses are defined on a per-type basis, using the :doc:`mass <mass>`
command. This means each particle's mass is indexed by its atom
*type*.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use atom_style hybrid sphere dipole, which will assign both a
diameter and dipole moment to each particle.
A few styles define the per-atom *rmass* attribute which can also be
added using the :doc:`fix property/atom <fix_property_atom>` command.
In this case each particle stores its own mass. Atom styles that have
a per-atom rmass may define it indirectly through setting particle
diameter and density on a per-particle basis. If both per-type mass
and per-atom *rmass* are defined (e.g. in a hybrid style), the
per-atom mass will take precedence in any operation which which works
with both flavors of mass.
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
----------
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *bpm/sphere* style is part of the BPM package.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand. Note that this style is part of the CG-DNA package.
The *dpd* style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the DPD-REACT package, and is not for use with
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity(edpd_cv).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering
density-dependent many-body interactions.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
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 *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
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetrating each other.
For the *spin* style, a magnetic spin is associated to each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *wavepacket* style is similar to *electron*, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical *etag* values.
For the *line* style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the *tri* style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
*template* style instead of the *bond*, *angle*, *molecular* styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
Additional information about specific atom styles
"""""""""""""""""""""""""""""""""""""""""""""""""
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -309,6 +282,148 @@ Note that there may be additional arguments required along with the
*bstyle* specification, in the atom_style body command. These
arguments are described on the :doc:`Howto body <Howto_body>` doc page.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole vector mu is defined for each
point particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use the command `atom_style hybrid sphere dipole`, which will
assign both a diameter and dipole moment to each particle. This also
requires using an integrator with a "/sphere" suffix like :doc:`fix
nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
and the "update dipole" or "update dlm" parameters to the fix
commands.
The *dpd* style is for reactive dissipative particle dynamics (DPD)
particles. Note that it is part of the DPD-REACT package, and is not
required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
commands, which only require the attributes from atom_style *atomic*.
Atom_style *dpd* extends DPD particle properties with internal
temperature (dpdTheta), internal conductive energy (uCond), internal
mechanical energy (uMech), and internal chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity (edpd_cv).
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the *ellipsoid* style, particles can be ellipsoids which each
stores a shape vector with the 3 diameters of the ellipsoid and a
quaternion 4-vector with its orientation. Each particle stores a flag
in the ellipsoid vector which indicates whether it is an ellipsoid (1)
or a point particle (0).
For the *line* style, particles can be are idealized line segments
which store a per-particle mass and length and orientation (i.e. the
end points of the line segment). Each particle stores a flag in the
line vector which indicates whether it is a line segment (1) or a
point particle (0).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering density-dependent
many-body interactions.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *smd* style is for Smooth Particle Mach dynamics. Both fluids and
solids can be modeled. Particles store the mass and volume of an
integration point, a kernel diameter used for calculating the field
variables (e.g. stress and deformation) and a contact radius for
calculating repulsive forces which prevent individual physical bodies
from penetrating each other.
The *sph* style is for smoothed particle hydrodynamics (SPH) particles
which store a density (rho), energy (esph), and heat capacity (cv).
For the *spin* style, a magnetic spin is associated with each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
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 *wavepacket* style is similar to the *electron* style, but the
electrons may consist of several Gaussian wave packets, summed up with
coefficients cs= (cs_re,cs_im). Each of the wave packets is treated
as a separate particle in LAMMPS, wave packets belonging to the same
electron must have identical *etag* values.
The *sphere* and *bpm/sphere* styles allow particles to be either point
particles or finite-size particles. If the *radius* attribute is >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by using 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 for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. These styles also
take an optional 0 or 1 argument. A value of 0 means the radius of
each sphere is constant for the duration of the simulation (this is
the default). 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.
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms only
store a template index and template atom to identify which molecule and
which atom-within-the-molecule they represent. Using the *template*
style instead of the *bond*, *angle*, *molecular* styles can save memory
for systems comprised of a large number of small molecules, all of a
single type (or small number of types). See the paper by Grime and
Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
advantageous for large-scale coarse-grained systems. The
``examples/template`` directory has a few demo inputs and examples
showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should ensure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
For the *tri* style, particles can be planar triangles which each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle). Each particle stores a flag in the tri
vector which indicates whether it is a triangle (1) or a point
particle (0).
----------
Typically, simulations require only a single (non-hybrid) atom style.
@ -326,11 +441,12 @@ dipole". When a hybrid style is used, atoms store and communicate the
union of all quantities implied by the individual styles.
When using the *hybrid* style, you cannot combine the *template* style
with another molecular style that stores bond,angle,etc info on a
with another molecular style that stores bond, angle, etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see the :doc:`Modify <Modify>` doc page.
LAMMPS can be extended with new atom styles as well as new body styles;
see the corresponding manual page on :doc:`modifying & extending LAMMPS
<Modify_atom>`.
----------
@ -346,54 +462,20 @@ This command cannot be used after the simulation box is defined by a
Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :doc:`Build package
<Build_package>` page for more info.
The *amoeba* style is part of the AMOEBA package.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
The *line* and *tri* styles are part of the ASPHERE package.
The *body* style is part of the BODY package.
The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *oxdna* style is part of the CG-DNA package for coarse-grained
simulation of DNA and RNA.
The *electron* style is part of the EFF package for :doc:`electronic
force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
<Build_package>` page for more info. The table above lists which package
is required for individual atom styles.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
Default
"""""""
The default atom style is atomic. If atom_style sphere is used its
default argument is 0.
The default atom style is *atomic*. If atom_style *sphere* or
*bpm/sphere* is used, its default argument is 0.
----------

4
doc/src/bond_bpm_rotational.rst
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@ -147,8 +147,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

4
doc/src/bond_bpm_spring.rst
View File

@ -113,8 +113,8 @@ By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces by setting
the *overlay/pair* keyword to *yes*. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the :doc:`how to
<Howto_bpm>` page on BPMs.
restrictions. Further details can be found in the :doc:`how to <Howto_bpm>`
page on BPMs.
.. versionadded:: 28Mar2023

19
doc/src/bond_lepton.rst
View File

@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
bond_style lepton
bond_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
bond_style lepton
bond_style lepton no_offset
bond_coeff 1 1.5 "k*r^2; k=250.0"
bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@ -40,6 +50,13 @@ constant *K* of 200.0 energy units:
U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that he value U is 0.0
for $r = r_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical

7
doc/src/dihedral_charmm.rst
View File

@ -3,6 +3,7 @@
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
.. index:: dihedral_style charmmfsw/kk
dihedral_style charmm command
=============================
@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
dihedral_style charmmfsw command
================================
Accelerator Variants: *charmmfsw/kk*
Syntax
""""""
@ -144,7 +147,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

2
doc/src/fix_halt.rst
View File

@ -183,4 +183,4 @@ Related commands
Default
"""""""
The option defaults are error = hard, message = yes, and path = ".".
The option defaults are error = soft, message = yes, and path = ".".

96
doc/src/fix_neb.rst
View File

@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
force/distance units.
With a value of *ideal*, the spring force is computed as suggested in
ref`(WeinanE) <WeinanE>`
:ref:`(WeinanE) <WeinanE>`
.. math::
@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
equally spaced. I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
climbing replica is off, where *i* is the replica number). The
*meanDist* is the average distance between replicas. Note that in this
case the specified *Kspring* is in force units. When the climbing replica
is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
each side of the climbing image. Note that the *ideal* form of nudging
can often be more effective at keeping the replicas equally spaced before
climbing, then equally spaced either side of the climbing image whilst
climbing.
case the specified *Kspring* is in force units. When the climbing
replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
separately each side of the climbing image. Note that the *ideal* form
of nudging can often be more effective at keeping the replicas equally
spaced before climbing, then equally spaced either side of the climbing
image whilst climbing.
With a value of *equal* the spring force is computed as for *ideal*
when the climbing replica is off, promoting equidistance. When the climbing
With a value of *equal* the spring force is computed as for *ideal* when
the climbing replica is off, promoting equidistance. When the climbing
replica is on, the spring force is computed to promote equidistant
absolute differences in energy, rather than distance, each side of
the climbing image:
absolute differences in energy, rather than distance, each side of the
climbing image:
.. math::
@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
*meanEdist* is the average absolute energy difference between
replicas up to the climbing image or from the climbing image
to the final image, for images before or after the climbing
image respectively. :math:`ED_{ideal}` is the corresponding
cumulative sum of average absolute energy differences in
each case, in close analogy to *ideal*. This form of nudging
is to aid schemes which integrate forces along, or near to,
NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
*meanEdist* is the average absolute energy difference between replicas
up to the climbing image or from the climbing image to the final image,
for images before or after the climbing image
respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
average absolute energy differences in each case, in close analogy to
*ideal*. This form of nudging is to aid schemes which integrate forces
along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
----------
The keyword *perp* specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too strongly kinked. It can
The keyword *perp* specifies if and how a perpendicular nudging force is
computed. It adds a spring force perpendicular to the path in order to
prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
:ref:`(Maras) <Maras1>` for details.
resolution is poor. I.e. when few replicas are used; see :ref:`(Maras)
<Maras1>` for details.
The perpendicular spring force is given by
@ -181,10 +180,10 @@ force is added.
By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word *end*, additional
forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy E to the
target energy ETarget.
respective local minima. By using the key word *end*, additional forces
can be applied to the first and/or last replicas, to enable them to
relax toward a MEP while constraining their energy E to the target
energy ETarget.
If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
specified replica becomes:
@ -197,33 +196,33 @@ specified replica becomes:
The "spring" constant on the difference in energies is the specified
*Kspring3* value.
When *estyle* is specified as *first*, the force is applied to the
first replica. When *estyle* is specified as *last*, the force is
applied to the last replica. Note that the *end* keyword can be used
twice to add forces to both the first and last replicas.
When *estyle* is specified as *first*, the force is applied to the first
replica. When *estyle* is specified as *last*, the force is applied to
the last replica. Note that the *end* keyword can be used twice to add
forces to both the first and last replicas.
For both these *estyle* settings, the target energy *ETarget* is set
to the initial energy of the replica (at the start of the NEB
calculation).
If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
force is applied to the last replica, but the target energy *ETarget*
is continuously set to the energy of the first replica, as it evolves
force is applied to the last replica, but the target energy *ETarget* is
continuously set to the energy of the first replica, as it evolves
during the NEB relaxation.
The difference between these two *estyle* options is as follows. When
*estyle* is specified as *last/efirst*, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying *estyle* as *last/efirst/middle* which will alter the
inter-replica force applied to intermediate replicas by removing the
contribution of the gradient to the inter-replica force. This will
only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
inter-replica force applied to the intermediate replicas (neither first
or last). If the initial path is too far from the MEP, an intermediate
replica may relax "faster" and reach a lower energy than the last
replica. In this case the intermediate replica will be relaxing toward
its own local minima. This behavior can be prevented by specifying
*estyle* as *last/efirst/middle* which will alter the inter-replica
force applied to intermediate replicas by removing the contribution of
the gradient to the inter-replica force. This will only be done if a
particular intermediate replica has a lower energy than the first
replica. This should effectively prevent the intermediate replicas from
over-relaxing.
After converging a NEB calculation using an *estyle* of
*last/efirst/middle*, you should check that all intermediate replicas
@ -237,9 +236,10 @@ target energy.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

2
doc/src/fix_qeq.rst
View File

@ -232,8 +232,6 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These qeq fixes are not compatible with the GPU and USER-INTEL packages.
These qeq fixes will ignore electric field contributions from
:doc:`fix efield <fix_efield>`.

138
doc/src/molecule.rst
View File

@ -126,14 +126,50 @@ molecule (header keyword = inertia).
Format of a molecule file
"""""""""""""""""""""""""
The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
.. code-block::
# Water molecule. TIP3P geometry
# header section:
3 atoms
2 bonds
1 angles
# body section:
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
first line of the header and thus of the molecule file is *always*
skipped; it typically contains a description of the file or a comment
from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values
in body particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
.. list-table::
:header-rows: 1
:widths: auto
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
* - Number(s)
- Keyword
- Meaning
- Default Value
* - N
- atoms
- # of atoms N in molecule
- 0
* - Nb
- bonds
- # of bonds Nb in molecule
- 0
* - Na
- angles
- # of angles Na in molecule
- 0
* - Nd
- dihedrals
- # of dihedrals Nd in molecule
- 0
* - Ni
- impropers
- # of impropers Ni in molecule
- 0
* - Nf
- fragments
- # of fragments Nf in molecule
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
* - Mtotal
- mass
- total mass of molecule
- computed
* - Xc Yc Zc
- com
- coordinates of center-of-mass of molecule
- computed
* - Ixx Iyy Izz Ixy Ixz Iyz
- inertia
- 6 components of inertia tensor of molecule
- computed
For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
this quantity itself if needed, assuming the molecules consist of a set
of point particles or finite-size particles (with a non-zero diameter)
that do **not** overlap. If finite-size particles in the molecule
**do** overlap, LAMMPS will not account for the overlap effects when
calculating any of these 3 quantities, so you should pre-compute them
yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@ -188,7 +261,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
----------
.. versionadded:: TBD
*Dipoles* section:
* one line per atom
* line syntax: ID mux muy muz
* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
This section is only allowed for :doc:`atom styles <atom_style>` that
support particles with point dipoles, e.g. atom_style dipole. If not
listed, the default dipole component of each atom in the molecule is set
to 0.0.
----------
*Masses* section:
* one line per atom

13
doc/src/neb.rst
View File

@ -10,7 +10,7 @@ Syntax
neb etol ftol N1 N2 Nevery file-style arg keyword values
* etol = stopping tolerance for energy (energy units)
* etol = stopping tolerance for energy (dimensionless)
* ftol = stopping tolerance for force (force units)
* N1 = max # of iterations (timesteps) to run initial NEB
* N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@ -89,10 +89,11 @@ potentials, and the starting configuration when the neb command is
issued should be the same for every replica.
In a NEB calculation each replica is connected to other replicas by
inter-replica nudging forces. These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
neb command. The group used to define the fix neb command defines the
NEB atoms which are the only ones that inter-replica springs are
applied to. If the group does not include all atoms, then non-NEB
inter-replica nudging forces. These forces are imposed by the
:doc:`fix neb <fix_neb>` command, which must be used in conjunction
with the neb command. The group used to define the fix neb command
defines the NEB atoms which are the only ones that inter-replica springs
are applied to. If the group does not include all atoms, then non-NEB
atoms have no inter-replica springs and the forces they feel and their
motion is computed in the usual way due only to other atoms within
their replica. Conceptually, the non-NEB atoms provide a background
@ -445,7 +446,7 @@ Related commands
""""""""""""""""
:doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix viscous <fix_viscous>`
:doc:`fix viscous <fix_viscous>`, :doc:`fix neb <fix_neb>`
Default
"""""""

26
doc/src/package.rst
View File

@ -344,12 +344,10 @@ specify additional flags for the runtime build.
----------
The *intel* style invokes settings associated with the use of the
INTEL package. All of its settings, except the *omp* and *mode*
keywords, are ignored if LAMMPS was not built with Xeon Phi
co-processor support. All of its settings, including the *omp* and
*mode* keyword are applicable if LAMMPS was built with co-processor
support.
The *intel* style invokes settings associated with the use of the INTEL
package. The keywords *balance*, *ghost*, *tpc*, and *tptask* are
**only** applicable if LAMMPS was built with Xeon Phi co-processor
support and are otherwise ignored.
The *Nphi* argument sets the number of co-processors per node.
This can be set to any value, including 0, if LAMMPS was not
@ -474,13 +472,13 @@ If the *neigh/thread* keyword is set to *off*, then the KOKKOS package
threads only over atoms. However, for small systems, this may not expose
enough parallelism to keep a GPU busy. When this keyword is set to *on*,
the KOKKOS package threads over both atoms and neighbors of atoms. When
using *neigh/thread* *on*, a full neighbor list must also be used. Using
*neigh/thread* *on* may be slower for large systems, so this this option
is turned on by default only when there are 16K atoms or less owned by
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
potentials support this keyword yet, and only thread over atoms. Many
simple pairwise potentials such as Lennard-Jones do support threading
over both atoms and neighbors.
using *neigh/thread* *on*, the :doc:`newton pair <newton>` setting must
be "off". Using *neigh/thread* *on* may be slower for large systems, so
this this option is turned on by default only when running on one or
more GPUs and there are 16k atoms or less owned by an MPI rank. Not all
KOKKOS-enabled potentials support this keyword yet, and only thread over
atoms. Many simple pairwise potentials such as Lennard-Jones do support
threading over both atoms and neighbors.
If the *neigh/transpose* keyword is set to *off*, then the KOKKOS
package will use the same memory layout for building the neighbor list on
@ -732,7 +730,7 @@ comm = device, sort = device, neigh/transpose = off, gpu/aware = on. When
LAMMPS can safely detect that GPU-aware MPI is not available, the default value
of gpu/aware becomes "off". For CPUs or Xeon Phis, the option defaults are
neigh = half, neigh/qeq = half, newton = on, binsize = 0.0, comm = no, and sort
= no. The option neigh/thread = on when there are 16K atoms or less on an MPI
= no. For GPUs, option neigh/thread = on when there are 16k atoms or less on an MPI
rank, otherwise it is "off". These settings are made automatically by the
required "-k on" :doc:`command-line switch <Run_options>`. You can change them
by using the package kokkos command in your input script or via the :doc:`-pk

39
doc/src/pair_aip_water_2dm.rst
View File

@ -22,13 +22,24 @@ Examples
.. code-block:: LAMMPS
pair_style hybrid/overlay aip/water/2dm 16.0 1
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
pair_coeff * * aip/water/2dm CBNOH.aip.water.2dm C Ow Hw
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm CBNOH.aip.water.2dm C Ow Hw
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 3 4 1 1 0.1546 10 8.5 coul/shield 16.0 1
pair_coeff 1*2 1*2 none
pair_coeff 3 3 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 3 4 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 4 4 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm CBNOH.aip.water.2dm B N Ow Hw
pair_coeff 1 3 coul/shield 1.333
pair_coeff 1 4 coul/shield 1.333
pair_coeff 2 3 coul/shield 1.333
pair_coeff 2 4 coul/shield 1.333
Description
"""""""""""
@ -37,7 +48,7 @@ Description
The *aip/water/2dm* style computes the anisotropic interfacial potential
(AIP) potential for interfaces of water with two-dimensional (2D)
materials as described in :ref:`(Feng) <Feng>`.
materials as described in :ref:`(Feng1) <Feng1>` and :ref:`(Feng2) <Feng2>`.
.. math::
@ -62,12 +73,12 @@ larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
.. note::
This pair style uses the atomic normal vector definition from
:ref:`(Feng) <Feng>`), where the atomic normal vectors of the
:ref:`(Feng1) <Feng1>`), where the atomic normal vectors of the
hydrogen atoms are assumed to lie along the corresponding
oxygen-hydrogen bonds and the normal vector of the central oxygen
atom is defined as their average.
The provided parameter file, ``COH.aip.water.2dm``, is intended for use
The provided parameter file, ``CBNOH.aip.water.2dm``, is intended for use
with *metal* :doc:`units <units>`, with energies in meV. Two additional
parameters, *S*, and *rcut* are included in the parameter file. *S* is
designed to facilitate scaling of energies; *rcut* is the cutoff for an
@ -77,7 +88,7 @@ the calculation of the normals for all atom pairs.
.. note::
The parameters presented in the provided parameter file,
``COH.aip.water.2dm``, are fitted with the taper function enabled by
``CBNOH.aip.water.2dm``, are fitted with the taper function enabled by
setting the cutoff equal to 16.0 Angstrom. Using a different cutoff
or taper function setting should be carefully checked as they can
lead to significant errors. These parameters provide a good
@ -134,7 +145,7 @@ if LAMMPS was built with that package. See the :doc:`Build package
This pair style requires the newton setting to be *on* for pair
interactions.
The ``COH.aip.water.2dm`` potential file provided with LAMMPS is
The ``CBNOH.aip.water.2dm`` potential file provided with LAMMPS is
parameterized for *metal* units. You can use this pair style with any
LAMMPS units, but you would need to create your own potential file with
parameters in the appropriate units, if your simulation does not use
@ -162,6 +173,10 @@ tap_flag = 1
----------
.. _Feng:
.. _Feng1:
**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).
**(Feng1)** Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
.. _Feng2:
**(Feng2)** Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).

7
doc/src/pair_charmm.rst
View File

@ -16,6 +16,7 @@
.. index:: pair_style lj/charmm/coul/msm/omp
.. index:: pair_style lj/charmmfsw/coul/charmmfsh
.. index:: pair_style lj/charmmfsw/coul/long
.. index:: pair_style lj/charmmfsw/coul/long/kk
pair_style lj/charmm/coul/charmm command
========================================
@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
pair_style lj/charmmfsw/coul/long command
=========================================
Accelerator Variants: *lj/charmmfsw/coul/long/kk*
Syntax
""""""
@ -281,7 +284,9 @@ page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

20
doc/src/pair_ilp_tmd.rst
View File

@ -22,12 +22,12 @@ Examples
.. code-block:: LAMMPS
pair_style hybrid/overlay ilp/tmd 16.0 1
pair_coeff * * ilp/tmd MoS2.ILP Mo S S
pair_coeff * * ilp/tmd TMD.ILP Mo S S
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL W Se Se
pair_coeff * * ilp/tmd TMD.ILP Mo S S W Se Se
Description
"""""""""""
@ -36,7 +36,7 @@ Description
The *ilp/tmd* style computes the registry-dependent interlayer
potential (ILP) potential for transition metal dichalcogenides (TMD)
as described in :ref:`(Ouyang7) <Ouyang7>`.
as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
.. math::
@ -69,7 +69,7 @@ calculating the normals.
each atom `i`, its six nearest neighboring atoms belonging to the same
sub-layer are chosen to define the normal vector `{\bf n}_i`.
The parameter file (e.g. MoS2.ILP), is intended for use with *metal*
The parameter file (e.g. TMD.ILP), is intended for use with *metal*
:doc:`units <units>`, with energies in meV. Two additional parameters,
*S*, and *rcut* are included in the parameter file. *S* is designed to
facilitate scaling of energies. *rcut* is designed to build the neighbor
@ -77,7 +77,7 @@ list for calculating the normals for each atom pair.
.. note::
The parameters presented in the parameter file (e.g. MoS2.ILP),
The parameters presented in the parameter file (e.g. TMD.ILP),
are fitted with taper function by setting the cutoff equal to 16.0
Angstrom. Using different cutoff or taper function should be careful.
These parameters provide a good description in both short- and long-range
@ -133,10 +133,10 @@ if LAMMPS was built with that package. See the :doc:`Build package
This pair style requires the newton setting to be *on* for pair
interactions.
The MoS2.ILP potential file provided with LAMMPS (see the potentials
The TMD.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your own
custom MoS2.ILP potential file with coefficients listed in the appropriate
custom TMD.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands
@ -164,3 +164,7 @@ tap_flag = 1
.. _Ouyang7:
**(Ouyang7)** W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
.. _Jiang:
**(Jiang)** W. Jiang, et al., J. Phys. Chem. A, 127, 46, 9820-9830 (2023).

6
doc/src/pair_lepton.rst
View File

@ -72,7 +72,7 @@ interactions between particles which depend on the distance and have a
cutoff. The potential function must be provided as an expression string
using "r" as the distance variable. With pair style *lepton/coul* one
may additionally reference the charges of the two atoms of the pair with
"qi" and "qj", respectively. With pair style *lepton/coul* one may
"qi" and "qj", respectively. With pair style *lepton/sphere* one may
instead reference the radii of the two atoms of the pair with "radi" and
"radj", respectively; this is half of the diameter that can be set in
:doc:`data files <read_data>` or the :doc:`set command <set>`.
@ -166,8 +166,8 @@ mixing. Thus, expressions for *all* I,J pairs must be specified
explicitly.
Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
option for shifting the energy of the pair interaction so that it is
0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
option for shifting the potential energy of the pair interaction so that
it is 0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
The :doc:`pair_modify table <pair_modify>` options are not relevant for
the these pair styles.

3
doc/src/run_style.rst
View File

@ -329,7 +329,8 @@ Restrictions
The *verlet/split* style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the *respa/omp* style is available
only if the OPENMP package was included. See the :doc:`Build package
<Build_package>` page for more info.
<Build_package>` page for more info. It is not compatible with
kspace styles from the INTEL package.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are

9
doc/utils/sphinx-config/false_positives.txt
View File

@ -125,6 +125,7 @@ antisymmetry
anton
Antonelli
api
apolar
Apoorva
Appl
Appshaw
@ -151,6 +152,7 @@ asphericity
Asq
assignee
assively
associativity
Asta
Astart
Astop
@ -792,11 +794,13 @@ dispersionflag
dissipative
Dissipative
distharm
distutils
dl
dlabel
dlambda
DLAMMPS
dll
dlm
dlopen
dm
dmax
@ -1014,6 +1018,7 @@ Ercolessi
Erdmann
erf
erfc
erforce
Erhart
erorate
erose
@ -2234,8 +2239,10 @@ Mohd
Mohles
mol
Mol
molatom
molfile
Molfile
molindex
MolPairStyle
moltemplate
momb
@ -2568,6 +2575,7 @@ ns
Ns
Nsample
Nskip
nspecial
Nspecies
nsq
Nstart
@ -3876,6 +3884,7 @@ versa
Verstraelen
ves
vflag
vfrac
vhi
vibrational
Vij

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -110,6 +110,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_variable);
ADDSYM(extract_variable_datatype);
ADDSYM(set_variable);
ADDSYM(set_string_variable);
ADDSYM(set_internal_variable);
ADDSYM(variable_info);
ADDSYM(gather_atoms);

6
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -152,9 +152,11 @@ struct _liblammpsplugin {
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
void *(*extract_variable)(void *, const char *, const char *);
int (*extract_variable_datatype)(void *, const char *);
int (*set_variable)(void *, char *, char *);
int (*set_variable)(void *, const char *, const char *);
int (*set_string_variable)(void *, const char *, const char *);
int (*set_internal_variable)(void *, const char *, double);
int (*variable_info)(void *, int, char *, int);
void (*gather_atoms)(void *, const char *, int, int, void *);

18
examples/COUPLE/simple/simple.cpp
View File

@ -67,7 +67,7 @@ int main(int narg, char **arg)
FILE *fp;
if (me == 0) {
fp = fopen(arg[2],"r");
if (fp == NULL) {
if (fp == nullptr) {
printf("ERROR: Could not open LAMMPS input script\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
@ -78,14 +78,14 @@ int main(int narg, char **arg)
// (could just send it to proc 0 of comm_lammps and let it Bcast)
// all LAMMPS procs call input->one() on the line
LAMMPS *lmp = NULL;
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
LAMMPS *lmp = nullptr;
if (lammps == 1) lmp = new LAMMPS(0,nullptr,comm_lammps);
int n;
char line[1024];
while (1) {
while (true) {
if (me == 0) {
if (fgets(line,1024,fp) == NULL) n = 0;
if (fgets(line,1024,fp) == nullptr) n = 0;
else n = strlen(line) + 1;
if (n == 0) fclose(fp);
}
@ -101,8 +101,8 @@ int main(int narg, char **arg)
// put coords back into LAMMPS
// run a single step with changed coords
double *x = NULL;
double *v = NULL;
double *x = nullptr;
double *v = nullptr;
if (lammps == 1) {
lmp->input->one("run 10");
@ -147,7 +147,7 @@ int main(int narg, char **arg)
// create_atoms() to create new ones with old coords, vels
// initial thermo should be same as step 20
int *type = NULL;
int *type = nullptr;
if (lammps == 1) {
int natoms = static_cast<int> (lmp->atom->natoms);
@ -155,7 +155,7 @@ int main(int narg, char **arg)
for (int i = 0; i < natoms; i++) type[i] = 1;
lmp->input->one("delete_atoms group all");
lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
lammps_create_atoms(lmp,natoms,nullptr,type,x,v,nullptr,0);
lmp->input->one("run 10");
}

369
examples/PACKAGES/cgdna/util/generate.py
View File

@ -22,22 +22,26 @@
"""
Import basic modules
"""
# for python2/3 compatibility
from __future__ import print_function
import sys, os, timeit
from timeit import default_timer as timer
start_time = timer()
"""
Try to import numpy; if failed, import a local version mynumpy
Try to import numpy; if failed, import a local version mynumpy
which needs to be provided
"""
try:
import numpy as np
except:
print >> sys.stderr, "numpy not found. Exiting."
print("numpy not found. Exiting.", file=sys.stderr)
sys.exit(1)
"""
Check that the required arguments (box offset and size in simulation units
Check that the required arguments (box offset and size in simulation units
and the sequence file were provided
"""
try:
@ -45,8 +49,8 @@ try:
box_length = float(sys.argv[2])
infile = sys.argv[3]
except:
print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences")
print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences"), file=sys.stderr)
sys.exit(1)
box = np.array ([box_length, box_length, box_length])
@ -57,8 +61,7 @@ try:
inp = open (infile, 'r')
inp.close()
except:
print >> sys.stderr, "Could not open file '%s' for reading. \
Aborting." % infile
print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
sys.exit(2)
# return parts of a string
@ -86,7 +89,7 @@ Define auxiliary variables for the construction of a helix
# center of the double strand
CM_CENTER_DS = POS_BASE + 0.2
# ideal distance between base sites of two nucleotides
# ideal distance between base sites of two nucleotides
# which are to be base paired in a duplex
BASE_BASE = 0.3897628551303122
@ -118,7 +121,7 @@ strandnum = []
bonds = []
"""
"""
Convert local body frame to quaternion DOF
"""
def exyz_to_quat (mya1, mya3):
@ -135,25 +138,25 @@ def exyz_to_quat (mya1, mya3):
# compute other components from it
if q0sq >= 0.25:
myquat[0] = np.sqrt(q0sq)
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
myquat[0] = np.sqrt(q0sq)
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
elif q1sq >= 0.25:
myquat[1] = np.sqrt(q1sq)
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
myquat[1] = np.sqrt(q1sq)
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
elif q2sq >= 0.25:
myquat[2] = np.sqrt(q2sq)
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
myquat[2] = np.sqrt(q2sq)
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
elif q3sq >= 0.25:
myquat[3] = np.sqrt(q3sq)
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
myquat[3] = np.sqrt(q3sq)
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
myquat[2]*myquat[2] + myquat[3]*myquat[3])
@ -169,62 +172,62 @@ Adds a strand to the system by appending it to the array of previous strands
"""
def add_strands (mynewpositions, mynewa1s, mynewa3s):
overlap = False
# This is a simple check for each of the particles where for previously
# placed particles i we check whether it overlaps with any of the
# This is a simple check for each of the particles where for previously
# placed particles i we check whether it overlaps with any of the
# newly created particles j
print >> sys.stdout, "## Checking for overlaps"
print( "## Checking for overlaps", file=sys.stdout)
for i in xrange(len(positions)):
for i in range(len(positions)):
p = positions[i]
pa1 = a1s[i]
p = positions[i]
pa1 = a1s[i]
for j in xrange (len(mynewpositions)):
for j in range (len(mynewpositions)):
q = mynewpositions[j]
qa1 = mynewa1s[j]
q = mynewpositions[j]
qa1 = mynewa1s[j]
# skip particles that are anyway too far away
dr = p - q
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) > RC2:
continue
# skip particles that are anyway too far away
dr = p - q
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) > RC2:
continue
# base site and backbone site of the two particles
# base site and backbone site of the two particles
p_pos_back = p + pa1 * POS_BACK
p_pos_base = p + pa1 * POS_BASE
q_pos_back = q + qa1 * POS_BACK
q_pos_base = q + qa1 * POS_BASE
# check for no overlap between the two backbone sites
# check for no overlap between the two backbone sites
dr = p_pos_back - q_pos_back
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BACK:
overlap = True
# check for no overlap between the two base sites
# check for no overlap between the two base sites
dr = p_pos_base - q_pos_base
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BASE:
overlap = True
# check for no overlap between backbone site of particle p
# with base site of particle q
# check for no overlap between backbone site of particle p
# with base site of particle q
dr = p_pos_back - q_pos_base
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) < RC2_BACK_BASE:
overlap = True
# check for no overlap between base site of particle p and
# backbone site of particle q
# check for no overlap between base site of particle p and
# backbone site of particle q
dr = p_pos_base - q_pos_back
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) < RC2_BACK_BASE:
overlap = True
# exit if there is an overlap
# exit if there is an overlap
if overlap:
return False
@ -237,10 +240,10 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
a1s.append (p)
for p in mynewa3s:
a3s.append (p)
# calculate quaternion from local body frame and append
for ia in xrange(len(mynewpositions)):
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
quaternions.append(mynewquaternions)
# calculate quaternion from local body frame and append
for ia in range(len(mynewpositions)):
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
quaternions.append(mynewquaternions)
return True
@ -281,7 +284,7 @@ def get_rotation_matrix(axis, anglest):
[olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
"""
Generates the position and orientation vectors of a
Generates the position and orientation vectors of a
(single or double) strand from a sequence string
"""
def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
@ -295,76 +298,75 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
# overall direction of the helix
dir = np.array(dir, dtype=float)
if sequence == None:
sequence = np.random.randint(1, 5, bp)
sequence = np.random.randint(1, 5, bp)
# the elseif here is most likely redundant
# the elseif here is most likely redundant
elif len(sequence) != bp:
n = bp - len(sequence)
sequence += np.random.randint(1, 5, n)
print >> sys.stderr, "sequence is too short, adding %d random bases" % n
n = bp - len(sequence)
sequence += np.random.randint(1, 5, n)
print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
# normalize direction
dir_norm = np.sqrt(np.dot(dir,dir))
if dir_norm < 1e-10:
print >> sys.stderr, "direction must be a valid vector, \
defaulting to (0, 0, 1)"
dir = np.array([0, 0, 1])
print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
dir = np.array([0, 0, 1])
else: dir /= dir_norm
# find a vector orthogonal to dir to act as helix direction,
# if not provided switch off random orientation
if perp is None or perp is False:
v1 = np.random.random_sample(3)
v1 -= dir * (np.dot(dir, v1))
v1 /= np.sqrt(sum(v1*v1))
v1 = np.random.random_sample(3)
v1 -= dir * (np.dot(dir, v1))
v1 /= np.sqrt(sum(v1*v1))
else:
v1 = perp;
v1 = perp;
# generate rotational matrix representing the overall rotation of the helix
R0 = get_rotation_matrix(dir, rot)
# rotation matrix corresponding to one step along the helix
R = get_rotation_matrix(dir, [1, "bp"])
# set the vector a1 (backbone to base) to v1
# set the vector a1 (backbone to base) to v1
a1 = v1
# apply the global rotation to a1
# apply the global rotation to a1
a1 = np.dot(R0, a1)
# set the position of the fist backbone site to start_pos
rb = np.array(start_pos)
# set a3 to the direction of the helix
a3 = dir
for i in range(bp):
# work out the position of the centre of mass of the nucleotide
rcdm = rb - CM_CENTER_DS * a1
# append to newpositions
mynewpositions.append(rcdm)
mynewa1s.append(a1)
mynewa3s.append(a3)
# if we are not at the end of the helix, we work out a1 and rb for the
# next nucleotide along the helix
if i != bp - 1:
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
rcdm = rb - CM_CENTER_DS * a1
# if we are working on a double strand, we do a cycle similar
# append to newpositions
mynewpositions.append(rcdm)
mynewa1s.append(a1)
mynewa3s.append(a3)
# if we are not at the end of the helix, we work out a1 and rb for the
# next nucleotide along the helix
if i != bp - 1:
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
# if we are working on a double strand, we do a cycle similar
# to the previous one but backwards
if double == True:
a1 = -a1
a3 = -dir
R = R.transpose()
for i in range(bp):
rcdm = rb - CM_CENTER_DS * a1
mynewpositions.append (rcdm)
mynewa1s.append (a1)
mynewa3s.append (a3)
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
a1 = -a1
a3 = -dir
R = R.transpose()
for i in range(bp):
rcdm = rb - CM_CENTER_DS * a1
mynewpositions.append (rcdm)
mynewa1s.append (a1)
mynewa3s.append (a3)
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
assert (len (mynewpositions) > 0)
@ -391,10 +393,10 @@ def read_strands(filename):
try:
infile = open (filename)
except:
print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
sys.exit(2)
# This block works out the number of nucleotides and strands by reading
# This block works out the number of nucleotides and strands by reading
# the number of non-empty lines in the input file and the number of letters,
# taking the possible DOUBLE keyword into account.
nstrands, nnucl, nbonds = 0, 0, 0
@ -406,30 +408,29 @@ def read_strands(filename):
if line[:6] == 'DOUBLE':
line = line.split()[1]
length = len(line)
print >> sys.stdout, "## Found duplex of %i base pairs" % length
print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
nnucl += 2*length
nstrands += 2
nbonds += (2*length-2)
nbonds += (2*length-2)
else:
line = line.split()[0]
length = len(line)
print >> sys.stdout, \
"## Found single strand of %i bases" % length
print( "## Found single strand of %i bases" % length, file=sys.stdout)
nnucl += length
nstrands += 1
nbonds += length-1
nbonds += length-1
# rewind the sequence input file
infile.seek(0)
print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
# generate the data file in LAMMPS format
try:
out = open ("data.oxdna", "w")
except:
print >> sys.stderr, "Could not open data file for writing. Aborting."
print( "Could not open data file for writing. Aborting.", file=sys.stderr)
sys.exit(2)
lines = infile.readlines()
nlines = len(lines)
i = 1
@ -440,115 +441,114 @@ def read_strands(filename):
line = line.upper().strip()
# skip empty lines
if len(line) == 0:
i += 1
continue
if len(line) == 0:
i += 1
continue
# block for duplexes: last argument of the generate function
# is set to 'True'
# block for duplexes: last argument of the generate function
# is set to 'True'
if line[:6] == 'DOUBLE':
line = line.split()[1]
length = len(line)
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
basetype.append(seq[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# create the sequence of the second strand as made of
# complementary bases
seq2 = [5-s for s in seq]
seq2.reverse()
# create the sequence of the second strand as made of
# complementary bases
seq2 = [5-s for s in seq]
seq2.reverse()
myns += 1
for b in xrange(length):
basetype.append(seq2[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq2[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# generate random position of the first nucleotide
print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
# generate random position of the first nucleotide
cdm = box_offset + np.random.random_sample(3) * box
# generate the random direction of the helix
# generate the random direction of the helix
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
# use the generate function defined above to create
# the position and orientation vector of the strand
# use the generate function defined above to create
# the position and orientation vector of the strand
newpositions, newa1s, newa3s = generate_strand(len(line), \
sequence=seq, dir=axis, start_pos=cdm, double=True)
sequence=seq, dir=axis, start_pos=cdm, double=True)
# generate a new position for the strand until it does not overlap
# with anything already present
start = timer()
# with anything already present
start = timer()
while not add_strands(newpositions, newa1s, newa3s):
cdm = box_offset + np.random.random_sample(3) * box
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
newpositions, newa1s, newa3s = generate_strand(len(line), \
sequence=seq, dir=axis, start_pos=cdm, double=True)
print >> sys.stdout, "## Trying %i" % i
end = timer()
print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl)
sequence=seq, dir=axis, start_pos=cdm, double=True)
print( "## Trying %i" % i, file=sys.stdout)
end = timer()
print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
# block for single strands: last argument of the generate function
# is set to 'False'
# block for single strands: last argument of the generate function
# is set to 'False'
else:
length = len(line)
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
basetype.append(seq[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# generate random position of the first nucleotide
# generate random position of the first nucleotide
cdm = box_offset + np.random.random_sample(3) * box
# generate the random direction of the helix
# generate the random direction of the helix
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
print >> sys.stdout, \
"## Created single strand of %i bases" % length
print("## Created single strand of %i bases" % length, file=sys.stdout)
newpositions, newa1s, newa3s = generate_strand(length, \
sequence=seq, dir=axis, start_pos=cdm, double=False)
start = timer()
start = timer()
while not add_strands(newpositions, newa1s, newa3s):
cdm = box_offset + np.random.random_sample(3) * box
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
axis /= np.sqrt(np.dot(axis, axis))
newpositions, newa1s, newa3s = generate_strand(length, \
sequence=seq, dir=axis, start_pos=cdm, double=False)
sequence=seq, dir=axis, start_pos=cdm, double=False)
print >> sys.stdout, "## Trying %i" % (i)
end = timer()
print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl)
end = timer()
print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
i += 1
# sanity check
if not len(positions) == nnucl:
print len(positions), nnucl
print( len(positions), nnucl )
raise AssertionError
out.write('# LAMMPS data file\n')
@ -580,44 +580,41 @@ def read_strands(filename):
out.write('Atoms\n')
out.write('\n')
for i in xrange(nnucl):
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
% (i+1, basetype[i], \
positions[i][0], positions[i][1], positions[i][2], \
strandnum[i]))
for i in range(nnucl):
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
out.write('\n')
out.write('# Atom-ID, translational, rotational velocity\n')
out.write('Velocities\n')
out.write('\n')
for i in xrange(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
out.write('\n')
out.write('# Atom-ID, shape, quaternion\n')
out.write('Ellipsoids\n')
out.write('\n')
for i in xrange(nnucl):
out.write(\
"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
out.write('\n')
out.write('# Bond topology\n')
out.write('Bonds\n')
out.write('\n')
for i in xrange(nbonds):
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
for i in range(nbonds):
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
out.close()
print >> sys.stdout, "## Wrote data to 'data.oxdna'"
print >> sys.stdout, "## DONE"
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
print("## DONE", file=sys.stdout)
# call the above main() function, which executes the program
read_strands (infile)
@ -627,4 +624,6 @@ runtime = end_time-start_time
hours = runtime/3600
minutes = (runtime-np.rint(hours)*3600)/60
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)

75
examples/PACKAGES/cgdna/util/generate_simple.py
View File

@ -1,5 +1,8 @@
# Setup tool for oxDNA input in LAMMPS format.
# for python2/3 compatibility
from __future__ import print_function
import math,numpy as np,sys,os
# system size
@ -250,59 +253,59 @@ def duplex_array():
qrot3=math.sin(0.5*twist)
for letter in strand[2]:
temp1=[]
temp2=[]
temp1=[]
temp2=[]
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
temp1.append(shape)
temp2.append(shape)
temp1.append(shape)
temp2.append(shape)
temp1.append(quat1)
temp2.append(quat2)
temp1.append(quat1)
temp2.append(quat2)
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
nucleotide.append(temp1)
compstrand.append(temp2)
nucleotide.append(temp1)
compstrand.append(temp2)
for ib in range(len(compstrand)):
nucleotide.append(compstrand[len(compstrand)-1-ib])
nucleotide.append(compstrand[len(compstrand)-1-ib])
for ib in range(len(comptopo)):
topology.append(comptopo[ib])
topology.append(comptopo[ib])
return

1
examples/PACKAGES/interlayer/aip_water_2dm/CBNOH.aip.water.2dm Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/CBNOH.aip.water.2dm

1
examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm
View File

@ -1 +0,0 @@
../../../../potentials/COH.aip.water.2dm

1
examples/PACKAGES/interlayer/ilp_tmds/MoS2.ILP
View File

@ -1 +0,0 @@
../../../../potentials/MoS2.ILP

1
examples/PACKAGES/interlayer/ilp_tmds/TMD.ILP Symbolic link
View File

@ -0,0 +1 @@
../../../../potentials/TMD.ILP

2
examples/PACKAGES/interlayer/ilp_tmds/in.mos2
View File

@ -12,7 +12,7 @@ mass 4 95.94
pair_style hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
pair_coeff * * sw/mod 1 tmd.sw.mod Mo S S NULL NULL NULL
pair_coeff * * sw/mod 2 tmd.sw.mod NULL NULL NULL Mo S S
pair_coeff * * ilp/tmd MoS2.ILP Mo S S Mo S S
pair_coeff * * ilp/tmd TMD.ILP Mo S S Mo S S
# Calculate the pair potential
compute 0 all pair ilp/tmd

2
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
View File

@ -40,7 +40,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo_style custom step temp press density f_myrxns[*]
thermo 100

4
examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt
View File

@ -26,7 +26,7 @@ read_data large_nylon_melt.data.gz &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
extra/special/per/atom 25
velocity all create 800.0 4928459 dist gaussian
@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 800 800 100
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
thermo_style custom step temp press density f_myrxns[*] # cumulative reaction counts
# restart 100 restart1 restart2

5
examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
View File

@ -20,7 +20,8 @@ improper_style class2
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_epoxy.data
read_data tiny_epoxy.data &
extra/special/per/atom 25
velocity all create 300.0 4928459 dist gaussian
@ -44,7 +45,7 @@ fix rxns all bond/react stabilization yes statted_grp .03 &
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
thermo_style custom step temp f_rxns[*]
run 2000

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -54,7 +54,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -47,7 +47,7 @@ fix myrxns all bond/react stabilization no &
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
View File

@ -51,7 +51,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
thermo_style custom step temp press density f_rxn1[*]
run 10000

54
fortran/lammps.f90
View File

@ -118,6 +118,8 @@ MODULE LIBLAMMPS
PROCEDURE :: extract_fix => lmp_extract_fix
PROCEDURE :: extract_variable => lmp_extract_variable
PROCEDURE :: set_variable => lmp_set_variable
PROCEDURE :: set_string_variable => lmp_set_string_variable
PROCEDURE :: set_internal_variable => lmp_set_internal_variable
PROCEDURE, PRIVATE :: lmp_gather_atoms_int
PROCEDURE, PRIVATE :: lmp_gather_atoms_double
GENERIC :: gather_atoms => lmp_gather_atoms_int, &
@ -557,6 +559,21 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: lammps_set_variable
END FUNCTION lammps_set_variable
FUNCTION lammps_set_string_variable(handle, name, str) BIND(C)
IMPORT :: c_int, c_ptr
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, name, str
INTEGER(c_int) :: lammps_set_string_variable
END FUNCTION lammps_set_string_variable
FUNCTION lammps_set_internal_variable(handle, name, val) BIND(C)
IMPORT :: c_int, c_ptr, c_double
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, name
REAL(c_double), VALUE :: val
INTEGER(c_int) :: lammps_set_internal_variable
END FUNCTION lammps_set_internal_variable
SUBROUTINE lammps_gather_atoms(handle, name, type, count, data) BIND(C)
IMPORT :: c_int, c_ptr
IMPLICIT NONE
@ -1631,6 +1648,43 @@ CONTAINS
END IF
END SUBROUTINE lmp_set_variable
! equivalent function to lammps_set_string_variable
SUBROUTINE lmp_set_string_variable(self, name, str)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name, str
INTEGER :: err
TYPE(c_ptr) :: Cstr, Cname
Cstr = f2c_string(str)
Cname = f2c_string(name)
err = lammps_set_string_variable(self%handle, Cname, Cstr)
CALL lammps_free(Cname)
CALL lammps_free(Cstr)
IF (err /= 0) THEN
CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, &
'WARNING: unable to set string variable "' // name &
// '" [Fortran/set_variable]')
END IF
END SUBROUTINE lmp_set_string_variable
! equivalent function to lammps_set_internal_variable
SUBROUTINE lmp_set_internal_variable(self, name, val)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name
REAL(KIND=c_double), INTENT(IN) :: val
INTEGER :: err
TYPE(c_ptr) :: Cstr, Cname
Cname = f2c_string(name)
err = lammps_set_internal_variable(self%handle, Cname, val)
CALL lammps_free(Cname)
IF (err /= 0) THEN
CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, &
'WARNING: unable to set internal variable "' // name &
// '" [Fortran/set_variable]')
END IF
END SUBROUTINE lmp_set_internal_variable
! equivalent function to lammps_gather_atoms (for integers)
SUBROUTINE lmp_gather_atoms_int(self, name, count, data)
CLASS(lammps), INTENT(IN) :: self

4
lib/gpu/Makefile.cuda
View File

@ -134,11 +134,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
$(GPU_LIB): $(OBJS) $(CUDPP)
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
@cp $(EXTRAMAKE) Makefile.lammps
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

4
lib/gpu/Makefile.cuda_mps
View File

@ -133,11 +133,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
$(GPU_LIB): $(OBJS) $(CUDPP)
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
@cp $(EXTRAMAKE) Makefile.lammps
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

4
lib/gpu/Makefile.hip
View File

@ -98,10 +98,10 @@ HIP_GPU_OPTS += $(HIP_OPTS) -I./
ifeq (spirv,$(HIP_PLATFORM))
HIP_HOST_OPTS += -fPIC
HIP_GPU_CC = $(HIP_PATH)/bin/hipcc -c
HIP_GPU_OPTS_S =
HIP_GPU_OPTS_S =
HIP_GPU_OPTS_E =
HIP_KERNEL_SUFFIX = .cpp
HIP_LIBS_TARGET =
HIP_LIBS_TARGET =
export HCC_AMDGPU_TARGET := $(HIP_ARCH)
else ifeq (clang,$(HIP_COMPILER))
HIP_HOST_OPTS += -fPIC

2
lib/gpu/Makefile.lammps.mac_ocl
View File

@ -2,4 +2,4 @@
gpu_SYSINC = -DFFT_SINGLE
gpu_SYSLIB = -framework OpenCL
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.lammps.mingw-cross
View File

@ -2,5 +2,5 @@
# settings for OpenCL builds
gpu_SYSINC =
gpu_SYSLIB = -Wl,--enable-stdcall-fixup -L../../tools/mingw-cross$(LIBOBJDIR) -Wl,-Bdynamic,-lOpenCL,-Bstatic
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.lammps.opencl
View File

@ -2,4 +2,4 @@
gpu_SYSINC =
gpu_SYSLIB = -lOpenCL
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.linux
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.linux_multi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA complied for multiple compute capabilities
# - Add your GPU to CUDA_CODE
# ------------------------------------------------------------------------- */

4
lib/gpu/Makefile.linux_opencl
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL - Mixed precision
# ------------------------------------------------------------------------- */
@ -11,7 +11,7 @@ EXTRAMAKE = Makefile.lammps.opencl
LMP_INC = -DLAMMPS_SMALLBIG
OCL_INC =
OCL_INC =
OCL_CPP = mpic++ -std=c++11 -O3 -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
OCL_LINK = -lOpenCL
OCL_PREC = -D_SINGLE_DOUBLE

2
lib/gpu/Makefile.mac_opencl
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.mac_opencl_mpi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.oneapi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Linux Makefile for Intel oneAPI - Mixed precision
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.oneapi_prof
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Linux Makefile for Intel oneAPI - Mixed precision (with timing enabled)
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.serial
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA without MPI libraries
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

4
lib/gpu/Nvidia.makefile
View File

@ -11,7 +11,7 @@ HOST_H = lal_answer.h lal_atom.h lal_balance.h lal_base_atomic.h lal_base_amoeba
lal_base_charge.h lal_base_dipole.h lal_base_dpd.h \
lal_base_ellipsoid.h lal_base_three.h lal_device.h lal_neighbor.h \
lal_neighbor_shared.h lal_pre_ocl_config.h $(NVD_H)
# Source files
SRCS := $(wildcard ./lal_*.cpp)
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
@ -127,7 +127,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.cubin *.linkinfo

2
lib/gpu/Nvidia.makefile_multi
View File

@ -89,7 +89,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

6
lib/gpu/geryon/nvd_device.h
View File

@ -138,7 +138,7 @@ class UCL_Device {
/** \note You cannot delete the default stream **/
inline void pop_command_queue() {
if (_cq.size()<2) return;
CU_SAFE_CALL_NS(cuStreamDestroy(_cq.back()));
cuStreamDestroy(_cq.back());
_cq.pop_back();
}
@ -426,8 +426,8 @@ void UCL_Device::clear() {
if (_device>-1) {
for (int i=1; i<num_queues(); i++) pop_command_queue();
#if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxSetCurrent(_old_context));
CU_SAFE_CALL_NS(cuDevicePrimaryCtxRelease(_cu_device));
cuCtxSetCurrent(_old_context);
cuDevicePrimaryCtxRelease(_cu_device);
#else
cuCtxDestroy(_context);
#endif

2
lib/gpu/geryon/ocl_memory.h
View File

@ -108,7 +108,7 @@ inline int _host_alloc(mat_type &mat, copy_type &cm, const size_t n,
return UCL_MEMORY_ERROR;
*mat.host_ptr() = (typename mat_type::data_type*)
clEnqueueMapBuffer(cm.cq(),mat.cbegin(),CL_TRUE,
map_perm,0,n,0,NULL,NULL,NULL);
map_perm,0,n,0,NULL,NULL,NULL);
mat.cq()=cm.cq();
CL_SAFE_CALL(clRetainCommandQueue(mat.cq()));

6
lib/gpu/lal_amoeba.cu
View File

@ -2033,13 +2033,13 @@ __kernel void k_amoeba_special15(__global int * dev_nbor,
const __global tagint *restrict special15,
const int inum, const int nall, const int nbor_pitch,
const int t_per_atom) {
int tid, ii, offset, n_stride, i;
int tid, ii, offset, n_stride, j;
atom_info(t_per_atom,ii,tid,offset);
if (ii<inum) {
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,j,numj,
n_stride,nbor_end,nbor);
int n15 = nspecial15[ii];
@ -2048,7 +2048,7 @@ __kernel void k_amoeba_special15(__global int * dev_nbor,
int sj=dev_packed[nbor];
int which = sj >> SBBITS & 3;
int j = sj & NEIGHMASK;
j = sj & NEIGHMASK;
tagint jtag = tag[j];
if (!which) {

2
lib/gpu/lal_base_sph.cpp
View File

@ -195,7 +195,7 @@ void BaseSPHT::compute(const int f_ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const int nlocal) {
double **host_v) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;

4
lib/gpu/lal_base_sph.h
View File

@ -15,7 +15,7 @@
***************************************************************************/
#ifndef LAL_BASE_SPH_H
#define LAL_BASE_DPD_H
#define LAL_BASE_SPH_H
#include "lal_device.h"
#include "lal_balance.h"
@ -132,7 +132,7 @@ class BaseSPH {
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **v, const int nlocal);
double **v);
/// Pair loop with device neighboring
int** compute(const int ago, const int inum_full, const int nall,

1
lib/gpu/lal_coul_slater_long.cu
View File

@ -102,6 +102,7 @@ __kernel void k_coul_slater_long(const __global numtyp4 *restrict x_,
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * scale[mtype] * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));

4
lib/gpu/lal_coul_slater_long.h
View File

@ -13,8 +13,8 @@
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_Coul_Slater_Long_H
#define LAL_Coul_Slater_Long_H
#ifndef LAL_COUL_SLATER_LONG_H
#define LAL_COUL_SLATER_LONG_H
#include "lal_base_charge.h"

6
lib/gpu/lal_eam.cpp
View File

@ -303,7 +303,7 @@ double EAMT::host_memory_usage() const {
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then compute atom energies/forces
// Copy nbor list from host if necessary and then compute per-atom fp
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EAMT::compute(const int f_ago, const int inum_full, const int nlocal,
@ -379,7 +379,7 @@ void EAMT::compute(const int f_ago, const int inum_full, const int nlocal,
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU and then compute per-atom densities
// Reneighbor on GPU and then compute per-atom fp
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** EAMT::compute(const int ago, const int inum_full, const int nall,
@ -461,7 +461,7 @@ int** EAMT::compute(const int ago, const int inum_full, const int nall,
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then calculate forces, virials,..
// Update per-atom fp, and then calculate forces, virials,..
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EAMT::compute2(int *ilist, const bool eflag, const bool vflag,

12
lib/gpu/lal_edpd.cu
View File

@ -324,8 +324,8 @@ __kernel void k_edpd(const __global numtyp4 *restrict x_,
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
@ -401,10 +401,8 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
__local numtyp4 sc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 kc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
@ -567,7 +565,7 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
// heat transfer
if (r < coeff2w) {
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
@ -581,10 +579,10 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
factor += kcx*T_pow.x + kcy*T_pow.y + kcz*T_pow.z + kcw*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti )/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);

10
lib/gpu/lal_hippo.cu
View File

@ -1225,7 +1225,9 @@ __kernel void k_hippo_udirect2b(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_charge();
#endif
acctyp _fieldp[6];
for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
@ -1410,7 +1412,9 @@ __kernel void k_hippo_umutual2b(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_charge();
#endif
acctyp _fieldp[6];
for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
@ -2452,13 +2456,13 @@ __kernel void k_hippo_special15(__global int * dev_nbor,
const __global tagint *restrict special15,
const int inum, const int nall, const int nbor_pitch,
const int t_per_atom) {
int tid, ii, offset, n_stride, i;
int tid, ii, offset, n_stride, j;
atom_info(t_per_atom,ii,tid,offset);
if (ii<inum) {
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,j,numj,
n_stride,nbor_end,nbor);
int n15 = nspecial15[ii];
@ -2467,7 +2471,7 @@ __kernel void k_hippo_special15(__global int * dev_nbor,
int sj=dev_packed[nbor];
int which = sj >> SBBITS & 3;
int j = sj & NEIGHMASK;
j = sj & NEIGHMASK;
tagint jtag = tag[j];
if (!which) {

16
lib/gpu/lal_mdpd.cu
View File

@ -210,13 +210,12 @@ __kernel void k_mdpd(const __global numtyp4 *restrict x_,
const numtyp rhoi = extra[i].x;
numtyp factor_dpd, factor_sqrt;
numtyp factor_dpd;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -240,22 +239,21 @@ __kernel void k_mdpd(const __global numtyp4 *restrict x_,
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
@ -322,10 +320,8 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
@ -339,7 +335,6 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
const numtyp sigmaij=coeff_in[ONETYPE].w;
const numtyp cutij=coeff2_in[ONETYPE].x;
const numtyp cut_rij=coeff2_in[ONETYPE].y;
const numtyp cutsqij=coeff2_in[ONETYPE].z;
const numtyp cutsq_p=cutsq[ONETYPE];
#endif
@ -412,7 +407,6 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
#endif
numtyp wc = (numtyp)1.0 - r/cutij;
@ -421,7 +415,7 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;

6
lib/gpu/lal_sph_heatconduction.cu
View File

@ -70,7 +70,9 @@ __kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_pair();
#endif
acctyp dEacc = (acctyp)0;
@ -171,7 +173,9 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
#endif
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_pair();
#endif
acctyp dEacc = (acctyp)0;
@ -234,7 +238,7 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// total thermal energy increment
numtyp D = coeffx; // alpha[itype][jtype] diffusion coefficient
numtyp deltaE = (numtyp)2.0 * mass_itype * mass_jtype / (mass_itype + mass_jtype);

4
lib/gpu/lal_sph_heatconduction.h
View File

@ -13,8 +13,8 @@
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_SPH_LJ_H
#define LAL_SPH_LJ_H
#ifndef LAL_SPH_HEATCONDUCTION_H
#define LAL_SPH_HEATCONDUCTION_H
#include "lal_base_sph.h"

4
lib/gpu/lal_sph_heatconduction_ext.cpp
View File

@ -110,10 +110,10 @@ void sph_heatconduction_gpu_compute(const int ago, const int inum_full, const in
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHHeatConductionMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_heatconduction_gpu_get_extra_data(double *host_rho, double *host_esph) {

4
lib/gpu/lal_sph_lj.cu
View File

@ -362,7 +362,7 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// function call to LJ EOS
numtyp fcj[2];
LJEOS2(rhoj, esphj, cvj, fcj);
@ -404,7 +404,7 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {

4
lib/gpu/lal_sph_lj_ext.cpp
View File

@ -110,10 +110,10 @@ void sph_lj_gpu_compute(const int ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph, double *host_cv) {

8
lib/gpu/lal_sph_taitwater.cu
View File

@ -145,9 +145,9 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
@ -321,7 +321,7 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
@ -356,7 +356,7 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {

4
lib/gpu/lal_sph_taitwater_ext.cpp
View File

@ -114,10 +114,10 @@ void sph_taitwater_gpu_compute(const int ago, const int inum_full, const int nal
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHTaitwaterMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_taitwater_gpu_get_extra_data(double *host_rho) {

2
lib/kokkos/core/src/Kokkos_Printf.hpp
View File

@ -31,7 +31,7 @@ namespace Kokkos {
// backends. The GPU backends always return 1 and NVHPC only compiles if we
// don't ask for the return value.
template <typename... Args>
KOKKOS_FUNCTION void printf(const char* format, Args... args) {
KOKKOS_FORCEINLINE_FUNCTION void printf(const char* format, Args... args) {
#ifdef KOKKOS_ENABLE_SYCL
// Some compilers warn if "args" is empty and format is not a string literal
if constexpr (sizeof...(Args) == 0)

2
lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Instance.hpp
View File

@ -219,8 +219,6 @@ KOKKOS_DEPRECATED void OpenMP::partition_master(F const& f, int num_partitions,
Exec::validate_partition_impl(prev_instance->m_pool_size, num_partitions,
partition_size);
OpenMP::memory_space space;
#pragma omp parallel num_threads(num_partitions)
{
Exec thread_local_instance(partition_size);

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