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Merge branch 'develop' into general-triclinic

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This commit is contained in:
Axel Kohlmeyer
2024-01-04 21:10:50 -05:00
parent e1be6c09f7 0e2a065f6b
commit c6d1cbef5a
536 changed files with 23786 additions and 19860 deletions
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6
.github/workflows/codeql-analysis.yml vendored
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@ -30,12 +30,12 @@ jobs:
fetch-depth: 2
- name: Setup Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
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/compile-msvc.yml vendored
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@ -24,7 +24,7 @@ jobs:
fetch-depth: 2
- name: Select Python version
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: '3.11'

20
cmake/CMakeLists.txt
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@ -971,6 +971,20 @@ if(PKG_KOKKOS)
endif()
endif()
if(PKG_KSPACE)
if (LMP_HEFFTE)
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: heFFTe")
if (HEFFTE_BACKEND)
message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
else()
message(STATUS "heFFTe backend: stock (builtin FFT implementation, tested for corrected but not optimized for production)")
endif()
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
message(STATUS "Using double precision FFTs")
endif()
else()
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: ${FFT}")
if(FFT_SINGLE)
@ -983,6 +997,11 @@ if(PKG_KSPACE)
else()
message(STATUS "Using non-threaded FFTs")
endif()
if (FFT_HEFFTE)
message(STATUS "Using distributed algorithms from heFTTe")
else()
message(STATUS "Using builtin distributed algorithms")
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if(FFT STREQUAL "KISS")
@ -1001,6 +1020,7 @@ if(PKG_KSPACE)
endif()
endif()
endif()
endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")
endif()

4
cmake/Modules/Packages/GPU.cmake
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@ -151,10 +151,10 @@ if(GPU_API STREQUAL "CUDA")
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
foreach(CU_OBJ ${GPU_GEN_OBJS})
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)

36
cmake/Modules/Packages/KSPACE.cmake
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@ -46,6 +46,42 @@ else()
target_compile_definitions(lammps PRIVATE -DFFT_KISS)
endif()
option(FFT_USE_HEFFTE "Use heFFTe as the distributed FFT engine, overrides the FFT option." OFF)
if(FFT_USE_HEFFTE)
# if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
set(HEFFTE_COMPONENTS "FFTW")
set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
set(HEFFTE_COMPONENTS "MKL")
set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
else()
message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
endif()
find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
if (NOT Heffte_FOUND) # download and build
include(FetchContent)
FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
URL "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
)
FetchContent_Populate(HEFFTE_PROJECT)
add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
target_link_libraries(Heffte::Heffte INTERFACE Heffte)
endif()
target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
target_link_libraries(lammps PRIVATE Heffte::Heffte)
endif()
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

11
cmake/presets/gpu-cuda.cmake Normal file
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@ -0,0 +1,11 @@
# preset that enables GPU and selects CUDA API
set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
set(GPU_PREC "mixed" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

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)

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"];
}

3
doc/src/Bibliography.rst
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@ -562,6 +562,9 @@ Bibliography
**(Kumar)**
Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
**(Lafourcade)**
Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
**(Lamoureux and Roux)**
G.\ Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

43
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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -518,6 +521,8 @@ The following options are available.
make fix-errordocs # remove error docs in header files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
make check-docs # search for several issues in the manual
make check-version # list files with pending release version tags
make check # run all check targets from above
These should help to make source and documentation files conforming

51
doc/src/Build_settings.rst
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@ -44,6 +44,14 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS, but other libraries can be faster.
LAMMPS can use them if they are available on your system.
.. versionadded:: TBD
Alternatively, LAMMPS can use the `heFFTe
<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
communication algorithms, which comes with many optimizations for
special cases, e.g. leveraging available 2D and 3D FFTs in the back end
libraries and better pipelining for packing and communication.
.. tabs::
.. tab:: CMake build
@ -53,6 +61,7 @@ LAMMPS can use them if they are available on your system.
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
.. note::
@ -76,6 +85,16 @@ LAMMPS can use them if they are available on your system.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
-D Heffte_ROOT=path # path to an existing heFFTe installation
.. note::
heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
default internal FFT implementation; however, this stock back
end is intended for testing purposes only and is not optimized
for production runs.
.. tab:: Traditional make
@ -111,6 +130,24 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link.
Traditional make can also link to heFFTe using an existing installation
.. code-block:: make
include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
FFT_PATH =
FFT_LIB = $(heffte_link) $(heffte_libs)
The heFFTe install path will contain `HeffteMakefile.in`.
which will define the `heffte_` include variables needed to link to heFFTe from
an external project using traditional make.
The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
omitting the variable will default to the `stock` back end.
The heFFTe `stock` back end is intended to be used for testing and debugging,
but is not performance optimized for large scale production runs.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
@ -170,6 +207,16 @@ Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
When using ``-DFFT_HEFFTE`` CMake will first look for an existing
install with hints provided by ``-DHeffte_ROOT``, as recommended by the
CMake standard and note that the name is case sensitive. If CMake cannot
find a heFFTe installation with the correct back end (e.g., FFTW or
MKL), it will attempt to download and build the library automatically.
In this case, LAMMPS CMake will also accept all heFFTe specific
variables listed in the `heFFTe documentation
<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
and those variables will be passed into the heFFTe build.
----------
.. _size:
@ -463,8 +510,8 @@ Exception handling when using LAMMPS as a library
LAMMPS errors do not kill the calling code, but throw an exception. In
the C-library interface, the call stack is unwound and control returns
to the caller, e.g. to Python or a code that is coupled to LAMMPS and
the error status can be queried. When using C++ directly, the calling
to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
error status can then be queried. When using C++ directly, the calling
code has to be set up to *catch* exceptions thrown from within LAMMPS.
.. note::

3
doc/src/Commands_compute.rst
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@ -100,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`nbond/atom <compute_nbond_atom>`
* :doc:`omega/chunk <compute_omega_chunk>`
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
* :doc:`pace <compute_pace>`
* :doc:`pair <compute_pair>`
* :doc:`pair/local <compute_pair_local>`
* :doc:`pe <compute_pe>`
@ -117,11 +118,13 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`rattlers/atom <compute_rattlers_atom>`
* :doc:`rdf <compute_rdf>`
* :doc:`reaxff/atom (k) <compute_reaxff_atom>`
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slcsa/atom <compute_slcsa_atom>`
* :doc:`slice <compute_slice>`
* :doc:`smd/contact/radius <compute_smd_contact_radius>`
* :doc:`smd/damage <compute_smd_damage>`

4
doc/src/Commands_fix.rst
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@ -239,10 +239,10 @@ OPT.
* :doc:`store/force <fix_store_force>`
* :doc:`store/state <fix_store_state>`
* :doc:`tdpd/source <fix_dpd_source>`
* :doc:`temp/berendsen <fix_temp_berendsen>`
* :doc:`temp/berendsen (k) <fix_temp_berendsen>`
* :doc:`temp/csld <fix_temp_csvr>`
* :doc:`temp/csvr <fix_temp_csvr>`
* :doc:`temp/rescale <fix_temp_rescale>`
* :doc:`temp/rescale (k) <fix_temp_rescale>`
* :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
* :doc:`tfmc <fix_tfmc>`
* :doc:`tgnpt/drude <fix_tgnh_drude>`

16
doc/src/Commands_pair.rst
View File

@ -87,7 +87,7 @@ OPT.
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/slater/long (g) <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/tt <pair_coul_tt>`
@ -110,7 +110,7 @@ OPT.
* :doc:`eam/he <pair_eam>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd <pair_mesodpd>`
* :doc:`edpd (g) <pair_mesodpd>`
* :doc:`eff/cut <pair_eff>`
* :doc:`eim (o) <pair_eim>`
* :doc:`exp6/rx (k) <pair_exp6_rx>`
@ -158,14 +158,14 @@ OPT.
* :doc:`lj/cut (gikot) <pair_lj>`
* :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/cut/soft (go) <pair_fep_soft>`
* :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/debye/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/long/cs <pair_cs>`
* :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
* :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/coul/long/soft (go) <pair_fep_soft>`
* :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
@ -202,7 +202,7 @@ OPT.
* :doc:`lubricate/poly (o) <pair_lubricate>`
* :doc:`lubricateU <pair_lubricateU>`
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_mesodpd>`
* :doc:`mdpd (g) <pair_mesodpd>`
* :doc:`mdpd/rhosum <pair_mesodpd>`
* :doc:`meam (k) <pair_meam>`
* :doc:`meam/ms (k) <pair_meam>`
@ -268,11 +268,11 @@ OPT.
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`sph/heatconduction <pair_sph_heatconduction>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj <pair_sph_lj>`
* :doc:`sph/lj (g) <pair_sph_lj>`
* :doc:`sph/rhosum <pair_sph_rhosum>`
* :doc:`sph/taitwater <pair_sph_taitwater>`
* :doc:`sph/taitwater (g) <pair_sph_taitwater>`
* :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`
* :doc:`spin/dipole/cut <pair_spin_dipole>`
* :doc:`spin/dipole/long <pair_spin_dipole>`

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

135
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
@ -274,9 +274,7 @@ Tests for using the Fortran module are in the ``unittest/fortran``
folder. Since they are also using the GoogleTest library, they require
to also implement test wrappers in C++ that will call fortran functions
which provide a C function interface through ISO_C_BINDINGS that will in
turn call the functions in the LAMMPS Fortran module. This part of the
unit tests is incomplete since the Fortran module it is based on is
incomplete as well.
turn call the functions in the LAMMPS Fortran module.
Tests for the C++-style library interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -397,10 +395,10 @@ compare with the reference and also start from the data file. A final
check will use multi-cutoff r-RESPA (if supported by the pair style) at
a 1:1 split and compare to the Verlet results. These sets of tests are
run with multiple test fixtures for accelerated styles (OPT, OPENMP,
INTEL) and for the latter two with 4 OpenMP threads enabled. For
these tests the relative error (epsilon) is lowered by a common factor
due to the additional numerical noise, but the tests are still comparing
to the same reference data.
INTEL, KOKKOS (OpenMP only)) and for the latter three with 4 OpenMP
threads enabled. For these tests the relative error (epsilon) is lowered
by a common factor due to the additional numerical noise, but the tests
are still comparing to the same reference data.
Additional tests will check whether all listed extract keywords are
supported and have the correct dimensionality and the final set of tests
@ -434,17 +432,19 @@ The ``test_pair_style`` tester is used with 4 categories of test inputs:
pair style is defined, but the computation of the pair style contributions
is disabled.
The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
fashion and share support functions with the pair style tester. The final
group of tests in this section is for fix styles that add/manipulate forces
and velocities, e.g. for time integration, thermostats and more.
The ``test_bond_style``, ``test_angle_style``, ``test_dihedral_style``, and
``test_improper_style`` tester programs are set up in a similar fashion and
share support functions with the pair style tester. The final group of
tests in this section is for fix styles that add/manipulate forces and
velocities, e.g. for time integration, thermostats and more.
Adding a new test is easiest done by copying and modifying an existing test
for a style that is similar to one to be tested. The file name should follow
the naming conventions described above and after copying the file, the first
step is to replace the style names where needed. The coefficient values
do not have to be meaningful, just in a reasonable range for the given system.
It does not matter if some forces are large, for as long as they do not diverge.
Adding a new test is easiest done by copying and modifying an existing YAML
file for a style that is similar to one to be tested. The file name should
follow the naming conventions described above and after copying the file,
the first step is to replace the style names where needed. The coefficient
values do not have to be meaningful, just in a reasonable range for the
given system. It does not matter if some forces are large, for as long as
they do not diverge.
The template input files define a large number of index variables at the top
that can be modified inside the YAML file to control the behavior. For example,
@ -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.

10
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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.

21
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@ -193,11 +193,14 @@ file changed):
write_data tip4p-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small
a TIP4P molecule file. Because of using :doc:`fix rigid/small
<fix_rigid>` no bonds need to be defined and thus no extra storage needs
to be reserved for them, but we need to switch to atom style full or use
:doc:`fix property/atom mol <fix_property_atom>` so that fix
rigid/nvt/small can identify rigid bodies by their molecule ID:
to be reserved for them, but we need to either switch to atom style full
or use :doc:`fix property/atom mol <fix_property_atom>` so that fix
rigid/small can identify rigid bodies by their molecule ID. Also a
:doc:`neigh_modify exclude <neigh_modify>` command is added to exclude
computing intramolecular non-bonded interactions, since those are
removed by the rigid fix anyway:
.. code-block:: LAMMPS
@ -216,17 +219,17 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
pair_coeff 2 2 0.0 1.0
pair_coeff 3 3 0.0 1.0
fix mol all property/atom mol
fix mol all property/atom mol ghost yes
molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
velocity all create 300.0 5463576
fix integrate all rigid/small molecule langevin 300.0 300.0 100.0 2345634
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000
thermo 2000
run 40000
write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule:

14
doc/src/Howto_tip5p.rst
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@ -81,11 +81,13 @@ long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
Below is the code for a LAMMPS input file for setting up a simulation of
TIP5P water with a molecule file. Because of using :doc:`fix
rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
extra storage needs to be reserved for them, but we need to switch to
rigid/small <fix_rigid>` no bonds need to be defined and thus no extra
storage needs to be reserved for them, but we need to either switch to
atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
so that fix rigid/nvt/small can identify rigid bodies by their molecule
ID:
so that fix rigid/small can identify rigid bodies by their molecule ID.
Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
exclude computing intramolecular non-bonded interactions, since those
are removed by the rigid fix anyway:
.. code-block:: LAMMPS
@ -107,11 +109,11 @@ ID:
fix mol all property/atom mol
molecule water tip5p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
fix integrate all rigid/small molecule langevin 300.0 300.0 50.0 235664
reset_timestep 0
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke
thermo 1000

16
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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;
* **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*
* **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* 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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@ -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.

2
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@ -2226,7 +2226,7 @@ and third order tensor from finite differences.
**Install:**
The PHONON package requires that also the :ref:`KSPACE <PKG-KSPACE>`
The fix phonon command also requires that the :ref:`KSPACE <PKG-KSPACE>`
package is installed.

10
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@ -1,11 +1,11 @@
Handling LAMMPS errors
**********************
The shared library is compiled with :ref:`C++ exception support
<exceptions>` to provide a better error handling experience. C++
exceptions allow capturing errors on the C++ side and rethrowing them on
the Python side. This way LAMMPS errors can be handled through the
Python exception handling mechanism.
LAMMPS and the LAMMPS library are compiled with :ref:`C++ exception support
<exceptions>` to provide a better error handling experience. LAMMPS errors
trigger throwing a C++ exception. These exceptions allow capturing errors on
the C++ side and rethrowing them on the Python side. This way LAMMPS errors
can be handled through the Python exception handling mechanism.
.. code-block:: python

19
doc/src/Run_output.rst
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@ -49,14 +49,17 @@ simulation. An example set of statistics is shown here:
----------
The first section provides a global loop timing summary. The *loop time*
is the total wall-clock time for the simulation to run. The
*Performance* line is provided for convenience to help predict how long
it will take to run a desired physical simulation and to have numbers
useful for performance comparison between different simulation settings
or system sizes. The *CPU use* line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP threads
(or 1 of not using OpenMP). Lower numbers correspond to delays due to
file I/O or insufficient thread utilization.
is the total wall-clock time for the MD steps of the simulation run,
excluding the time for initialization and setup (i.e. the parts that may
be skipped with :doc:`run N pre no <run>`). The *Performance* line is
provided for convenience to help predict how long it will take to run a
desired physical simulation and to have numbers useful for performance
comparison between different simulation settings or system sizes. The
*CPU use* line provides the CPU utilization per MPI task; it should be
close to 100% times the number of OpenMP threads (or 1 if not using
OpenMP). Lower numbers correspond to delays due to file I/O or
insufficient thread utilization from parts of the code that have not
been multi-threaded.
----------

3
doc/src/compute.rst
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@ -264,6 +264,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
* :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
* :doc:`pace <compute_pace>` - atomic cluster expansion descriptors and related quantities
* :doc:`pair <compute_pair>` - values computed by a pair style
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
* :doc:`pe <compute_pe>` - potential energy
@ -281,11 +282,13 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
* :doc:`rattlers/atom <compute_rattlers_atom>` - identify under-coordinated rattler atoms
* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reaxff/atom <compute_reaxff_atom>` - extract ReaxFF bond information
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
* :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
* :doc:`slcsa/atom <compute_slcsa_atom>` - perform Supervised Learning Crystal Structure Analysis (SL-CSA)
* :doc:`slice <compute_slice>` - extract values from global vector or array
* :doc:`smd/contact/radius <compute_smd_contact_radius>` - contact radius for Smooth Mach Dynamics
* :doc:`smd/damage <compute_smd_damage>` - damage status of SPH particles in Smooth Mach Dynamics

253
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@ -0,0 +1,253 @@
.. index:: compute pace
compute pace command
========================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID pace ace_potential_filename ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* pace = style name of this compute command
* ace_potential_filename = file name (in the .yace or .ace format from :doc:`pace pair_style <pair_pace>`) including ACE hyper-parameters, bonds, and generalized coupling coefficients
* keyword = *bikflag* or *dgradflag*
.. parsed-literal::
*bikflag* value = *0* or *1*
*0* = descriptors are summed over atoms of each type
*1* = descriptors are listed separately for each atom
*dgradflag* value = *0* or *1*
*0* = descriptor gradients are summed over atoms of each type
*1* = descriptor gradients are listed separately for each atom pair
Examples
""""""""
.. code-block:: LAMMPS
compute pace all pace coupling_coefficients.yace
compute pace all pace coupling_coefficients.yace 0 1
compute pace all pace coupling_coefficients.yace 1 1
Description
"""""""""""
.. versionadded:: TBD
This compute calculates a set of quantities related to the atomic
cluster expansion (ACE) descriptors of the atoms in a group. ACE
descriptors are highly general atomic descriptors, encoding the radial
and angular distribution of neighbor atoms, up to arbitrary bond order
(rank). The detailed mathematical definition is given in the paper by
:ref:`(Drautz) <Drautz19>`. These descriptors are used in the
:doc:`pace pair_style <pair_pace>`. Quantities obtained from `compute
pace` are related to those used in :doc:`pace pair_style <pair_pace>` to
evaluate atomic energies, forces, and stresses for linear ACE models.
For example, the energy for a linear ACE model is calculated as:
:math:`E=\sum_i^{N\_atoms} \sum_{\boldsymbol{\nu}} c_{\boldsymbol{\nu}}
B_{i,\boldsymbol{\boldsymbol{\nu}}}`. The ACE descriptors for atom `i`
:math:`B_{i,\boldsymbol{\nu}}`, and :math:`c_{\nu}` are linear model
parameters. The detailed definition and indexing convention for ACE
descriptors is given in :ref:`(Drautz) <Drautz19>`. In short, body
order :math:`N`, angular character, radial character, and chemical
elements in the *N-body* descriptor are encoded by :math:`\nu`. In the
:doc:`pace pair_style <pair_pace>`, the linear model parameters and the
ACE descriptors are combined for efficient evaluation of energies and
forces. The details and benefits of this efficient implementation are
given in :ref:`(Lysogorskiy) <Lysogorskiy21>`, but the combined
descriptors and linear model parameters for the purposes of `compute
pace` may be expressed in terms of the ACE descriptors mentioned above.
:math:`c_{\boldsymbol{\nu}} B_{i,\boldsymbol{\nu}}= \sum_{\boldsymbol{\nu}' \in \boldsymbol{\nu} } \big[ c_{\boldsymbol{\nu}} C(\boldsymbol{\nu}') \big] A_{i,\boldsymbol{\nu}'}`
where the bracketed terms on the right-hand side are the combined functions
with linear model parameters typically provided in the `<name>.yace` potential
file for `pace pair_style`. When these bracketed terms are multiplied by the
products of the atomic base from :ref:`(Drautz) <Drautz19>`,
:math:`A_{i,\boldsymbol{\nu'}}`, the ACE descriptors are recovered but they
are also scaled by linear model parameters. The generalized coupling coefficients,
written in short-hand here as :math:`C(\boldsymbol{\nu}')`, are the generalized
Clebsch-Gordan or generalized Wigner symbols. It may be desirable to reverse the
combination of these descriptors and the linear model parameters so that the
ACE descriptors themselves may be used. The ACE descriptors and their gradients
are often used when training ACE models, performing custom data analysis,
generalizing ACE model forms, and other tasks that involve direct computation of
descriptors. The key utility of `compute pace` is that it can compute the ACE
descriptors and gradients so that these tasks can be performed during a LAMMPS
simulation or so that LAMMPS can be used as a driver for tasks like ACE model
parameterization. To see how this command can be used within a Python workflow
to train ACE potentials, see the examples in
`FitSNAP <https://github.com/FitSNAP/FitSNAP>`_. Examples on using outputs from
this compute to construct general ACE potential forms are demonstrated in
:ref:`(Goff) <Goff23>`. The various keywords and inputs to `compute pace`
determine what ACE descriptors and related quantities are returned in a compute
array.
The coefficient file, `<name>.yace`, ultimately defines the number of ACE
descriptors to be computed, their maximum body-order, the degree of angular
character they have, the degree of radial character they have, the chemical
character (which element-element interactions are encoded by descriptors),
and other hyper-parameters defined in :ref:`(Drautz) <Drautz19>`. These may
be modeled after the potential files in :doc:`pace pair_style <pair_pace>`,
and have the same format. Details on how to generate the coefficient files
to train ACE models may be found in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
The keyword *bikflag* determines whether or not to list the descriptors of
each atom separately, or sum them together and list in a single row. If
*bikflag* is set to *0* then a single descriptor row is used, which contains
the per-atom ACE descriptors :math:`B_{i,\boldsymbol{\nu}}` summed over all
atoms *i* to produce :math:`B_{\boldsymbol{\nu}}`. If *bikflag* is set to
*1* this is replaced by a separate per-atom ACE descriptor row for each atom.
In this case, the entries in the final column for these rows are set to zero.
The keyword *dgradflag* determines whether to sum atom gradients or list
them separately. If *dgradflag* is set to 0, the ACE
descriptor gradients w.r.t. atom *j* are summed over all atoms *i'*
of, which may be useful when training linear ACE models on atomic forces.
If *dgradflag* is set to 1, gradients are listed separately for each pair of atoms.
Each row corresponds
to a single term :math:`\frac{\partial {B_{i,\boldsymbol{\nu}}}}{\partial {r}^a_j}`
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. This also changes the number of columns to be equal to the number of
ACE descriptors, with 3 additional columns representing the indices :math:`i`,
:math:`j`, and :math:`a`, as explained more in the Output info section below.
The option *dgradflag=1* requires that *bikflag=1*.
.. note::
It is noted here that in contrast to :doc:`pace pair_style <pair_pace>`,
the *.yace* file for `compute pace` typically should not contain linear
parameters for an ACE potential. If :math:`c_{\nu}` are included,
the value of the descriptor will not be returned in the `compute` array,
but instead, the energy contribution from that descriptor will be returned.
Do not do this unless it is the desired behavior.
*In short, you should not plug in a '.yace' for a pace potential into this
compute to evaluate descriptors.*
.. note::
*Generalized Clebsch-Gordan or Generalized Wigner symbols (with appropriate
factors) must be used to evaluate ACE descriptors with this compute.* There
are multiple ways to define the generalized coupling coefficients. Because
of this, this compute will not revert your potential file to a coupling
coefficient file. Instead this compute allows the user to supply coupling
coefficients that follow any convention.
.. note::
Using *dgradflag* = 1 produces a global array with :math:`N + 3N^2 + 1` rows
which becomes expensive for systems with more than 1000 atoms.
.. note::
If you have a bonded system, then the settings of :doc:`special_bonds
<special_bonds>` command can remove pairwise interactions between
atoms in the same bond, angle, or dihedral. This is the default
setting for the :doc:`special_bonds <special_bonds>` command, and
means those pairwise interactions do not appear in the neighbor list.
Because this fix uses the neighbor list, it also means those pairs
will not be included in the calculation. One way to get around this,
is to write a dump file, and use the :doc:`rerun <rerun>` command to
compute the ACE descriptors for snapshots in the dump file.
The rerun script can use a :doc:`special_bonds <special_bonds>`
command that includes all pairs in the neighbor list.
----------
Output info
"""""""""""
Compute *pace* evaluates a global array. The columns are arranged into
*ntypes* blocks, listed in order of atom type *I*\ . Each block contains
one column for each ACE descriptor, the same as for compute
*sna/atom*\ in :doc:`compute snap <compute_sna_atom>`. A final column contains the corresponding energy, force
component on an atom, or virial stress component. The rows of the array
appear in the following order:
* 1 row: *pace* average descriptor values for all atoms of type *I*
* 3\*\ *n* force rows: quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID and run up to the total number of atoms, *n*.
* 6 rows: *virial* quantities summed for all atoms of type *I*
For example, if :math:`\# \; B_{i, \boldsymbol{\nu}}` =30 and ntypes=1, the number of columns in the
The number of columns in the global array generated by *pace* are 31, and
931, respectively, while the number of rows is 1+3\*\ *n*\ +6, where *n*
is the total number of atoms.
If the *bik* keyword is set to 1, the structure of the pace array is expanded.
The first :math:`N` rows of the pace array
correspond to :math:`\# \; B_{i,\boldsymbol{\nu}}` instead of a single row summed over atoms :math:`i`.
In this case, the entries in the final column for these rows
are set to zero. Also, each row contains only non-zero entries for the
columns corresponding to the type of that atom. This is not true in the case
of *dgradflag* keyword = 1 (see below).
If the *dgradflag* keyword is set to 1, this changes the structure of the
global array completely.
Here the per-atom quantities are replaced with rows corresponding to
descriptor gradient components on single atoms:
.. math::
\frac{\partial {B_{i,\boldsymbol{\nu}} }}{\partial {r}^a_j}
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. The rows are
organized in chunks, where each chunk corresponds to an atom with global index
:math:`j`. The rows in an atom :math:`j` chunk correspond to
atoms with global index :math:`i`. The total number of rows for
these descriptor gradients is therefore :math:`3N^2`.
The number of columns is equal to the number of ACE descriptors,
plus 3 additional left-most columns representing the global atom indices
:math:`i`, :math:`j`,
and Cartesian direction :math:`a` (0, 1, 2, for x, y, z).
The first 3 columns of the first :math:`N` rows belong to the reference
potential force components. The remaining K columns contain the
:math:`B_{i,\boldsymbol{\nu}}` per-atom descriptors corresponding to the non-zero entries
obtained when *bikflag* = 1.
The first column of the last row, after the first
:math:`N + 3N^2` rows, contains the reference potential
energy. The virial components are not used with this option. The total number of
rows is therefore :math:`N + 3N^2 + 1` and the number of columns is :math:`K + 3`.
These values can be accessed by any command that uses global values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
Restrictions
""""""""""""
These computes are part of the ML-PACE package. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_style pace <pair_pace>`
:doc:`pair_style snap <pair_snap>`
:doc:`compute snap <compute_sna_atom>`
Default
"""""""
The optional keyword defaults are *bikflag* = 0,
*dgradflag* = 0
----------
.. _Drautz19:
**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
.. _Lysogorskiy21:
**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
.. _Goff23:
**(Goff)** Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).

4
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@ -1,7 +1,7 @@
.. index:: compute rattlers/atom
compute rattlers/atom command
========================
=============================
Syntax
""""""
@ -35,7 +35,7 @@ Description
.. versionadded:: TBD
Define a compute that identifies rattlers in a system. Rattlers are often
identified in granular or glassy packings as undercoordinated atoms that
identified in granular or glassy packings as under-coordinated atoms that
do not have the required number of contacts to constrain their translational
degrees of freedom. Such atoms are not considered rigid and can often freely
rattle around in the system. This compute identifies rattlers which can be

97
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@ -0,0 +1,97 @@
.. index:: compute reaxff/atom
.. index:: compute reaxff/atom/kk
compute reaxff/atom command
===========================
Accelerator Variants: *reaxff/atom/kk*
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID reaxff/atom attribute args ... keyword value ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* reaxff/atom = name of this compute command
* attribute = *pair*
.. parsed-literal::
*pair* args = nsub
nsub = *n*-instance of a sub-style, if a pair style is used multiple times in a hybrid style
* keyword = *bonds*
.. parsed-literal::
*bonds* value = *no* or *yes*
*no* = ignore list of local bonds
*yes* = include list of local bonds
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all reaxff/atom bonds yes
Description
"""""""""""
.. versionadded:: TBD
Define a computation that extracts bond information computed by the ReaxFF
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
By default, it produces per-atom data that includes the following columns:
* abo = atom bond order (sum of all bonds)
* nlp = number of lone pairs
* nb = number of bonds
Bonds will only be included if its atoms are in the group.
In addition, if ``bonds`` is set to ``yes``, the compute will also produce a
local array of all bonds on the current processor whose atoms are in the group.
The columns of each entry of this local array are:
* id_i = atom i id of bond
* id_j = atom j id of bond
* bo = bond order of bond
Output info
"""""""""""
This compute calculates a per-atom array and local array depending on the
number of keywords. The number of rows in the local array is the number of
bonds as described above. Both per-atom and local array have 3 columns.
The arrays can be accessed by any command that uses local and per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` page for
an overview of LAMMPS output options.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
The compute reaxff/atom command requires that the :doc:`pair_style reaxff
<pair_reaxff>` is invoked. This fix is part of the REAXFF package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`
Default
"""""""
The option defaults are *bonds* = *no*.

2
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@ -68,7 +68,7 @@ reciprocal lattice nodes. The mesh spacing is defined either (a) by
the entire simulation domain or (b) manually using selected values as
shown in the 2D diagram below.
.. image:: img/saed_mesh.jpg
.. image:: img/saed_mesh.png
:scale: 75%
:align: center

162
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@ -0,0 +1,162 @@
.. index:: compute slcsa/atom
compute slcsa/atom command
============================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID slcsa/atom twojmax nclasses db_mean_descriptor_file lda_file lr_decision_file lr_bias_file maha_file value
* ID, group-ID are documented in :doc:`compute <compute>` command
* slcsa/atom = style name of this compute command
* twojmax = band limit for bispectrum components (non-negative integer)
* nclasses = number of crystal structures used in the database for the classifier SL-CSA
* db_mean_descriptor_file = file name of file containing the database mean descriptor
* lda_file = file name of file containing the linear discriminant analysis matrix for dimension reduction
* lr_decision_file = file name of file containing the scaling matrix for logistic regression classification
* lr_bias_file = file name of file containing the bias vector for logistic regression classification
* maha_file = file name of file containing for each crystal structure: the Mahalanobis distance threshold for sanity check purposes, the average reduced descriptor and the inverse of the corresponding covariance matrix
* c_ID[*] = compute ID of previously required *compute sna/atom* command
Examples
""""""""
.. code-block:: LAMMPS
compute b1 all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.3
compute b2 all slcsa/atom 8 4 mean_descriptors.dat lda_scalings.dat lr_decision.dat lr_bias.dat maha_thresholds.dat c_b1[*]
Description
"""""""""""
.. versionadded:: TBD
Define a computation that performs the Supervised Learning Crystal
Structure Analysis (SL-CSA) from :ref:`(Lafourcade) <Lafourcade2023_1>`
for each atom in the group. The SL-CSA tool takes as an input a per-atom
descriptor (bispectrum) that is computed through the *compute sna/atom*
command and then proceeds to a dimension reduction step followed by a
logistic regression in order to assign a probable crystal structure to
each atom in the group. The SL-CSA tool is pre-trained on a database
containing :math:`C` distinct crystal structures from which a crystal
structure classifier is derived and a tutorial to build such a tool is
available at `SL-CSA <https://github.com/lafourcadep/SL-CSA>`_.
The first step of the SL-CSA tool consists in performing a dimension
reduction of the per-atom descriptor :math:`\mathbf{B}^i \in
\mathbb{R}^{D}` through the Linear Discriminant Analysis (LDA) method,
leading to a new projected descriptor
:math:`\mathbf{x}^i=\mathrm{P}_\mathrm{LDA}(\mathbf{B}^i):\mathbb{R}^D
\rightarrow \mathbb{R}^{d=C-1}`:
.. math::
\mathbf{x}^i = \mathbf{C}^T_\mathrm{LDA} \cdot (\mathbf{B}^i - \mu^\mathbf{B}_\mathrm{db})
where :math:`\mathbf{C}^T_\mathrm{LDA} \in \mathbb{R}^{D \times d}` is
the reduction coefficients matrix of the LDA model read in file
*lda_file*, :math:`\mathbf{B}^i \in \mathbb{R}^{D}` is the bispectrum of
atom :math:`i` and :math:`\mu^\mathbf{B}_\mathrm{db} \in \mathbb{R}^{D}`
is the average descriptor of the entire database. The latter is computed
from the average descriptors of each crystal structure read from the
file *mean_descriptors_file*.
The new projected descriptor with dimension :math:`d=C-1` allows for a
good separation of different crystal structures fingerprints in the
latent space.
Once the dimension reduction step is performed by means of LDA, the new
descriptor :math:`\mathbf{x}^i \in \mathbb{R}^{d=C-1}` is taken as an
input for performing a multinomial logistic regression (LR) which
provides a score vector
:math:`\mathbf{s}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
\rightarrow \mathbb{R}^C` defined as:
.. math::
\mathbf{s}^i = \mathbf{b}_\mathrm{LR} + \mathbf{D}_\mathrm{LR} \cdot {\mathbf{x}^i}^T
with :math:`\mathbf{b}_\mathrm{LR} \in \mathbb{R}^C` and
:math:`\mathbf{D}_\mathrm{LR} \in \mathbb{R}^{C \times d}` the bias
vector and decision matrix of the LR model after training both read in
files *lr_fil1* and *lr_file2* respectively.
Finally, a probability vector
:math:`\mathbf{p}^i=\mathrm{P}_\mathrm{LR}(\mathbf{x}^i):\mathbb{R}^d
\rightarrow \mathbb{R}^C` is defined as:
.. math::
\mathbf{p}^i = \frac{\mathrm{exp}(\mathbf{s}^i)}{\sum\limits_{j} \mathrm{exp}(s^i_j) }
from which the crystal structure assigned to each atom with descriptor
:math:`\mathbf{B}^i` and projected descriptor :math:`\mathbf{x}^i` is
computed as the *argmax* of the probability vector
:math:`\mathbf{p}^i`. Since the logistic regression step systematically
attributes a crystal structure to each atom, a sanity check is needed to
avoid misclassification. To this end, a per-atom Mahalanobis distance to
each crystal structure *CS* present in the database is computed:
.. math::
d_\mathrm{Mahalanobis}^{i \rightarrow \mathrm{CS}} = \sqrt{(\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS})^\mathrm{T} \cdot \mathbf{\Sigma}^{-1}_\mathrm{CS} \cdot (\mathbf{x}^i - \mathbf{\mu}^\mathbf{x}_\mathrm{CS}) }
where :math:`\mathbf{\mu}^\mathbf{x}_\mathrm{CS} \in \mathbb{R}^{d}` is
the average projected descriptor of crystal structure *CS* in the
database and where :math:`\mathbf{\Sigma}_\mathrm{CS} \in \mathbb{R}^{d
\times d}` is the corresponding covariance matrix. Finally, if the
Mahalanobis distance to crystal structure *CS* for atom *i* is greater
than the pre-determined threshold, no crystal structure is assigned to
atom *i*. The Mahalanobis distance thresholds are read in file
*maha_file* while the covariance matrices are read in file
*covmat_file*.
The `SL-CSA <https://github.com/lafourcadep/SL-CSA>`_ framework provides
an automatic computation of the different matrices and thresholds
required for a proper classification and writes down all the required
files for calling the *compute slcsa/atom* command.
The *compute slcsa/atom* command requires that the :doc:`compute
sna/atom <compute_sna_atom>` command is called before as it takes the
resulting per-atom bispectrum as an input. In addition, it is crucial
that the value *twojmax* is set to the same value of the value *twojmax*
used in the *compute sna/atom* command, as well as that the value
*nclasses* is set to the number of crystal structures used in the
database to train the SL-CSA tool.
Output info
"""""""""""
By default, this compute computes the Mahalanobis distances to the
different crystal structures present in the database in addition to
assigning a crystal structure for each atom as a per-atom vector, which
can be accessed by any command that uses per-atom values from a compute
as input. See the :doc:`Howto output <Howto_output>` page for an
overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`compute sna/atom <compute_sna_atom>`
Default
"""""""
none
----------
.. _Lafourcade2023_1:
**(Lafourcade)** Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica,
`Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_

39
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View File

@ -45,7 +45,7 @@ Syntax
* w_1, w_2,... = list of neighbor weights, one for each type
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag* or *nnn* or *wmode* or *delta*
.. parsed-literal::
@ -82,6 +82,16 @@ Syntax
*0* = descriptor gradients are summed over atoms of each type
*1* = descriptor gradients are listed separately for each atom pair
* additional keyword = *nnn* or *wmode* or *delta*
.. parsed-literal::
*nnn* value = number of considered nearest neighbors to compute the bispectrum over a target specific number of neighbors (only implemented for compute sna/atom)
*wmode* value = weight function for finding optimal cutoff to match the target number of neighbors (required if nnn used, only implemented for compute sna/atom)
*0* = heavyside weight function
*1* = hyperbolic tangent weight function
*delta* value = transition interval centered at cutoff distance for hyperbolic tangent weight function (ignored if wmode=0, required if wmode=1, only implemented for compute sna/atom)
Examples
""""""""
@ -94,6 +104,7 @@ Examples
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.2
Description
"""""""""""
@ -433,6 +444,25 @@ requires that *bikflag=1*.
The rerun script can use a :doc:`special_bonds <special_bonds>`
command that includes all pairs in the neighbor list.
The keyword *nnn* allows for the calculation of the bispectrum over a
specific target number of neighbors. This option is only implemented for
the compute *sna/atom*\ . An optimal cutoff radius for defining the
neighborhood of the central atom is calculated by means of a dichotomy
algorithm. This iterative process allows to assign weights to
neighboring atoms in order to match the total sum of weights with the
target number of neighbors. Depending on the radial weight function
used in that process, the cutoff radius can fluctuate a lot in the
presence of thermal noise. Therefore, in addition to the *nnn* keyword,
the keyword *wmode* allows to choose whether a Heaviside (*wmode* = 0)
function or a Hyperbolic tangent function (*wmode* = 1) should be used.
If the Heaviside function is used, the cutoff radius exactly matches the
distance between the central atom an its *nnn*'th neighbor. However, in
the case of the hyperbolic tangent function, the dichotomy algorithm
allows to span the weights over a distance *delta* in order to reduce
fluctuations in the resulting local atomic environment fingerprint. The
detailed formalism is given in the paper by Lafourcade et
al. :ref:`(Lafourcade) <Lafourcade2023_2>`.
----------
Output info
@ -585,6 +615,7 @@ Related commands
""""""""""""""""
:doc:`pair_style snap <pair_snap>`
:doc:`compute slcsa/atom <compute_slcsa_atom>`
Default
"""""""
@ -592,6 +623,7 @@ Default
The optional keyword defaults are *rmin0* = 0,
*switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
*bnormflag* = 0, *wselfallflag* = 0, *switchinnerflag* = 0,
*nnn* = -1, *wmode* = 0, *delta* = 1.e-3
----------
@ -623,3 +655,8 @@ of Angular Momentum, World Scientific, Singapore (1987).
.. _Ellis2021:
**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
.. _Lafourcade2023_2:
**(Lafourcade)** Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica,
`Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_

10
doc/src/compute_stress_atom.rst
View File

@ -127,11 +127,11 @@ result in more consistent heat flux values for angle, dihedrals,
improper and constraint force contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution all of the
virial contribution terms are included in the per-atom stress tensor.
If any extra keywords are listed, only those terms are summed to
compute the tensor. The *virial* keyword means include all terms
except the kinetic energy *ke*\ .
If no extra keywords are listed, the kinetic contribution *and* all
of the virial contribution terms are included in the per-atom stress
tensor. If any extra keywords are listed, only those terms are
summed to compute the tensor. The *virial* keyword means include all
terms except the kinetic energy *ke*\ .
Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.

21
doc/src/compute_stress_mop.rst
View File

@ -18,7 +18,7 @@ Syntax
* style = *stress/mop* or *stress/mop/profile*
* dir = *x* or *y* or *z* is the direction normal to the plane
* args = argument specific to the compute style
* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* or *dihedral* (one or more can be specified)
.. parsed-literal::
@ -68,15 +68,13 @@ Verlet algorithm.
.. versionadded:: 15Jun2023
contributions from bond and angle potentials
contributions from bond, angle and dihedral potentials
Between one and six keywords can be used to indicate which contributions
Between one and seven keywords can be used to indicate which contributions
to the stress must be computed: total stress (total), kinetic stress
(kin), configurational stress (conf), stress due to bond stretching
(bond), stress due to angle bending (angle) and/or due to pairwise
non-bonded interactions (pair). The angle keyword is currently
available only for the *stress/mop* command and **not** the
*stress/mop/profile* command.
(bond), stress due to angle bending (angle), stress due to dihedral terms (dihedral)
and/or due to pairwise non-bonded interactions (pair).
NOTE 1: The configurational stress is computed considering all pairs of
atoms where at least one atom belongs to group group-ID.
@ -134,14 +132,9 @@ size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* does not work with more than two-body pair
*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
interactions, long range (kspace) interactions and
angle/dihedral/improper intramolecular interactions. Similarly, compute
*stress/mop* does not work with more than two-body pair interactions,
long range (kspace) interactions and dihedral/improper intramolecular
interactions but works with all bond interactions with the class method
single() implemented and all angle interactions with the class method
born_matrix() implemented.
improper intramolecular interactions.
Related commands
""""""""""""""""

2
doc/src/fix_adapt.rst
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@ -221,7 +221,7 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`table <pair_table>` | table_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`ufm <pair_ufm>` | epsilon,sigma | type pairs |
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`wf/cut <pair_wf_cut>` | epsilon,sigma,nu,mu | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

20
doc/src/fix_adapt_fep.rst
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@ -123,19 +123,29 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born/gauss <pair_born_gauss>` | biga0,biga1,r0 | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/cut <pair_coul>` | scale | type pairs |
| :doc:`coul/cut, coul/cut/global <pair_coul>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/cut/soft <pair_fep_soft>` | lambda | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/debye <pair_coul>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/long, coul/msm <pair_coul>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/long/soft <pair_fep_soft>` | scale, lambda | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`eam <pair_eam>` | scale | type pairs |
| :doc:`coul/slater/long <pair_coul_slater>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`coul/streitz <pair_coul>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`eam, eam/alloy, eam/fs <pair_eam>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`harmonic/cut <pair_harmonic_cut>` | k | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`gauss <pair_gauss>` | a | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
@ -163,6 +173,8 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`lj/sf/dipole/sf <pair_dipole>` | epsilon,sigma,scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`meam <pair_meam>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`mie/cut <pair_mie>` | epsilon,sigma,gamR,gamA | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`morse, morse/smooth/linear <pair_morse>` | d0,r0,alpha | type pairs |
@ -173,12 +185,16 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | e0,r0,nn,mm | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`snap <pair_snap>` | scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`soft <pair_soft>` | a | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`ufm <pair_ufm>` | epsilon,sigma,scale | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`wf/cut <pair_wf_cut>` | epsilon,sigma,nu,mu | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
.. note::

2
doc/src/fix_halt.rst
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@ -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 = ".".

4
doc/src/fix_nh_uef.rst
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@ -23,7 +23,7 @@ Syntax
.. parsed-literal::
keyword = *erate* or *ext* or *strain* or *temp* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
*erate* values = e_x e_y = engineering strain rates (required)
*erate* values = e_x e_y = true strain rates (required)
*ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions
sets the external dimensions used to calculate the scalar pressure
*strain* values = e_x e_y = initial strain
@ -62,7 +62,7 @@ performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
<fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
commands.
The applied flow field is set by the *eps* keyword. The values
The applied flow field is set by the *erate* keyword. The values
*edot_x* and *edot_y* correspond to the strain rates in the xx and yy
directions. It is implicitly assumed that the flow field is
traceless, and therefore the strain rate in the zz direction is eqal

8
doc/src/fix_phonon.rst
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@ -181,10 +181,10 @@ This fix assumes a crystalline system with periodical lattice. The
temperature of the system should not exceed the melting temperature to
keep the system in its solid state.
This fix is part of the PHONON package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This fix requires LAMMPS be built with an FFT library. See the :doc:`Build settings <Build_settings>` page for details.
This fix is part of the PHONON package. It is only enabled if LAMMPS
was built with that package. This fix also requires LAMMPS to be built
with 3d-FFT support which is included in the KSPACE package. See the
:doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""

7
doc/src/fix_temp_berendsen.rst
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@ -1,8 +1,11 @@
.. index:: fix temp/berendsen
.. index:: fix temp/berendsen/kk
fix temp/berendsen command
==========================
Accelerator Variants: *temp/berendsen/kk*
Syntax
""""""
@ -118,6 +121,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

7
doc/src/fix_temp_rescale.rst
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@ -1,8 +1,11 @@
.. index:: fix temp/rescale
.. index:: fix temp/rescale/kk
fix temp/rescale command
========================
Accelerator Variants: *temp/rescale/kk*
Syntax
""""""
@ -125,6 +128,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
.. include:: accel_styles.rst
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

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doc/src/molecule.rst
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@ -164,8 +164,8 @@ defining a *body* particle, which requires setting the number of
* 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
* 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

26
doc/src/package.rst
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@ -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

33
doc/src/pair_aip_water_2dm.rst
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@ -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 * * 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).

3
doc/src/pair_coul_slater.rst
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@ -1,6 +1,7 @@
.. index:: pair_style coul/slater
.. index:: pair_style coul/slater/cut
.. index:: pair_style coul/slater/long
.. index:: pair_style coul/slater/long/gpu
pair_style coul/slater command
==============================
@ -11,6 +12,8 @@ pair_style coul/slater/cut command
pair_style coul/slater/long command
===================================
Accelerator Variants: *coul/slater/long/gpu*
Syntax
""""""

6
doc/src/pair_fep_soft.rst
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@ -1,8 +1,10 @@
.. index:: pair_style lj/cut/soft
.. index:: pair_style lj/cut/soft/omp
.. index:: pair_style lj/cut/coul/cut/soft
.. index:: pair_style lj/cut/coul/cut/soft/gpu
.. index:: pair_style lj/cut/coul/cut/soft/omp
.. index:: pair_style lj/cut/coul/long/soft
.. index:: pair_style lj/cut/coul/long/soft/gpu
.. index:: pair_style lj/cut/coul/long/soft/omp
.. index:: pair_style lj/cut/tip4p/long/soft
.. index:: pair_style lj/cut/tip4p/long/soft/omp
@ -27,12 +29,12 @@ Accelerator Variants: *lj/cut/soft/omp*
pair_style lj/cut/coul/cut/soft command
=======================================
Accelerator Variants: *lj/cut/coul/cut/soft/omp*
Accelerator Variants: *lj/cut/coul/cut/soft/gpu*, *lj/cut/coul/cut/soft/omp*
pair_style lj/cut/coul/long/soft command
========================================
Accelerator Variants: *lj/cut/coul/long/soft/omp*
Accelerator Variants: *lj/cut/coul/long/soft/gpu*, *lj/cut/coul/long/soft/omp*
pair_style lj/cut/tip4p/long/soft command
=========================================

20
doc/src/pair_ilp_tmd.rst
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@ -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_mesodpd.rst
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@ -1,14 +1,20 @@
.. index:: pair_style edpd
.. index:: pair_style edpd/gpu
.. index:: pair_style mdpd
.. index:: pair_style mdpd/gpu
.. index:: pair_style mdpd/rhosum
.. index:: pair_style tdpd
pair_style edpd command
=======================
Accelerator Variants: *edpd/gpu*
pair_style mdpd command
=======================
Accelerator Variants: *mdpd/gpu*
pair_style mdpd/rhosum command
==============================

3
doc/src/pair_reaxff.rst
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@ -373,7 +373,8 @@ Related commands
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
:doc:`fix reaxff/species <fix_reaxff_species>`
:doc:`fix reaxff/species <fix_reaxff_species>`,
:doc:`compute reaxff/atom <compute_reaxff_atom>`
Default
"""""""

3
doc/src/pair_sph_heatconduction.rst
View File

@ -1,8 +1,11 @@
.. index:: pair_style sph/heatconduction
.. index:: pair_style sph/heatconduction/gpu
pair_style sph/heatconduction command
=====================================
Accelerator Variants: *sph/heatconduction/gpu*
Syntax
""""""

3
doc/src/pair_sph_lj.rst
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@ -1,8 +1,11 @@
.. index:: pair_style sph/lj
.. index:: pair_style sph/lj/gpu
pair_style sph/lj command
=========================
Accelerator Variants: *sph/lj/gpu*
Syntax
""""""

3
doc/src/pair_sph_taitwater.rst
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@ -1,8 +1,11 @@
.. index:: pair_style sph/taitwater
.. index:: pair_style sph/taitwater/gpu
pair_style sph/taitwater command
================================
Accelerator Variants: *sph/taitwater/gpu*
Syntax
""""""

3
doc/src/run_style.rst
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@ -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

18
doc/utils/sphinx-config/false_positives.txt
View File

@ -80,6 +80,7 @@ Alessandro
Alexey
ali
aliceblue
Allera
Allinger
allocatable
allocator
@ -732,6 +733,7 @@ dem
Dendrimer
dendritic
Denniston
Denoual
dephase
dephasing
dequidt
@ -803,6 +805,7 @@ dispersionflag
dissipative
Dissipative
distharm
distutils
dl
dlabel
dlambda
@ -873,6 +876,7 @@ Dunweg
Dupend
Dupont
dUs
Duval
dV
dvector
dVx
@ -1312,6 +1316,7 @@ Gonzalez-Melchor
googlemail
googletest
Gordan
Goryaeva
Goudeau
GPa
GPL
@ -1398,12 +1403,14 @@ hcp
hdnnp
HDNNP
Hearn
Heaviside
heatconduction
heatflow
Hebbeker
Hebenstreit
Hecht
Heenen
heFFTe
Hendrik
Henin
Henkelman
@ -1862,6 +1869,7 @@ lbl
LBtype
lcbop
ld
lda
ldfftw
ldg
lebedeva
@ -1983,6 +1991,7 @@ lossy
Lozovik
lps
lpsapi
lr
lrt
lsfftw
lt
@ -2025,7 +2034,10 @@ magelec
Maginn
magneton
magnetons
maha
Mahalanobis
Mahoney
Maillet
mainboard
mainboards
makefile
@ -2204,6 +2216,7 @@ mintcream
Mintmire
Miron
mis
misclassification
Mises
Mishin
Mishra
@ -2312,6 +2325,7 @@ multicomponent
multicore
multielectron
multinode
multinomial
multiphysics
Multipole
multiscale
@ -2403,6 +2417,7 @@ Nbtypes
Nbytes
nc
Nc
nclasses
nchunk
Nchunk
ncoeff
@ -2817,6 +2832,7 @@ pIm
pimd
Piola
pIp
pipelining
Pisarev
Pishevar
Pitera
@ -3369,6 +3385,7 @@ Skylake
slateblue
slategray
slater
slcsa
Slepoy
Sliozberg
sLL
@ -4049,6 +4066,7 @@ xy
xyz
xz
xzhou
yace
Yade
yade
yaff

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");
}

1
examples/PACKAGES/dpd-meso/mdpd/in.mdpd
View File

@ -16,6 +16,7 @@ neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
comm_modify vel yes
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd

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

9
examples/PACKAGES/pace/README.md Normal file
View File

@ -0,0 +1,9 @@
# This folder contains examples for pace in LAMMPS
## Compute pace usage
compute/latte_cell_0.data # lammps data file with C-H-O structure
compute/latte_cell_0.xyz # xyz file with C-H-O structure
compute/coupling_coefficients.yace # .yace file containing coupling coefficients (or ACE potential parameters)
compute/in.compute # input file for calling `compute pace`

294
examples/PACKAGES/pace/compute/coupling_coefficients.yace Normal file
View File

@ -0,0 +1,294 @@
elements: [H, N, O]
E0: [0.000000, 0.000000, 0.000000]
deltaSplineBins: 0.001000
embeddings:
0: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
1: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
2: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
bonds:
[0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.0, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[0, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[0, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[1, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[1, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 4.4, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[1, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[2, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[2, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
[2, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
functions:
0:
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
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- {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 0], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
1:
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
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- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
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- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
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- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
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- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 1, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
2:
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 2, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [2, 2, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
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- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 2, 2], ns: [1, 1, 1], ls: [2, 1, 1], ms_combs: [-2, 1, 1, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 2, -1, -1], ctildes: [0.25819888974716115, -0.18257418583505536, -0.18257418583505536, 0.10540925533894599, 0.21081851067789198, 0.10540925533894599, -0.18257418583505536, -0.18257418583505536, 0.25819888974716115]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 2, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 0], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
- {mu0: 2, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}

22
examples/PACKAGES/pace/compute/in.compute Normal file
View File

@ -0,0 +1,22 @@
#info all out log
units metal
atom_style atomic
boundary p p p
atom_modify map hash
boundary p p p
read_data latte_cell_0.data
mass 1 1.00
mass 2 14.00
mass 3 15.999
# potential settings
pair_style zero 5.7
pair_coeff * *
compute pace all pace coupling_coefficients.yace 1 0
thermo 1
thermo_style custom step temp c_pace[1][183]
run 0

172
examples/PACKAGES/pace/compute/latte_cell_0.data Normal file
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@ -0,0 +1,172 @@
latte_cell_0.data (written by ASE)
161 atoms
3 atom types
0.0 12 xlo xhi
0.0 12 ylo yhi
0.0 12 zlo zhi
Atoms
1 3 1.2688096799999999 2.0079938400000001 2.7446829899999998
2 1 1.5343068200000001 2.0638766500000001 3.7105626900000002
3 1 1.7848279600000001 2.6755003400000001 2.2268847200000002
4 1 1.56251195 1.1089126899999999 2.3978115199999999
5 1 11.61728216 5.71881094 2.4732045999999999
6 2 6.5501865600000002 4.7439566800000001 3.6526025500000001
7 1 6.4564895299999998 4.1571673000000002 2.6975267999999999
8 2 2.0835561 1.59406078 8.5498047600000007
9 1 1.1041162499999999 1.4971771599999999 8.1507879200000009
10 1 2.60115534 2.2945960400000001 7.95374187
11 1 1.9817723300000001 2.0194066400000001 9.5128239400000005
12 1 0.99333338000000004 3.6983907299999998 8.1903947899999991
13 3 4.9484070999999998 5.3645501400000004 9.16152503
14 1 9.0716170599999995 9.3748453999999999 4.2276462400000003
15 2 0.30864418999999998 7.7136657499999997 2.9274995599999998
16 1 0.47661671 10.1807211 3.71160091
17 1 1.07465334 7.8226921999999997 3.5771466900000002
18 1 0.38402249999999999 8.3770493300000002 2.1748437100000002
19 1 11.435413410000001 7.7903735999999997 3.4040245499999999
20 3 6.1570384599999999 10.25988474 3.50899568
21 1 5.5932224399999999 9.5632944700000007 3.1446559000000001
22 2 1.7785569000000001 7.6312579300000003 9.1488452299999992
23 1 2.5594048599999999 6.96832838 9.3069700199999996
24 1 2.12441551 8.4547986999999996 8.6428622900000001
25 1 1.04552782 7.1697722800000001 8.5894244999999998
26 1 0.34824445999999998 10.17844028 9.1629463799999993
27 3 5.9638830399999998 10.723709400000001 9.4568803900000002
28 1 6.5890835699999997 10.926486110000001 8.7981925800000003
29 2 7.1065890400000002 1.83029753 3.3452543600000002
30 1 6.9229304999999997 1.8465022099999999 4.3089037100000001
31 1 8.0780433600000006 1.9303052199999999 3.2089521400000001
32 1 5.6795373600000003 10.471831630000001 4.3244390499999996
33 1 6.82999417 0.95850113000000003 2.9815288199999999
34 2 11.383805349999999 4.6301225199999996 2.5393688399999998
35 1 0.37927047000000003 4.1943216300000001 2.59073807
36 3 5.2376410099999999 1.91523463 9.7240636400000007
37 1 4.7887202499999999 2.7036936499999999 9.5698142300000004
38 1 9.8129906699999996 9.2075140700000002 4.08265499
39 1 4.7980879500000002 1.1403494700000001 9.6739962800000008
40 1 5.4455845600000004 2.0102099999999998 10.620773509999999
41 3 0.90954338999999995 4.6240093199999999 8.3108110600000007
42 1 11.909735319999999 4.7483814000000004 8.2500624600000005
43 2 7.3223424499999998 7.5866457 3.0245226500000002
44 1 7.4470362200000002 8.3169646700000008 3.7148003300000001
45 1 6.9073805300000002 7.9385021 2.1723768699999999
46 1 5.5542868500000004 5.1176065800000003 3.7655251999999999
47 1 6.8124309500000004 6.7778811599999997 3.3973232499999999
48 2 0.29575823000000001 11.04303794 3.1016142499999999
49 1 0.86490721999999998 11.83879228 3.6389974500000002
50 3 6.85201686 8.0846369300000003 8.8762878799999996
51 1 7.3351430100000004 7.4263498700000001 9.3821674799999997
52 1 6.7919613300000004 7.7595477199999996 7.9716174799999999
53 1 3.8990487699999998 6.4283490399999996 8.8832409600000002
54 1 5.95997296 9.9329723199999993 9.4746654699999997
55 3 11.403658979999999 10.371960359999999 9.2766092199999992
56 1 10.983666360000001 9.5157199800000001 9.1478757300000009
57 3 1.5223279700000001 5.3327331100000004 0.57537605999999997
58 1 2.3815113999999999 5.7251991200000001 0.77945295999999997
59 1 0.92079957000000001 6.0931282299999996 0.62203253000000003
60 3 11.23490924 2.9153355200000002 6.7585064099999999
61 1 10.792340190000001 2.9755225099999998 5.9000018399999998
62 1 10.751242059999999 2.1896156000000002 7.1807401500000001
63 3 11.39027944 7.3462855600000001 6.7258299499999996
64 1 10.92025679 6.69831954 7.2776696599999999
65 1 11.12238028 7.0632020999999998 5.8394107799999997
66 3 8.4684319499999994 10.71736286 10.60018556
67 1 8.5672201599999998 11.420466080000001 11.25794033
68 1 9.0803109800000001 10.04804949 10.9406517
69 3 6.5851757299999996 9.9940623399999993 6.5574614899999997
70 1 7.0276325799999997 10.76096604 6.1723333699999996
71 1 5.7419327400000002 10.384583920000001 6.8228822999999998
72 3 1.7600546399999999 1.01771919 5.4926787700000004
73 1 1.9704209100000001 1.01748419 6.4429703700000003
74 1 1.42973007 0.11076352 5.3470644900000002
75 1 2.61130613 9.7034123700000006 10.450306830000001
76 3 3.05086908 10.48131334 10.085189310000001
77 1 3.0032693199999998 10.93357295 9.3652121000000008
78 3 6.4631532199999997 8.7652058299999993 11.967847969999999
79 1 6.4506808400000004 9.6596595300000008 11.588956019999999
80 1 5.6611629700000003 8.3535737700000006 11.638443329999999
81 3 1.1745999300000001 5.2420690800000003 5.1001449699999997
82 1 1.31932881 5.5236392399999996 6.0128966300000002
83 1 0.58053834999999998 4.4898134599999997 5.2325565000000003
84 3 6.7275549699999999 0.78840874999999999 7.3817280900000002
85 1 6.3887965600000003 1.54670982 6.8634520400000003
86 1 7.6791783999999996 0.94039024000000004 7.2649461000000004
87 3 8.5476657199999995 0.0064750299999999997 5.0450514100000001
88 1 8.8736290899999997 11.10484108 4.8601807900000003
89 1 8.0477597599999999 0.20198361000000001 4.2357399400000002
90 3 1.2895030000000001 8.4280097900000008 11.82038504
91 1 1.4766666399999999 8.1087866399999999 10.87290333
92 1 2.10220669 8.1947620200000006 0.29510553
93 3 9.6797907599999995 6.4207335499999996 4.3469150599999997
94 1 8.9271530099999996 6.72940235 3.7974122399999999
95 1 10.20024126 5.9167739199999998 3.66976111
96 3 3.57411616 6.7041021699999996 3.8825478499999999
97 1 2.8894899500000002 6.1560529800000001 4.2980848099999998
98 1 4.3613707699999997 6.4304732400000004 4.3804965400000002
99 3 4.7506556 11.441853350000001 1.12537088
100 1 4.0861192800000001 10.748523670000001 1.1923347099999999
101 1 5.5035301600000004 10.965688249999999 0.73651277000000004
102 3 9.5254526399999992 4.8994443900000002 8.3732284099999994
103 1 8.7885959800000002 4.3508043900000004 8.6632831400000008
104 1 9.6149067499999994 4.6084911499999999 7.4540068699999997
105 3 4.1970746700000001 1.34592128 3.67401439
106 1 4.9437011999999996 0.74406280999999996 3.514068
107 1 4.1905534900000001 1.7730376000000001 2.7963049400000002
108 3 1.88232618 11.95451227 0.60024434000000004
109 1 2.0464587299999999 11.02454723 0.38329541
110 1 1.1518493700000001 0.17494340999999999 11.99928285
111 3 3.7593842199999998 11.01685511 6.4562050800000002
112 1 3.2125414299999999 10.4553747 5.8894917099999997
113 1 3.4166026899999999 10.821557670000001 7.3296563900000002
114 3 9.7039841399999993 3.95001545 11.894743249999999
115 1 10.461666060000001 3.9163117999999999 11.285435229999999
116 1 10.09834695 4.4026997400000001 0.68193007999999999
117 3 8.5639596400000002 3.5169507499999999 5.6224104199999996
118 1 8.3966650299999994 2.6262214699999999 5.2638164300000003
119 1 7.9695371399999999 4.0825059799999996 5.0049407400000003
120 3 9.6736245000000007 0.48030482000000002 7.9257577799999996
121 1 9.6131980400000003 11.883419180000001 7.1680923999999999
122 1 9.9784050299999993 11.90238635 8.63894187
123 3 3.9424153099999999 6.9650296699999998 11.60258943
124 1 4.2767152700000004 6.8460048999999996 10.670225220000001
125 1 4.6570638500000001 6.5129461500000003 0.091159879999999999
126 3 3.0570173199999999 9.6631958499999993 3.6611250599999998
127 1 2.5400490100000002 9.5743355000000001 2.8444047600000002
128 1 2.9314874400000002 8.7809807200000005 4.0425234200000002
129 3 7.4549612700000001 5.8430850799999998 11.011384720000001
130 1 8.1675884100000005 5.4639182799999997 10.47644287
131 1 6.7135573700000002 5.8393818399999997 10.361099749999999
132 3 9.8029139300000008 7.9578901699999998 10.21404942
133 1 10.38910242 8.3400641400000008 10.87949429
134 1 9.0637612000000001 7.6392374099999998 10.756928869999999
135 3 4.4963435599999997 4.1067935799999997 11.73387805
136 1 4.5473727899999998 4.9577970899999997 11.19223377
137 1 5.3588818399999996 4.1756111699999998 0.20355936999999999
138 3 9.5923448100000002 7.3418014600000001 1.34856172
139 1 8.8715593300000002 7.4776837199999999 2.05040471
140 1 9.0443221699999992 7.2732200799999998 0.54011714
141 3 7.0350963100000001 3.22348773 0.7070824
142 1 7.1784470499999999 4.1340314300000003 1.0184109699999999
143 1 7.7787854400000001 2.7888888399999998 1.15838887
144 3 9.2124107800000008 0.48085899999999998 1.21751966
145 1 9.6620436499999993 11.657271079999999 1.45318397
146 1 9.9404883900000005 1.11619136 1.18684594
147 3 1.19704207 9.5859959200000002 6.6190888899999996
148 1 0.25606413 9.6737366500000004 6.8319340899999998
149 1 1.2690051899999999 8.6249354900000004 6.5480112500000001
150 3 0.78256133999999999 2.6040609300000002 11.453408359999999
151 1 0.61502181 3.5607405999999999 11.40300991
152 1 1.55655312 2.5457368800000002 10.866733030000001
153 3 5.8627936099999998 7.1217054800000001 5.89173203
154 1 6.3432410700000004 7.9400136699999999 6.0855840299999997
155 1 5.5077296699999998 6.8468306800000001 6.7436875799999996
156 3 10.887828150000001 9.9637482500000001 0.51092815999999996
157 1 11.78841776 10.322043069999999 0.44704989000000001
158 1 11.02688182 9.2051906700000004 1.0976661299999999
159 3 3.93073389 4.1645674499999998 5.7137877000000001
160 1 4.6884062999999996 3.5788913299999998 5.5644605800000004
161 1 4.2956948500000003 4.7644888099999996 6.3801669700000003

163
examples/PACKAGES/pace/compute/latte_cell_0.xyz Normal file
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@ -0,0 +1,163 @@
161
Lattice="12.0 0.0 0.0 0.0 12.0 0.0 0.0 0.0 12.0" Properties=species:S:1:pos:R:3 pbc="T T T"
O 1.26880968 2.00799384 2.74468299
H 1.53430682 2.06387665 3.71056269
H 1.78482796 2.67550034 2.22688472
H 1.56251195 1.10891269 2.39781152
H 11.61728216 5.71881094 2.47320460
N 6.55018656 4.74395668 3.65260255
H 6.45648953 4.15716730 2.69752680
N 2.08355610 1.59406078 8.54980476
H 1.10411625 1.49717716 8.15078792
H 2.60115534 2.29459604 7.95374187
H 1.98177233 2.01940664 9.51282394
H 0.99333338 3.69839073 8.19039479
O 4.94840710 5.36455014 9.16152503
H 9.07161706 9.37484540 4.22764624
N 0.30864419 7.71366575 2.92749956
H 0.47661671 10.18072110 3.71160091
H 1.07465334 7.82269220 3.57714669
H 0.38402250 8.37704933 2.17484371
H 11.43541341 7.79037360 3.40402455
O 6.15703846 10.25988474 3.50899568
H 5.59322244 9.56329447 3.14465590
N 1.77855690 7.63125793 9.14884523
H 2.55940486 6.96832838 9.30697002
H 2.12441551 8.45479870 8.64286229
H 1.04552782 7.16977228 8.58942450
H 0.34824446 10.17844028 9.16294638
O 5.96388304 10.72370940 9.45688039
H 6.58908357 10.92648611 8.79819258
N 7.10658904 1.83029753 3.34525436
H 6.92293050 1.84650221 4.30890371
H 8.07804336 1.93030522 3.20895214
H 5.67953736 10.47183163 4.32443905
H 6.82999417 0.95850113 2.98152882
N 11.38380535 4.63012252 2.53936884
H 0.37927047 4.19432163 2.59073807
O 5.23764101 1.91523463 9.72406364
H 4.78872025 2.70369365 9.56981423
H 9.81299067 9.20751407 4.08265499
H 4.79808795 1.14034947 9.67399628
H 5.44558456 2.01021000 10.62077351
O 0.90954339 4.62400932 8.31081106
H 11.90973532 4.74838140 8.25006246
N 7.32234245 7.58664570 3.02452265
H 7.44703622 8.31696467 3.71480033
H 6.90738053 7.93850210 2.17237687
H 5.55428685 5.11760658 3.76552520
H 6.81243095 6.77788116 3.39732325
N 0.29575823 11.04303794 3.10161425
H 0.86490722 11.83879228 3.63899745
O 6.85201686 8.08463693 8.87628788
H 7.33514301 7.42634987 9.38216748
H 6.79196133 7.75954772 7.97161748
H 3.89904877 6.42834904 8.88324096
H 5.95997296 9.93297232 9.47466547
O 11.40365898 10.37196036 9.27660922
H 10.98366636 9.51571998 9.14787573
O 1.52232797 5.33273311 0.57537606
H 2.38151140 5.72519912 0.77945296
H 0.92079957 6.09312823 0.62203253
O 11.23490924 2.91533552 6.75850641
H 10.79234019 2.97552251 5.90000184
H 10.75124206 2.18961560 7.18074015
O 11.39027944 7.34628556 6.72582995
H 10.92025679 6.69831954 7.27766966
H 11.12238028 7.06320210 5.83941078
O 8.46843195 10.71736286 10.60018556
H 8.56722016 11.42046608 11.25794033
H 9.08031098 10.04804949 10.94065170
O 6.58517573 9.99406234 6.55746149
H 7.02763258 10.76096604 6.17233337
H 5.74193274 10.38458392 6.82288230
O 1.76005464 1.01771919 5.49267877
H 1.97042091 1.01748419 6.44297037
H 1.42973007 0.11076352 5.34706449
H 2.61130613 9.70341237 10.45030683
O 3.05086908 10.48131334 10.08518931
H 3.00326932 10.93357295 9.36521210
O 6.46315322 8.76520583 11.96784797
H 6.45068084 9.65965953 11.58895602
H 5.66116297 8.35357377 11.63844333
O 1.17459993 5.24206908 5.10014497
H 1.31932881 5.52363924 6.01289663
H 0.58053835 4.48981346 5.23255650
O 6.72755497 0.78840875 7.38172809
H 6.38879656 1.54670982 6.86345204
H 7.67917840 0.94039024 7.26494610
O 8.54766572 0.00647503 5.04505141
H 8.87362909 11.10484108 4.86018079
H 8.04775976 0.20198361 4.23573994
O 1.28950300 8.42800979 11.82038504
H 1.47666664 8.10878664 10.87290333
H 2.10220669 8.19476202 0.29510553
O 9.67979076 6.42073355 4.34691506
H 8.92715301 6.72940235 3.79741224
H 10.20024126 5.91677392 3.66976111
O 3.57411616 6.70410217 3.88254785
H 2.88948995 6.15605298 4.29808481
H 4.36137077 6.43047324 4.38049654
O 4.75065560 11.44185335 1.12537088
H 4.08611928 10.74852367 1.19233471
H 5.50353016 10.96568825 0.73651277
O 9.52545264 4.89944439 8.37322841
H 8.78859598 4.35080439 8.66328314
H 9.61490675 4.60849115 7.45400687
O 4.19707467 1.34592128 3.67401439
H 4.94370120 0.74406281 3.51406800
H 4.19055349 1.77303760 2.79630494
O 1.88232618 11.95451227 0.60024434
H 2.04645873 11.02454723 0.38329541
H 1.15184937 0.17494341 11.99928285
O 3.75938422 11.01685511 6.45620508
H 3.21254143 10.45537470 5.88949171
H 3.41660269 10.82155767 7.32965639
O 9.70398414 3.95001545 11.89474325
H 10.46166606 3.91631180 11.28543523
H 10.09834695 4.40269974 0.68193008
O 8.56395964 3.51695075 5.62241042
H 8.39666503 2.62622147 5.26381643
H 7.96953714 4.08250598 5.00494074
O 9.67362450 0.48030482 7.92575778
H 9.61319804 11.88341918 7.16809240
H 9.97840503 11.90238635 8.63894187
O 3.94241531 6.96502967 11.60258943
H 4.27671527 6.84600490 10.67022522
H 4.65706385 6.51294615 0.09115988
O 3.05701732 9.66319585 3.66112506
H 2.54004901 9.57433550 2.84440476
H 2.93148744 8.78098072 4.04252342
O 7.45496127 5.84308508 11.01138472
H 8.16758841 5.46391828 10.47644287
H 6.71355737 5.83938184 10.36109975
O 9.80291393 7.95789017 10.21404942
H 10.38910242 8.34006414 10.87949429
H 9.06376120 7.63923741 10.75692887
O 4.49634356 4.10679358 11.73387805
H 4.54737279 4.95779709 11.19223377
H 5.35888184 4.17561117 0.20355937
O 9.59234481 7.34180146 1.34856172
H 8.87155933 7.47768372 2.05040471
H 9.04432217 7.27322008 0.54011714
O 7.03509631 3.22348773 0.70708240
H 7.17844705 4.13403143 1.01841097
H 7.77878544 2.78888884 1.15838887
O 9.21241078 0.48085900 1.21751966
H 9.66204365 11.65727108 1.45318397
H 9.94048839 1.11619136 1.18684594
O 1.19704207 9.58599592 6.61908889
H 0.25606413 9.67373665 6.83193409
H 1.26900519 8.62493549 6.54801125
O 0.78256134 2.60406093 11.45340836
H 0.61502181 3.56074060 11.40300991
H 1.55655312 2.54573688 10.86673303
O 5.86279361 7.12170548 5.89173203
H 6.34324107 7.94001367 6.08558403
H 5.50772967 6.84683068 6.74368758
O 10.88782815 9.96374825 0.51092816
H 11.78841776 10.32204307 0.44704989
H 11.02688182 9.20519067 1.09766613
O 3.93073389 4.16456745 5.71378770
H 4.68840630 3.57889133 5.56446058
H 4.29569485 4.76448881 6.38016697

81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1 Normal file
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#info all out log
units metal
atom_style atomic
boundary p p p
atom_modify map hash
boundary p p p
read_data latte_cell_0.data
Reading data file ...
orthogonal box = (0 0 0) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
161 atoms
read_data CPU = 0.001 seconds
mass 1 1.00
mass 2 14.00
mass 3 15.999
# potential settings
pair_style zero 5.7
pair_coeff * *
compute pace all pace coupling_coefficients.yace 1 0
thermo 1
thermo_style custom step temp c_pace[1][183]
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute pace, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.993 | 6.993 | 6.993 Mbytes
Step Temp c_pace[1][183]
0 0 8.6885642
Loop time of 1.217e-06 on 1 procs for 0 steps with 161 atoms
164.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.217e-06 | | |100.00
Nlocal: 161 ave 161 max 161 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1754 ave 1754 max 1754 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14230 ave 14230 max 14230 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 28460 ave 28460 max 28460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 28460
Ave neighs/atom = 176.77019
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.4 Normal file
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
#info all out log
units metal
atom_style atomic
boundary p p p
atom_modify map hash
boundary p p p
read_data latte_cell_0.data
Reading data file ...
orthogonal box = (0 0 0) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
161 atoms
read_data CPU = 0.001 seconds
mass 1 1.00
mass 2 14.00
mass 3 15.999
# potential settings
pair_style zero 5.7
pair_coeff * *
compute pace all pace coupling_coefficients.yace 1 0
thermo 1
thermo_style custom step temp c_pace[1][183]
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute pace, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.97 | 6.97 | 6.971 Mbytes
Step Temp c_pace[1][183]
0 0 8.6885642
Loop time of 1.979e-06 on 4 procs for 0 steps with 161 atoms
164.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.979e-06 | | |100.00
Nlocal: 40.25 ave 44 max 35 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 1134.5 ave 1159 max 1117 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 3557.5 ave 4115 max 3189 min
Histogram: 2 0 0 0 0 1 0 0 0 1
FullNghs: 7115 ave 7755 max 6158 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 28460
Ave neighs/atom = 176.77019
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

1
examples/PACKAGES/sna_nnn_slcsa/Zr_mm.eam.fs Symbolic link
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../../../potentials/Zr_mm.eam.fs

879
examples/PACKAGES/sna_nnn_slcsa/data.zr_cell Normal file
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# Hcp Zr with box vectors H1=[2-1-10], H2=[-12-10], H3=[0001].
864 atoms
1 atom types
0.000000000000 19.374000000000 xlo xhi
0.000000000000 33.556752345839 ylo yhi
0.000000000000 30.846000000000 zlo zhi
Masses
1 91.22400000 # Zr
Atoms # atomic
1 1 0.000000000000 1.864264019213 2.570500000000
2 1 0.000000000000 0.000000000000 0.000000000000
3 1 1.614500000000 4.660660048033 2.570500000000
4 1 1.614500000000 2.796396028820 0.000000000000
5 1 3.229000000000 1.864264019213 2.570500000000
6 1 3.229000000000 0.000000000000 0.000000000000
7 1 4.843500000000 4.660660048033 2.570500000000
8 1 4.843500000000 2.796396028820 0.000000000000
9 1 6.458000000000 1.864264019213 2.570500000000
10 1 6.458000000000 0.000000000000 0.000000000000
11 1 8.072500000000 4.660660048033 2.570500000000
12 1 8.072500000000 2.796396028820 0.000000000000
13 1 9.687000000000 1.864264019213 2.570500000000
14 1 9.687000000000 0.000000000000 0.000000000000
15 1 11.301500000000 4.660660048033 2.570500000000
16 1 11.301500000000 2.796396028820 0.000000000000
17 1 12.916000000000 1.864264019213 2.570500000000
18 1 12.916000000000 0.000000000000 0.000000000000
19 1 14.530500000000 4.660660048033 2.570500000000
20 1 14.530500000000 2.796396028820 0.000000000000
21 1 16.145000000000 1.864264019213 2.570500000000
22 1 16.145000000000 0.000000000000 0.000000000000
23 1 17.759500000000 4.660660048033 2.570500000000
24 1 17.759500000000 2.796396028820 0.000000000000
25 1 0.000000000000 7.457056076853 2.570500000000
26 1 0.000000000000 5.592792057640 0.000000000000
27 1 1.614500000000 10.253452105673 2.570500000000
28 1 1.614500000000 8.389188086460 0.000000000000
29 1 3.229000000000 7.457056076853 2.570500000000
30 1 3.229000000000 5.592792057640 0.000000000000
31 1 4.843500000000 10.253452105673 2.570500000000
32 1 4.843500000000 8.389188086460 0.000000000000
33 1 6.458000000000 7.457056076853 2.570500000000
34 1 6.458000000000 5.592792057640 0.000000000000
35 1 8.072500000000 10.253452105673 2.570500000000
36 1 8.072500000000 8.389188086460 0.000000000000
37 1 9.687000000000 7.457056076853 2.570500000000
38 1 9.687000000000 5.592792057640 0.000000000000
39 1 11.301500000000 10.253452105673 2.570500000000
40 1 11.301500000000 8.389188086460 0.000000000000
41 1 12.916000000000 7.457056076853 2.570500000000
42 1 12.916000000000 5.592792057640 0.000000000000
43 1 14.530500000000 10.253452105673 2.570500000000
44 1 14.530500000000 8.389188086460 0.000000000000
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822 1 3.229000000000 22.371168230560 25.705000000000
823 1 4.843500000000 27.031828278593 28.275500000000
824 1 4.843500000000 25.167564259380 25.705000000000
825 1 6.458000000000 24.235432249773 28.275500000000
826 1 6.458000000000 22.371168230560 25.705000000000
827 1 8.072500000000 27.031828278593 28.275500000000
828 1 8.072500000000 25.167564259380 25.705000000000
829 1 9.687000000000 24.235432249773 28.275500000000
830 1 9.687000000000 22.371168230560 25.705000000000
831 1 11.301500000000 27.031828278593 28.275500000000
832 1 11.301500000000 25.167564259380 25.705000000000
833 1 12.916000000000 24.235432249773 28.275500000000
834 1 12.916000000000 22.371168230560 25.705000000000
835 1 14.530500000000 27.031828278593 28.275500000000
836 1 14.530500000000 25.167564259380 25.705000000000
837 1 16.145000000000 24.235432249773 28.275500000000
838 1 16.145000000000 22.371168230560 25.705000000000
839 1 17.759500000000 27.031828278593 28.275500000000
840 1 17.759500000000 25.167564259380 25.705000000000
841 1 0.000000000000 29.828224307413 28.275500000000
842 1 0.000000000000 27.963960288200 25.705000000000
843 1 1.614500000000 32.624620336233 28.275500000000
844 1 1.614500000000 30.760356317019 25.705000000000
845 1 3.229000000000 29.828224307413 28.275500000000
846 1 3.229000000000 27.963960288200 25.705000000000
847 1 4.843500000000 32.624620336233 28.275500000000
848 1 4.843500000000 30.760356317019 25.705000000000
849 1 6.458000000000 29.828224307413 28.275500000000
850 1 6.458000000000 27.963960288200 25.705000000000
851 1 8.072500000000 32.624620336233 28.275500000000
852 1 8.072500000000 30.760356317019 25.705000000000
853 1 9.687000000000 29.828224307413 28.275500000000
854 1 9.687000000000 27.963960288200 25.705000000000
855 1 11.301500000000 32.624620336233 28.275500000000
856 1 11.301500000000 30.760356317019 25.705000000000
857 1 12.916000000000 29.828224307413 28.275500000000
858 1 12.916000000000 27.963960288200 25.705000000000
859 1 14.530500000000 32.624620336233 28.275500000000
860 1 14.530500000000 30.760356317019 25.705000000000
861 1 16.145000000000 29.828224307413 28.275500000000
862 1 16.145000000000 27.963960288200 25.705000000000
863 1 17.759500000000 32.624620336233 28.275500000000
864 1 17.759500000000 30.760356317019 25.705000000000

55
examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lda_scalings.dat Normal file
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@ -0,0 +1,55 @@
0.65552758 -0.08218108 -0.23122826
2.03065849 0.46494117 0.87297750
-15.80180341 1.50484584 0.31669351
0.06060238 -0.47589059 -0.41017499
4.23928030 -2.27982958 4.87969884
-1.09746642 -1.28258171 2.03459312
5.48480653 -0.66345012 3.18471732
-1.57479966 0.17478998 -0.17156696
3.85779786 1.59890578 1.78936017
-1.14469715 -2.15823271 2.14353632
5.97160056 0.11573423 0.97653410
4.44645807 -0.15365582 -0.08773622
3.09452721 0.32439223 1.19779688
-1.22585061 -0.32185613 0.03949731
0.44816997 -1.11182687 0.26222208
0.19532128 0.30397832 -0.57154050
5.52432571 -0.76685448 0.32647935
6.37957282 -0.96148815 1.53439397
2.73798648 -0.69516327 1.73607004
0.94755899 0.41154702 -0.14095753
1.50733544 1.22254481 0.26284605
0.98313431 -1.24195379 0.59009611
-0.76518592 0.11605047 -0.00304658
-0.68335076 0.48935564 -0.53834507
1.86534260 -0.49032664 -0.06298849
1.52931829 0.64853878 -0.56286214
2.64217062 -1.37348638 0.22526281
0.18023516 0.03439864 0.77624538
2.02366558 0.35432524 0.76748492
0.80982907 0.31806067 0.08774175
1.57388194 -1.07822533 0.15886237
0.41345498 0.38916338 -0.29917607
-0.24819893 0.13763422 0.45471609
-2.27933523 -0.01771636 -0.20567577
1.52275665 0.35306670 0.21266257
0.28547991 1.05230832 1.16641438
0.97147437 -0.63973458 -0.37994470
0.48124764 0.03483500 -0.01982056
0.74502588 0.14367872 -0.24443596
0.48813660 0.15632903 -0.88469078
0.04886450 0.00882595 -0.47920447
0.03103900 -0.15091487 -0.41193682
-0.10106190 0.14911569 0.10727243
-0.15552036 -0.49286545 -0.04644942
0.27304084 0.35638954 1.13331445
0.57788886 -0.50269555 0.09110942
0.36780762 -0.08710371 -0.28478716
1.01678932 -0.42099561 -0.07317253
0.06561086 -0.27253002 -0.05366136
0.22266923 0.19999531 -0.30017173
-0.18666193 0.02576273 0.27752106
-0.76718071 0.61299522 0.58296511
0.60978530 0.04962900 -0.32796430
-0.11572649 0.03034386 -0.83005753
0.12675714 0.00004617 -0.37078106

1
examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_bias.dat Normal file
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@ -0,0 +1 @@
-6.32012657 5.62127377 1.19871662 -0.49986382

4
examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_decision.dat Normal file
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@ -0,0 +1,4 @@
-0.42810669 1.25467216 0.93144383
0.09624929 -0.80420088 0.48996738
-0.09865949 0.39991755 -0.69233982
0.43051689 -0.85038883 -0.72907140

20
examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mahalanobis_file.dat Normal file
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@ -0,0 +1,20 @@
5.0540
-23.8329 4.6638 3.9805
1.1377 0.1077 -0.0171
0.1077 0.8846 -0.2577
-0.0171 -0.2577 0.6783
5.2340
-21.2853 -6.1583 1.7948
1.7124 0.0341 0.1966
0.0341 0.6453 0.2880
0.1966 0.2880 1.8991
5.0360
-23.1593 1.3059 -5.7549
0.7496 -0.0806 -0.1101
-0.0806 1.1178 0.1667
-0.1101 0.1667 0.6711
7.9940
68.1971 0.1604 -0.0067
0.9663 -0.1846 0.6622
-0.1846 8.2371 0.9841
0.6622 0.9841 5.9601

55
examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mean_descriptor.dat Normal file
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@ -0,0 +1,55 @@
137.71497059
0.36342014
-2.78949838
1.75623090
-4.86893969
-2.31918628
-3.01873942
59.70217846
-8.31239311
-1.05113276
-4.08948813
11.70560234
17.48710737
42.43158755
-6.27727395
-1.46675636
-3.40739849
1.58674150
13.02515977
5.67885926
6.45692906
4.69273492
21.59764216
-7.68805780
-4.37357550
-5.79764719
0.53149261
-0.00723980
-2.47811316
-0.34939237
-4.59425510
-4.44056296
107.64051985
-9.32851480
-6.62214151
-5.69590145
22.80361437
9.47641390
2.25214024
-0.19403065
3.05386205
12.91756406
135.15381317
-9.93292065
-3.73311129
10.67039500
9.60945072
-0.03566872
21.97944941
6.70251772
74.60284853
-5.99090678
0.21877973
-1.19909174
1.37424965

57
examples/PACKAGES/sna_nnn_slcsa/in.slcsa Normal file
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@ -0,0 +1,57 @@
variable trequis equal 750.0
variable prequis_low equal 0.0
variable prequis_high equal 25.0e4
variable equilSteps equal 200
variable runSteps equal 2000
variable freqdump equal 200
variable pstime equal step*dt
variable sxx equal 1.e-4*pxx
variable syy equal 1.e-4*pyy
variable szz equal 1.e-4*pzz
variable sxy equal 1.e-4*pxy
variable sxz equal 1.e-4*pxz
variable syz equal 1.e-4*pyz
variable TK equal temp
variable PE equal pe
variable KE equal ke
variable V equal vol
dimension 3
boundary p p p
units metal
atom_style atomic
read_data data.zr_cell
replicate 1 5 5
change_box all triclinic
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
timestep 0.002
thermo 50
thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz
# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat
velocity all create ${trequis} 42345 dist gaussian
# 1st step : compute the bispectrum on 24 nearest neighbors
compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25
# 2nd step : perform dimension reduction + logistic regression
compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*]
#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
# for testing only. in production use dump as shown above
compute max_slcsa all reduce max c_slcsa[*]
compute min_slcsa all reduce min c_slcsa[*]
thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]
#fix 1 all nvt temp ${trequis} ${trequis} 0.100
fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
run ${equilSteps}

180
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1 Normal file
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@ -0,0 +1,180 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable trequis equal 750.0
variable prequis_low equal 0.0
variable prequis_high equal 25.0e4
variable equilSteps equal 200
variable runSteps equal 2000
variable freqdump equal 200
variable pstime equal step*dt
variable sxx equal 1.e-4*pxx
variable syy equal 1.e-4*pyy
variable szz equal 1.e-4*pzz
variable sxy equal 1.e-4*pxy
variable sxz equal 1.e-4*pxz
variable syz equal 1.e-4*pyz
variable TK equal temp
variable PE equal pe
variable KE equal ke
variable V equal vol
dimension 3
boundary p p p
units metal
atom_style atomic
read_data data.zr_cell
Reading data file ...
orthogonal box = (0 0 0) to (19.374 33.556752 30.846)
1 by 1 by 1 MPI processor grid
reading atoms ...
864 atoms
read_data CPU = 0.002 seconds
replicate 1 5 5
Replication is creating a 1x5x5 = 25 times larger system...
orthogonal box = (0 0 0) to (19.374 167.78376 154.23)
1 by 1 by 1 MPI processor grid
21600 atoms
replicate CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0)
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
Reading eam/fs potential file Zr_mm.eam.fs with DATE: 2007-06-11
timestep 0.002
thermo 50
thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz
# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat
velocity all create ${trequis} 42345 dist gaussian
velocity all create 750 42345 dist gaussian
# 1st step : compute the bispectrum on 24 nearest neighbors
compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25
# 2nd step : perform dimension reduction + logistic regression
compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*]
Files used:
database mean descriptor: dir.slcsa/mean_descriptor.dat
lda scalings : dir.slcsa/lda_scalings.dat
lr decision : dir.slcsa/lr_decision.dat
lr bias : dir.slcsa/lr_bias.dat
maha stats : dir.slcsa/mahalanobis_file.dat
For class 0 maha threshold = 5.054
mean B:
-23.8329
4.6638
3.9805
icov:
1.1377 0.1077 -0.0171
0.1077 0.8846 -0.2577
-0.0171 -0.2577 0.6783
For class 1 maha threshold = 5.234
mean B:
-21.2853
-6.1583
1.7948
icov:
1.7124 0.0341 0.1966
0.0341 0.6453 0.288
0.1966 0.288 1.8991
For class 2 maha threshold = 5.036
mean B:
-23.1593
1.3059
-5.7549
icov:
0.7496 -0.0806 -0.1101
-0.0806 1.1178 0.1667
-0.1101 0.1667 0.6711
For class 3 maha threshold = 7.994
mean B:
68.1971
0.1604
-0.0067
icov:
0.9663 -0.1846 0.6622
-0.1846 8.2371 0.9841
0.6622 0.9841 5.9601
#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
# for testing only. in production use dump as shown above
compute max_slcsa all reduce max c_slcsa[*]
compute min_slcsa all reduce min c_slcsa[*]
thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]
#fix 1 all nvt temp ${trequis} ${trequis} 0.100
fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri 0 0 1.0
run ${equilSteps}
run 200
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 4 31 29
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) pair eam/fs, perpetual, trim from (1)
attributes: half, newton on, cut 9.6
pair build: trim
stencil: none
bin: none
(3) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 31.9 | 31.9 | 31.9 Mbytes
Step PotEng KinEng Temp c_max_slcsa[1] c_max_slcsa[2] c_max_slcsa[3] c_max_slcsa[4] c_max_slcsa[5] c_min_slcsa[1] c_min_slcsa[2] c_min_slcsa[3] c_min_slcsa[4] c_min_slcsa[5]
0 -143297.23 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
50 -142154.08 1007.7164 360.9442 8.8091564 19.23244 4.2093382 113.87959 2 5.0327148 9.6817454 0.02610585 106.71863 2
100 -142365.33 1406.6559 503.83647 8.6272189 17.908949 2.9294666 113.75167 2 6.2058895 11.913521 0.033775944 108.66893 2
150 -142188.18 1432.0075 512.91691 8.6441961 18.176321 2.9277374 114.27958 2 5.5899425 10.521867 0.014919473 108.14526 2
200 -142000.4 1481.7247 530.72462 8.5895692 18.65646 3.1725758 114.55015 2 5.5955774 10.776385 0.061469343 108.35384 2
Loop time of 36.3759 on 1 procs for 200 steps with 21600 atoms
Performance: 0.950 ns/day, 25.261 hours/ns, 5.498 timesteps/s, 118.760 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0837 | 9.0837 | 9.0837 | 0.0 | 24.97
Neigh | 0.52896 | 0.52896 | 0.52896 | 0.0 | 1.45
Comm | 0.045416 | 0.045416 | 0.045416 | 0.0 | 0.12
Output | 26.548 | 26.548 | 26.548 | 0.0 | 72.98
Modify | 0.1493 | 0.1493 | 0.1493 | 0.0 | 0.41
Other | | 0.02088 | | | 0.06
Nlocal: 21600 ave 21600 max 21600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 36674 ave 36674 max 36674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.61729e+06 ave 2.61729e+06 max 2.61729e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 5.24007e+06 ave 5.24007e+06 max 5.24007e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5240069
Ave neighs/atom = 242.59579
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:43

180
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4 Normal file
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@ -0,0 +1,180 @@
LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable trequis equal 750.0
variable prequis_low equal 0.0
variable prequis_high equal 25.0e4
variable equilSteps equal 200
variable runSteps equal 2000
variable freqdump equal 200
variable pstime equal step*dt
variable sxx equal 1.e-4*pxx
variable syy equal 1.e-4*pyy
variable szz equal 1.e-4*pzz
variable sxy equal 1.e-4*pxy
variable sxz equal 1.e-4*pxz
variable syz equal 1.e-4*pyz
variable TK equal temp
variable PE equal pe
variable KE equal ke
variable V equal vol
dimension 3
boundary p p p
units metal
atom_style atomic
read_data data.zr_cell
Reading data file ...
orthogonal box = (0 0 0) to (19.374 33.556752 30.846)
1 by 2 by 2 MPI processor grid
reading atoms ...
864 atoms
read_data CPU = 0.002 seconds
replicate 1 5 5
Replication is creating a 1x5x5 = 25 times larger system...
orthogonal box = (0 0 0) to (19.374 167.78376 154.23)
1 by 2 by 2 MPI processor grid
21600 atoms
replicate CPU = 0.001 seconds
change_box all triclinic
Changing box ...
triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0)
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
Reading eam/fs potential file Zr_mm.eam.fs with DATE: 2007-06-11
timestep 0.002
thermo 50
thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz
# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat
velocity all create ${trequis} 42345 dist gaussian
velocity all create 750 42345 dist gaussian
# 1st step : compute the bispectrum on 24 nearest neighbors
compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25
# 2nd step : perform dimension reduction + logistic regression
compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*]
Files used:
database mean descriptor: dir.slcsa/mean_descriptor.dat
lda scalings : dir.slcsa/lda_scalings.dat
lr decision : dir.slcsa/lr_decision.dat
lr bias : dir.slcsa/lr_bias.dat
maha stats : dir.slcsa/mahalanobis_file.dat
For class 0 maha threshold = 5.054
mean B:
-23.8329
4.6638
3.9805
icov:
1.1377 0.1077 -0.0171
0.1077 0.8846 -0.2577
-0.0171 -0.2577 0.6783
For class 1 maha threshold = 5.234
mean B:
-21.2853
-6.1583
1.7948
icov:
1.7124 0.0341 0.1966
0.0341 0.6453 0.288
0.1966 0.288 1.8991
For class 2 maha threshold = 5.036
mean B:
-23.1593
1.3059
-5.7549
icov:
0.7496 -0.0806 -0.1101
-0.0806 1.1178 0.1667
-0.1101 0.1667 0.6711
For class 3 maha threshold = 7.994
mean B:
68.1971
0.1604
-0.0067
icov:
0.9663 -0.1846 0.6622
-0.1846 8.2371 0.9841
0.6622 0.9841 5.9601
#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
# for testing only. in production use dump as shown above
compute max_slcsa all reduce max c_slcsa[*]
compute min_slcsa all reduce min c_slcsa[*]
thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]
#fix 1 all nvt temp ${trequis} ${trequis} 0.100
fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0
fix 1 all npt temp 750 750 0.100 tri 0 0 1.0
run ${equilSteps}
run 200
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 4 31 29
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/tri
bin: standard
(2) pair eam/fs, perpetual, trim from (1)
attributes: half, newton on, cut 9.6
pair build: trim
stencil: none
bin: none
(3) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.26 | 11.45 | 11.64 Mbytes
Step PotEng KinEng Temp c_max_slcsa[1] c_max_slcsa[2] c_max_slcsa[3] c_max_slcsa[4] c_max_slcsa[5] c_min_slcsa[1] c_min_slcsa[2] c_min_slcsa[3] c_min_slcsa[4] c_min_slcsa[5]
0 -143297.23 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
50 -142154.08 1007.7164 360.9442 8.8091564 19.23244 4.2093382 113.87959 2 5.0327148 9.6817454 0.02610585 106.71863 2
100 -142365.33 1406.6559 503.83647 8.6272189 17.908949 2.9294666 113.75167 2 6.2058895 11.913521 0.033775944 108.66893 2
150 -142188.18 1432.0075 512.91691 8.6441961 18.176321 2.9277374 114.27958 2 5.5899425 10.521867 0.014919473 108.14526 2
200 -142000.4 1481.7247 530.72462 8.5895692 18.65646 3.1725758 114.55015 2 5.5955774 10.776385 0.061469343 108.35384 2
Loop time of 9.81677 on 4 procs for 200 steps with 21600 atoms
Performance: 3.521 ns/day, 6.817 hours/ns, 20.373 timesteps/s, 440.063 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6508 | 2.6589 | 2.6698 | 0.5 | 27.09
Neigh | 0.1516 | 0.15276 | 0.15406 | 0.3 | 1.56
Comm | 0.047132 | 0.058969 | 0.066095 | 3.2 | 0.60
Output | 6.8886 | 6.8886 | 6.8886 | 0.0 | 70.17
Modify | 0.046437 | 0.04661 | 0.046825 | 0.1 | 0.47
Other | | 0.01091 | | | 0.11
Nlocal: 5400 ave 5416 max 5393 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 12902.8 ave 12911 max 12888 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 654322 ave 655602 max 650912 min
Histogram: 1 0 0 0 0 0 0 0 0 3
FullNghs: 1.31002e+06 ave 1.31507e+06 max 1.30683e+06 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 5240065
Ave neighs/atom = 242.5956
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:11

7
examples/reaxff/in.reaxff.tatb
View File

@ -31,8 +31,15 @@ neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
compute bonds all reaxff/atom bonds yes
variable nqeq equal f_2
# dumps out the local bond information
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
# dumps out the peratom bond information
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &

2
lib/gpu/Makefile.linux_multi
View File

@ -65,7 +65,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC -allow-unsupported-compiler
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC -std=c++11
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias

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

@ -54,6 +54,6 @@ namespace ucl_opencl {
#include "ucl_print.h"
#undef UCL_PRINT_ALLOW
} // namespace ucl_cudart
} // namespace ucl_opencl
#endif

8
lib/gpu/lal_amoeba.cpp
View File

@ -281,13 +281,7 @@ int AmoebaT::polar_real(const int eflag, const int vflag) {
const int BX=this->block_size();
const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
/*
const int cus = this->device->gpu->cus();
while (GX < cus && GX > 1) {
BX /= 2;
GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
}
*/
this->time_pair.start();
// Build the short neighbor list if not done yet

6
lib/gpu/lal_base_dpd.cpp
View File

@ -56,7 +56,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name, const int onetype) {
const char *k_name, const int onetype,
const int extra_fields) {
screen=_screen;
int gpu_nbor=0;
@ -75,7 +76,8 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
bool charge = false;
bool rot = false;
bool vel = true;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel);
_extra_fields = extra_fields;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel,_extra_fields/4);
if (success!=0)
return success;

5
lib/gpu/lal_base_dpd.h
View File

@ -53,7 +53,7 @@ class BaseDPD {
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name,
const int onetype=0);
const int onetype=0, const int extra_fields=0);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead();
@ -167,7 +167,6 @@ class BaseDPD {
/// Atom Data
Atom<numtyp,acctyp> *atom;
// ------------------------ FORCE/ENERGY DATA -----------------------
Answer<numtyp,acctyp> *ans;
@ -199,7 +198,7 @@ class BaseDPD {
protected:
bool _compiled;
int _block_size, _threads_per_atom, _onetype;
int _block_size, _threads_per_atom, _onetype, _extra_fields;
double _max_bytes, _max_an_bytes;
double _gpu_overhead, _driver_overhead;
UCL_D_Vec<int> *_nbor_data;

362
lib/gpu/lal_base_sph.cpp Normal file
View File

@ -0,0 +1,362 @@
/***************************************************************************
base_sph.cpp
-------------------
Trung Nguyen (U Chicago)
Base class for SPH pair styles needing per-particle data for position,
velocity, and type.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#include "lal_base_sph.h"
namespace LAMMPS_AL {
#define BaseSPHT BaseSPH<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> global_device;
template <class numtyp, class acctyp>
BaseSPHT::BaseSPH() : _compiled(false), _max_bytes(0) {
device=&global_device;
ans=new Answer<numtyp,acctyp>();
nbor=new Neighbor();
pair_program=nullptr;
ucl_device=nullptr;
#if defined(LAL_OCL_EV_JIT)
pair_program_noev=nullptr;
#endif
}
template <class numtyp, class acctyp>
BaseSPHT::~BaseSPH() {
delete ans;
delete nbor;
k_pair_fast.clear();
k_pair.clear();
if (pair_program) delete pair_program;
#if defined(LAL_OCL_EV_JIT)
k_pair_noev.clear();
if (pair_program_noev) delete pair_program_noev;
#endif
}
template <class numtyp, class acctyp>
int BaseSPHT::bytes_per_atom_atomic(const int max_nbors) const {
return device->atom.bytes_per_atom()+ans->bytes_per_atom()+
nbor->bytes_per_atom(max_nbors);
}
template <class numtyp, class acctyp>
int BaseSPHT::init_atomic(const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, const double gpu_split,
FILE *_screen, const void *pair_program,
const char *k_name, const int onetype,
const int extra_fields) {
screen=_screen;
int gpu_nbor=0;
if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_NEIGH)
gpu_nbor=1;
else if (device->gpu_mode()==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
gpu_nbor=2;
int _gpu_host=0;
int host_nlocal=hd_balancer.first_host_count(nlocal,gpu_split,gpu_nbor);
if (host_nlocal>0)
_gpu_host=1;
_threads_per_atom=device->threads_per_atom();
bool charge = false;
bool rot = false;
bool vel = true;
_extra_fields = extra_fields;
int success=device->init(*ans,charge,rot,nlocal,nall,maxspecial,vel,_extra_fields/4);
if (success!=0)
return success;
if (ucl_device!=device->gpu) _compiled=false;
ucl_device=device->gpu;
atom=&device->atom;
_block_size=device->pair_block_size();
compile_kernels(*ucl_device,pair_program,k_name,onetype);
if (_threads_per_atom>1 && gpu_nbor==0) {
nbor->packing(true);
_nbor_data=&(nbor->dev_packed);
} else
_nbor_data=&(nbor->dev_nbor);
success = device->init_nbor(nbor,nlocal,host_nlocal,nall,maxspecial,_gpu_host,
max_nbors,cell_size,false,_threads_per_atom);
if (success!=0)
return success;
// Initialize host-device load balancer
hd_balancer.init(device,gpu_nbor,gpu_split);
// Initialize timers for the selected GPU
time_pair.init(*ucl_device);
time_pair.zero();
pos_tex.bind_float(atom->x,4);
vel_tex.bind_float(atom->v,4);
_max_an_bytes=ans->gpu_bytes()+nbor->gpu_bytes();
return success;
}
template <class numtyp, class acctyp>
void BaseSPHT::estimate_gpu_overhead() {
device->estimate_gpu_overhead(1,_gpu_overhead,_driver_overhead);
}
template <class numtyp, class acctyp>
void BaseSPHT::clear_atomic() {
// Output any timing information
acc_timers();
double avg_split=hd_balancer.all_avg_split();
_gpu_overhead*=hd_balancer.timestep();
_driver_overhead*=hd_balancer.timestep();
device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes,
_gpu_overhead,_driver_overhead,_threads_per_atom,screen);
time_pair.clear();
hd_balancer.clear();
nbor->clear();
ans->clear();
}
// ---------------------------------------------------------------------------
// Copy neighbor list from host
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int * BaseSPHT::reset_nbors(const int nall, const int inum, int *ilist,
int *numj, int **firstneigh, bool &success) {
success=true;
int mn=nbor->max_nbor_loop(inum,numj,ilist);
resize_atom(inum,nall,success);
resize_local(inum,mn,success);
if (!success)
return nullptr;
nbor->get_host(inum,ilist,numj,firstneigh,block_size());
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
if (bytes>_max_an_bytes)
_max_an_bytes=bytes;
return ilist;
}
// ---------------------------------------------------------------------------
// Build neighbor list on device
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
inline void BaseSPHT::build_nbor_list(const int inum, const int host_inum,
const int nall, double **host_x,
int *host_type, double *sublo,
double *subhi, tagint *tag,
int **nspecial, tagint **special,
bool &success) {
success=true;
resize_atom(inum,nall,success);
resize_local(inum,host_inum,nbor->max_nbors(),success);
if (!success)
return;
atom->cast_copy_x(host_x,host_type);
int mn;
nbor->build_nbor_list(host_x, inum, host_inum, nall, *atom, sublo, subhi,
tag, nspecial, special, success, mn, ans->error_flag);
double bytes=ans->gpu_bytes()+nbor->gpu_bytes();
if (bytes>_max_an_bytes)
_max_an_bytes=bytes;
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then calculate forces, virials,..
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void BaseSPHT::compute(const int f_ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
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) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
if (inum_full==0) {
host_start=0;
// Make sure textures are correct if realloc by a different hybrid style
resize_atom(0,nall,success);
zero_timers();
return;
}
int ago=hd_balancer.ago_first(f_ago);
int inum=hd_balancer.balance(ago,inum_full,cpu_time);
ans->inum(inum);
host_start=inum;
if (ago==0) {
reset_nbors(nall, inum, ilist, numj, firstneigh, success);
if (!success)
return;
}
atom->cast_x_data(host_x,host_type);
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
atom->add_v_data(host_v,tag);
const int red_blocks=loop(eflag,vflag);
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,ilist,red_blocks);
device->add_ans_object(ans);
hd_balancer.stop_timer();
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary and then compute forces, virials, energies
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseSPHT::compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time, bool &success,
double **host_v) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
if (inum_full==0) {
host_start=0;
// Make sure textures are correct if realloc by a different hybrid style
resize_atom(0,nall,success);
zero_timers();
return nullptr;
}
hd_balancer.balance(cpu_time);
int inum=hd_balancer.get_gpu_count(ago,inum_full);
ans->inum(inum);
host_start=inum;
// Build neighbor list on GPU if necessary
if (ago==0) {
build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
sublo, subhi, tag, nspecial, special, success);
if (!success)
return nullptr;
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
} else {
atom->cast_x_data(host_x,host_type);
atom->cast_v_data(host_v,tag);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
}
atom->add_v_data(host_v,tag);
*ilist=nbor->host_ilist.begin();
*jnum=nbor->host_acc.begin();
const int red_blocks=loop(eflag,vflag);
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
device->add_ans_object(ans);
hd_balancer.stop_timer();
return nbor->host_jlist.begin()-host_start;
}
template <class numtyp, class acctyp>
double BaseSPHT::host_memory_usage_atomic() const {
return device->atom.host_memory_usage()+nbor->host_memory_usage()+
4*sizeof(numtyp)+sizeof(BaseSPH<numtyp,acctyp>);
}
template <class numtyp, class acctyp>
void BaseSPHT::compile_kernels(UCL_Device &dev, const void *pair_str,
const char *kname, const int onetype) {
if (_compiled && _onetype==onetype)
return;
_onetype=onetype;
std::string s_fast=std::string(kname)+"_fast";
if (pair_program) delete pair_program;
pair_program=new UCL_Program(dev);
std::string oclstring = device->compile_string()+" -DEVFLAG=1";
if (_onetype) oclstring+=" -DONETYPE="+device->toa(_onetype);
pair_program->load_string(pair_str,oclstring.c_str(),nullptr,screen);
k_pair_fast.set_function(*pair_program,s_fast.c_str());
k_pair.set_function(*pair_program,kname);
pos_tex.get_texture(*pair_program,"pos_tex");
vel_tex.get_texture(*pair_program,"vel_tex");
#if defined(LAL_OCL_EV_JIT)
oclstring = device->compile_string()+" -DEVFLAG=0";
if (_onetype) oclstring+=" -DONETYPE="+device->toa(_onetype);
if (pair_program_noev) delete pair_program_noev;
pair_program_noev=new UCL_Program(dev);
pair_program_noev->load_string(pair_str,oclstring.c_str(),nullptr,screen);
k_pair_noev.set_function(*pair_program_noev,s_fast.c_str());
#else
k_pair_sel = &k_pair_fast;
#endif
_compiled=true;
#if defined(USE_OPENCL) && (defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0))
if (dev.has_subgroup_support()) {
size_t mx_subgroup_sz = k_pair_fast.max_subgroup_size(_block_size);
#if defined(LAL_OCL_EV_JIT)
mx_subgroup_sz = std::min(mx_subgroup_sz, k_pair_noev.max_subgroup_size(_block_size));
#endif
if (_threads_per_atom > (int)mx_subgroup_sz) _threads_per_atom = mx_subgroup_sz;
device->set_simd_size(mx_subgroup_sz);
}
#endif
}
template class BaseSPH<PRECISION,ACC_PRECISION>;
}

209
lib/gpu/lal_base_sph.h Normal file
View File

@ -0,0 +1,209 @@
/***************************************************************************
base_sph.h
-------------------
Trung Nguyen (U Chicago)
Base class for SPH pair styles needing per-particle data for position,
velocity, and type.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : December 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_BASE_SPH_H
#define LAL_BASE_DPD_H
#include "lal_device.h"
#include "lal_balance.h"
#include "mpi.h"
#ifdef USE_OPENCL
#include "geryon/ocl_texture.h"
#elif defined(USE_HIP)
#include "geryon/hip_texture.h"
#else
#include "geryon/nvd_texture.h"
#endif
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class BaseSPH {
public:
BaseSPH();
virtual ~BaseSPH();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
* \param k_name name for the kernel for force calculation
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init_atomic(const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const void *pair_program, const char *k_name,
const int onetype=0, const int extra_fields=0);
/// Estimate the overhead for GPU context changes and CPU driver
void estimate_gpu_overhead();
/// Check if there is enough storage for atom arrays and realloc if not
/** \param success set to false if insufficient memory **/
inline void resize_atom(const int inum, const int nall, bool &success) {
if (atom->resize(nall, success)) {
pos_tex.bind_float(atom->x,4);
vel_tex.bind_float(atom->v,4);
}
ans->resize(inum,success);
}
/// Check if there is enough storage for neighbors and realloc if not
/** \param nlocal number of particles whose nbors must be stored on device
* \param host_inum number of particles whose nbors need to copied to host
* \param current maximum number of neighbors
* \note olist_size=total number of local particles **/
inline void resize_local(const int inum, const int max_nbors, bool &success) {
nbor->resize(inum,max_nbors,success);
}
/// Check if there is enough storage for neighbors and realloc if not
/** \param nlocal number of particles whose nbors must be stored on device
* \param host_inum number of particles whose nbors need to copied to host
* \param current maximum number of neighbors
* \note host_inum is 0 if the host is performing neighboring
* \note nlocal+host_inum=total number local particles
* \note olist_size=0 **/
inline void resize_local(const int inum, const int host_inum,
const int max_nbors, bool &success) {
nbor->resize(inum,host_inum,max_nbors,success);
}
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear_atomic();
/// Returns memory usage on device per atom
int bytes_per_atom_atomic(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage_atomic() const;
/// Accumulate timers
inline void acc_timers() {
if (device->time_device()) {
nbor->acc_timers(screen);
time_pair.add_to_total();
atom->acc_timers();
ans->acc_timers();
}
}
/// Zero timers
inline void zero_timers() {
time_pair.zero();
atom->zero_timers();
ans->zero_timers();
}
/// Copy neighbor list from host
int * reset_nbors(const int nall, const int inum, int *ilist, int *numj,
int **firstneigh, bool &success);
/// Build neighbor list on device
void build_nbor_list(const int inum, const int host_inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, bool &success);
/// Pair loop with host neighboring
void compute(const int f_ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
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);
/// Pair loop with device neighboring
int** compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **numj, const double cpu_time, bool &success,
double **v);
// -------------------------- DEVICE DATA -------------------------
/// Device Properties and Atom and Neighbor storage
Device<numtyp,acctyp> *device;
/// Geryon device
UCL_Device *ucl_device;
/// Device Timers
UCL_Timer time_pair;
/// Host device load balancer
Balance<numtyp,acctyp> hd_balancer;
/// LAMMPS pointer for screen output
FILE *screen;
// --------------------------- ATOM DATA --------------------------
/// Atom Data
Atom<numtyp,acctyp> *atom;
// ------------------------ FORCE/ENERGY DATA -----------------------
Answer<numtyp,acctyp> *ans;
// --------------------------- NBOR DATA ----------------------------
/// Neighbor data
Neighbor *nbor;
// ------------------------- DEVICE KERNELS -------------------------
UCL_Program *pair_program, *pair_program_noev;
UCL_Kernel k_pair_fast, k_pair, k_pair_noev, *k_pair_sel;
inline int block_size() { return _block_size; }
inline void set_kernel(const int eflag, const int vflag) {
#if defined(LAL_OCL_EV_JIT)
if (eflag || vflag) k_pair_sel = &k_pair_fast;
else k_pair_sel = &k_pair_noev;
#endif
}
// --------------------------- TEXTURES -----------------------------
UCL_Texture pos_tex;
UCL_Texture vel_tex;
// ------------------------- COMMON VARS ----------------------------
protected:
bool _compiled;
int _block_size, _threads_per_atom, _onetype, _extra_fields;
double _max_bytes, _max_an_bytes;
double _gpu_overhead, _driver_overhead;
UCL_D_Vec<int> *_nbor_data;
void compile_kernels(UCL_Device &dev, const void *pair_string,
const char *k, const int onetype);
virtual int loop(const int eflag, const int vflag) = 0;
};
}
#endif

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/***************************************************************************
coul_slater_long_ext.cpp
------------------------
Trung Nguyen (U Chicago)
Class for acceleration of the coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#if defined(USE_OPENCL)
#include "coul_slater_long_cl.h"
#elif defined(USE_CUDART)
const char *coul_slater_long=0;
#else
#include "coul_slater_long_cubin.h"
#endif
#include "lal_coul_slater_long.h"
#include <cassert>
namespace LAMMPS_AL {
#define CoulSlaterLongT CoulSlaterLong<numtyp, acctyp>
extern Device<PRECISION,ACC_PRECISION> pair_gpu_device;
template <class numtyp, class acctyp>
CoulSlaterLongT::CoulSlaterLong() : BaseCharge<numtyp,acctyp>(), _allocated(false) {
}
template <class numtyp, class acctyp>
CoulSlaterLongT::~CoulSlaterLong() {
clear();
}
template <class numtyp, class acctyp>
int CoulSlaterLongT::bytes_per_atom(const int max_nbors) const {
return this->bytes_per_atom_atomic(max_nbors);
}
template <class numtyp, class acctyp>
int CoulSlaterLongT::init(const int ntypes, double **host_scale,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *_screen,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, double lamda) {
int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
gpu_split,_screen,coul_slater_long,"k_coul_slater_long");
if (success!=0)
return success;
int lj_types=ntypes;
shared_types=false;
int max_shared_types=this->device->max_shared_types();
if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
lj_types=max_shared_types;
shared_types=true;
}
_lj_types=lj_types;
// Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<lj_types*lj_types; i++)
host_write[i]=0.0;
scale.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack1(ntypes,lj_types,scale,host_write,host_scale);
sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
for (int i=0; i<4; i++) {
host_write[i]=host_special_coul[i];
}
ucl_copy(sp_cl,host_write,4,false);
_cut_coulsq=host_cut_coulsq;
_qqrd2e=qqrd2e;
_g_ewald=g_ewald;
_lamda=lamda;
_allocated=true;
this->_max_bytes=scale.row_bytes()+sp_cl.row_bytes();
return 0;
}
template <class numtyp, class acctyp>
void CoulSlaterLongT::reinit(const int ntypes, double **host_scale) {
UCL_H_Vec<numtyp> hscale(_lj_types*_lj_types,*(this->ucl_device),
UCL_WRITE_ONLY);
this->atom->type_pack1(ntypes,_lj_types,scale,hscale,host_scale);
}
template <class numtyp, class acctyp>
void CoulSlaterLongT::clear() {
if (!_allocated)
return;
_allocated=false;
scale.clear();
sp_cl.clear();
this->clear_atomic();
}
template <class numtyp, class acctyp>
double CoulSlaterLongT::host_memory_usage() const {
return this->host_memory_usage_atomic()+sizeof(CoulSlaterLong<numtyp,acctyp>);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int CoulSlaterLongT::loop(const int eflag, const int vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
int ainum=this->ans->inum();
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
if (shared_types) {
this->k_pair_sel->set_size(GX,BX);
this->k_pair_sel->run(&this->atom->x, &scale, &sp_cl,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv,
&eflag, &vflag, &ainum, &nbor_pitch,
&this->atom->q, &_cut_coulsq, &_qqrd2e, &_g_ewald,
&_lamda, &this->_threads_per_atom);
} else {
this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &scale, &_lj_types, &sp_cl,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->ans->force, &this->ans->engv, &eflag, &vflag,
&ainum, &nbor_pitch, &this->atom->q, &_cut_coulsq,
&_qqrd2e, &_g_ewald, &_lamda, &this->_threads_per_atom);
}
this->time_pair.stop();
return GX;
}
template class CoulSlaterLong<PRECISION,ACC_PRECISION>;
}

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// **************************************************************************
// coul_slater_long.cu
// -------------------
// Trung Nguyen (U Chicago)
//
// Device code for acceleration of the coul/slater/long pair style
//
// __________________________________________________________________________
// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
// __________________________________________________________________________
//
// begin : September 2023
// email : ndactrung@gmail.com
// ***************************************************************************
#if defined(NV_KERNEL) || defined(USE_HIP)
#include "lal_aux_fun1.h"
#ifndef _DOUBLE_DOUBLE
_texture( pos_tex,float4);
_texture( q_tex,float);
#else
_texture_2d( pos_tex,int4);
_texture( q_tex,int2);
#endif
#else
#define pos_tex x_
#define q_tex q_
#endif
__kernel void k_coul_slater_long(const __global numtyp4 *restrict x_,
const __global numtyp *restrict scale,
const int lj_types,
const __global numtyp *restrict sp_cl_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp sp_cl[4];
int n_stride;
local_allocate_store_charge();
sp_cl[0]=sp_cl_in[0];
sp_cl[1]=sp_cl_in[1];
sp_cl[2]=sp_cl_in[2];
sp_cl[3]=sp_cl_in[3];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, virial[6];
if (EVFLAG) {
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
numtyp qtmp; fetch(qtmp,i,q_tex);
numtyp lamdainv = ucl_recip(lamda);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int jtype=jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
int mtype=itype*lj_types+jtype;
if (rsq < cut_coulsq) {
numtyp r2inv=ucl_recip(rsq);
numtyp force, prefactor, _erfc;
numtyp r = ucl_rsqrt(r2inv);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
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);
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)));
force = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force *= r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
acctyp energy;
if (EVFLAG) energy=(acctyp)0.0;
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}
__kernel void k_coul_slater_long_fast(const __global numtyp4 *restrict x_,
const __global numtyp *restrict scale_in,
const __global numtyp *restrict sp_cl_in,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp3 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag, const int inum,
const int nbor_pitch,
const __global numtyp *restrict q_,
const numtyp cut_coulsq, const numtyp qqrd2e,
const numtyp g_ewald, const numtyp lamda,
const int t_per_atom) {
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
__local numtyp scale[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_cl[4];
int n_stride;
local_allocate_store_charge();
if (tid<4)
sp_cl[tid]=sp_cl_in[tid];
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES)
scale[tid]=scale_in[tid];
acctyp3 f;
f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
acctyp e_coul, virial[6];
if (EVFLAG) {
e_coul=(acctyp)0;
for (int i=0; i<6; i++) virial[i]=(acctyp)0;
}
__syncthreads();
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
numtyp qtmp; fetch(qtmp,i,q_tex);
int iw=ix.w;
int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
numtyp lamdainv = ucl_recip(lamda);
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
numtyp factor_coul;
factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
int mtype=itype+jx.w;
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq < cut_coulsq) {
numtyp r2inv=ucl_recip(rsq);
numtyp force, prefactor, _erfc;
numtyp r = ucl_rsqrt(r2inv);
numtyp grij = g_ewald * r;
numtyp expm2 = ucl_exp(-grij*grij);
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)));
force = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
if (factor_coul > (numtyp)0) force -= factor_coul*prefactor*((numtyp)1.0-slater_term);
force *= r2inv;
f.x+=delx*force;
f.y+=dely*force;
f.z+=delz*force;
if (EVFLAG && eflag) {
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
numtyp e = prefactor*(_erfc-e_slater);
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
e_coul += e;
}
if (EVFLAG && vflag) {
virial[0] += delx*delx*force;
virial[1] += dely*dely*force;
virial[2] += delz*delz*force;
virial[3] += delx*dely*force;
virial[4] += delx*delz*force;
virial[5] += dely*delz*force;
}
}
} // for nbor
} // if ii
acctyp energy;
if (EVFLAG) energy=(acctyp)0.0;
store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
vflag,ans,engv);
}

82
lib/gpu/lal_coul_slater_long.h Normal file
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@ -0,0 +1,82 @@
/***************************************************************************
coul_slater_long.h
-------------------
Trung Nguyen (U Chicago)
Class for acceleration of the coul/slater/long pair style.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_Coul_Slater_Long_H
#define LAL_Coul_Slater_Long_H
#include "lal_base_charge.h"
namespace LAMMPS_AL {
template <class numtyp, class acctyp>
class CoulSlaterLong : public BaseCharge<numtyp, acctyp> {
public:
CoulSlaterLong();
~CoulSlaterLong();
/// Clear any previous data and set up for a new LAMMPS run
/** \param max_nbors initial number of rows in the neighbor matrix
* \param cell_size cutoff + skin
* \param gpu_split fraction of particles handled by device
*
* Returns:
* - 0 if successful
* - -1 if fix gpu not found
* - -3 if there is an out of memory error
* - -4 if the GPU library was not compiled for GPU
* - -5 Double precision is not supported on card **/
int init(const int ntypes, double **scale,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
const double gpu_split, FILE *screen,
const double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, const double lamda);
/// Send updated coeffs from host to device (to be compatible with fix adapt)
void reinit(const int ntypes, double **scale);
/// Clear all host and device data
/** \note This is called at the beginning of the init() routine **/
void clear();
/// Returns memory usage on device per atom
int bytes_per_atom(const int max_nbors) const;
/// Total host memory used by library for pair style
double host_memory_usage() const;
// --------------------------- TYPE DATA --------------------------
/// scale
UCL_D_Vec<numtyp> scale;
/// Special Coul values [0-3]
UCL_D_Vec<numtyp> sp_cl;
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
/// Number of atom types
int _lj_types;
numtyp _cut_coulsq, _qqrd2e, _g_ewald, _lamda;
protected:
bool _allocated;
int loop(const int eflag, const int vflag);
};
}
#endif

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@ -0,0 +1,145 @@
/***************************************************************************
coul_slater_long_ext.cpp
------------------------
Trung Nguyen (U Chicago)
Functions for LAMMPS access to coul/slater/long acceleration routines.
__________________________________________________________________________
This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
__________________________________________________________________________
begin : September 2023
email : ndactrung@gmail.com
***************************************************************************/
#include <iostream>
#include <cassert>
#include <cmath>
#include "lal_coul_slater_long.h"
using namespace std;
using namespace LAMMPS_AL;
static CoulSlaterLong<PRECISION,ACC_PRECISION> CSLMF;
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int csl_gpu_init(const int ntypes, double **host_scale,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald, const double lamda) {
CSLMF.clear();
gpu_mode=CSLMF.device->gpu_mode();
double gpu_split=CSLMF.device->particle_split();
int first_gpu=CSLMF.device->first_device();
int last_gpu=CSLMF.device->last_device();
int world_me=CSLMF.device->world_me();
int gpu_rank=CSLMF.device->gpu_rank();
int procs_per_gpu=CSLMF.device->procs_per_gpu();
CSLMF.device->init_message(screen,"coul/slater/long",first_gpu,last_gpu);
bool message=false;
if (CSLMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing Device and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=CSLMF.init(ntypes, host_scale, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_coulsq,
host_special_coul, qqrd2e, g_ewald, lamda);
CSLMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=CSLMF.init(ntypes, host_scale, inum, nall, max_nbors, maxspecial,
cell_size, gpu_split, screen, host_cut_coulsq,
host_special_coul, qqrd2e, g_ewald, lamda);
CSLMF.device->serialize_init();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
CSLMF.estimate_gpu_overhead();
return init_ok;
}
// ---------------------------------------------------------------------------
// Copy updated coeffs from host to device
// ---------------------------------------------------------------------------
void csl_gpu_reinit(const int ntypes, double **host_scale) {
int world_me=CSLMF.device->world_me();
int gpu_rank=CSLMF.device->gpu_rank();
int procs_per_gpu=CSLMF.device->procs_per_gpu();
if (world_me==0)
CSLMF.reinit(ntypes, host_scale);
CSLMF.device->world_barrier();
for (int i=0; i<procs_per_gpu; i++) {
if (gpu_rank==i && world_me!=0)
CSLMF.reinit(ntypes, host_scale);
CSLMF.device->serialize_init();
}
}
void csl_gpu_clear() {
CSLMF.clear();
}
int** csl_gpu_compute_n(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd) {
return CSLMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
host_q, boxlo, prd);
}
void csl_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd) {
CSLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,
firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success,
host_q,nlocal,boxlo,prd);
}
double csl_gpu_bytes() {
return CSLMF.host_memory_usage();
}

38
lib/gpu/lal_device.cpp
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@ -364,6 +364,12 @@ int DeviceT::init_device(MPI_Comm /*world*/, MPI_Comm replica, const int ngpu,
} else
_neighbor_shared.setup_auto_cell_size(false,_user_cell_size,_simd_size);
#ifndef LAL_USE_OLD_NEIGHBOR
_use_old_nbor_build = 0;
#else
_use_old_nbor_build = 1;
#endif
return flag;
}
@ -510,9 +516,13 @@ int DeviceT::init(Answer<numtyp,acctyp> &ans, const bool charge,
gpu_nbor=1;
else if (_gpu_mode==Device<numtyp,acctyp>::GPU_HYB_NEIGH)
gpu_nbor=2;
// NOTE: enforce the hybrid mode (binning on the CPU)
// when not using sorting on the device
#if !defined(USE_CUDPP) && !defined(USE_HIP_DEVICE_SORT)
if (gpu_nbor==1) gpu_nbor=2;
#endif
// or when the device supports subgroups
#ifndef LAL_USE_OLD_NEIGHBOR
if (gpu_nbor==1) gpu_nbor=2;
#endif
@ -886,19 +896,31 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
}
if (times[5] > 0.0)
fprintf(screen,"Device Overhead: %.4f s.\n",times[5]/_replica_size);
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Lanes / atom: %d.\n",threads_per_atom);
fprintf(screen,"Vector width: %d.\n", simd_size());
fprintf(screen,"Prefetch mode: ");
if (_nbor_prefetch==2) fprintf(screen,"Intrinsics.\n");
else if (_nbor_prefetch==1) fprintf(screen,"API.\n");
else fprintf(screen,"None.\n");
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
if (nbor.gpu_nbor()==2)
fprintf(screen,"CPU Neighbor: %.4f s.\n",times[8]/_replica_size);
fprintf(screen,"CPU Cast/Pack: %.4f s.\n",times[4]/_replica_size);
fprintf(screen,"CPU Driver_Time: %.4f s.\n",times[6]/_replica_size);
fprintf(screen,"CPU Idle_Time: %.4f s.\n",times[7]/_replica_size);
fprintf(screen,"Average split: %.4f.\n",avg_split);
fprintf(screen,"Max Mem / Proc: %.2f MB.\n",max_mb);
fprintf(screen,"Prefetch mode: ");
if (_nbor_prefetch==2) fprintf(screen,"Intrinsics.\n");
else if (_nbor_prefetch==1) fprintf(screen,"API.\n");
else fprintf(screen,"None.\n");
fprintf(screen,"Vector width: %d.\n", simd_size());
fprintf(screen,"Lanes / atom: %d.\n",threads_per_atom);
fprintf(screen,"Pair block: %d.\n",_block_pair);
fprintf(screen,"Neigh block: %d.\n",_block_nbor_build);
if (nbor.gpu_nbor()==2) {
fprintf(screen,"Neigh mode: Hybrid (binning on host)");
if (_use_old_nbor_build == 1) fprintf(screen," - legacy\n");
else fprintf(screen," with subgroup support\n");
} else if (nbor.gpu_nbor()==1) {
fprintf(screen,"Neigh mode: Device");
if (_use_old_nbor_build == 1) fprintf(screen," - legacy\n");
else fprintf(screen," - with subgroup support\n");
} else if (nbor.gpu_nbor()==0)
fprintf(screen,"Neigh mode: Host\n");
fprintf(screen,"-------------------------------------");
fprintf(screen,"--------------------------------\n\n");

1
lib/gpu/lal_device.h
View File

@ -347,6 +347,7 @@ class Device {
int _pppm_block, _block_nbor_build, _block_cell_2d, _block_cell_id;
int _max_shared_types, _max_bio_shared_types, _pppm_max_spline;
int _nbor_prefetch;
int _use_old_nbor_build;
UCL_Program *dev_program;
UCL_Kernel k_zero, k_info;

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