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Merge branch 'develop' of github.com:lammps/lammps into compute_reaxff_bonds_local

Browse Source
This commit is contained in:
Stan Gerald Moore
2023-12-13 11:14:45 -07:00
parent 0cf4c9e7a3 0c4a1cb21d
commit 37cb1ce30f
831 changed files with 65657 additions and 18727 deletions
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6
.github/CODEOWNERS vendored
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@ -153,12 +153,12 @@ tools/vim/* @hammondkd
unittest/* @akohlmey
# cmake
cmake/* @rbberger
cmake/* @akohlmey
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
cmake/Modules/Packages/KIM.cmake @ellio167
cmake/presets/*.cmake @akohlmey
# python

6
.github/workflows/coverity.yml vendored
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@ -59,16 +59,13 @@ jobs:
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=SMALLBIG \
-D LAMMPS_EXCEPTIONS=off \
-D PKG_MESSAGE=on \
-D PKG_MPIIO=on \
-D PKG_ATC=on \
-D PKG_AWPMD=on \
-D PKG_BOCS=on \
-D PKG_EFF=on \
-D PKG_H5MD=on \
-D PKG_INTEL=on \
-D PKG_LATBOLTZ=on \
-D PKG_MANIFOLD=on \
-D PKG_MDI=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
@ -77,7 +74,6 @@ jobs:
-D PKG_PTM=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-D PKG_TALLY=on \
../cmake
- name: Run Coverity Scan

35
cmake/CMakeLists.txt
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@ -2,7 +2,6 @@
########################################
# CMake build system
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.16)
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
@ -106,7 +105,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
endif()
endif()
endif()
@ -428,6 +427,18 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
# lower C++ standard for fmtlib sources when using Intel classic compiler
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
PROPERTIES COMPILE_OPTIONS "-std=c++14")
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
@ -960,6 +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)
@ -972,6 +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")
@ -989,6 +1019,7 @@ if(PKG_KSPACE)
message(STATUS "Kokkos FFT: ${FFT}")
endif()
endif()
endif()
endif()
if(BUILD_DOC)
message(STATUS "<<< Building HTML Manual >>>")

4
cmake/Modules/LAMMPSUtils.cmake
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@ -83,12 +83,12 @@ function(check_for_autogen_files source_dir)
file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES})
get_filename_component(FILENAME "${_SRC}" NAME)
if(EXISTS ${source_dir}/${FILENAME})
message(FATAL_ERROR "\n########################################################################\n"
"Found header file(s) generated by the make-based build system\n"
"Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
"\n"
"Please run\n"
"make -C ${source_dir} purge\n"

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)

6
cmake/Modules/Packages/KOKKOS.cmake
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@ -50,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.2.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "731647b61a4233f568d583702e9cd6d1" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -76,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.1.00 REQUIRED CONFIG)
find_package(Kokkos 4.2.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

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})

31
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,15 +1,20 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# download library sources to build folder
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
# to make it easier to check local build without going through the public github releases
if(LOCAL_ML-PACE)
set(lib-pace "${LOCAL_ML-PACE}")
else()
# download library sources to build folder
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(STATUS "Downloading ${PACELIB_URL}")
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
@ -17,17 +22,19 @@ if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
endif()
else()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
endif()
# uncompress downloaded sources
execute_process(
# uncompress downloaded sources
execute_process(
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

11
cmake/presets/gpu-cuda.cmake Normal file
View File

@ -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)

2
cmake/presets/kokkos-cuda.cmake
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@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 August 2023" "2023-08-2"
.TH LAMMPS "1" "21 November 2023" "2023-11-21"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 August 2023
\- Molecular Dynamics Simulator. Version 21 November 2023
.SH SYNOPSIS
.B lmp

22
doc/src/Build_extras.rst
View File

@ -626,22 +626,22 @@ They must be specified in uppercase.
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
* - VEGA900
* - AMD_GFX906
- GPU
- AMD GPU MI25 GFX900
* - VEGA906
- AMD GPU MI50/MI60
* - AMD_GFX908
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI100 GFX908
* - VEGA90A
- AMD GPU MI200
* - AMD_GFX942
- GPU
- AMD GPU MI200 GFX90A
* - NAVI1030
- AMD GPU MI300
* - AMD_GFX1030
- GPU
- AMD GPU V620/W6800
* - NAVI1100
* - AMD_GFX1100
- GPU
- AMD GPU RX7900XTX
* - INTEL_GEN
@ -666,7 +666,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.0.1 of the Kokkos library.
This list was last updated for version 4.2 of the Kokkos library.
.. tabs::

44
doc/src/Build_settings.rst
View File

@ -43,6 +43,12 @@ When the KSPACE package is included in a LAMMPS build, the
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.
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 2D and 3D backend transforms and
better pipelining for packing and communication.
.. tabs::
@ -53,6 +59,7 @@ 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 +83,15 @@ 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 backend
-D Heffte_ROOT=path # path to an existing heFFTe installation
.. note::
heFFTe comes with a builtin stock backend for FFTs; however, the backend
is intended for testing purposes and is not performance optimized
for large scale production runs.
.. tab:: Traditional make
@ -111,6 +127,24 @@ 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 backend, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
omitting the variable will default to the `stock` backend.
The heFFTe `stock` backend 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 +204,16 @@ 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 backend (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:

4
doc/src/Commands_compute.rst
View File

@ -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>`
@ -115,8 +116,9 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`property/grid <compute_property_grid>`
* :doc:`property/local <compute_property_local>`
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`reaxff/atom (k) <compute_reaxff_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>`

5
doc/src/Commands_fix.rst
View File

@ -122,6 +122,7 @@ OPT.
* :doc:`mvv/tdpd <fix_mvv_dpd>`
* :doc:`neb <fix_neb>`
* :doc:`neb/spin <fix_neb_spin>`
* :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
* :doc:`nph (ko) <fix_nh>`
* :doc:`nph/asphere (o) <fix_nph_asphere>`
* :doc:`nph/body <fix_nph_body>`
@ -238,10 +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>`

15
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@ -88,7 +88,7 @@ The same functionality is available through
MPIIO package
-------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
@ -107,7 +107,7 @@ see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
MSCG package
------------
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
@ -126,6 +126,17 @@ syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-REAXC package
------------------
.. deprecated:: TBD
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
USER-CUDA package
-----------------

18
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@ -180,19 +180,11 @@ discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
environment variable, ``TEST_ARGS=-v``) it can be printed and used to
understand why tests fail unexpectedly.
Another complexity of these tests stems from the need to capture
situations where LAMMPS will stop with an error, i.e. handle so-called
"death tests". Here the LAMMPS code will operate differently depending
on whether it was configured to throw C++ exceptions on errors or call
either ``exit()`` or ``MPI_Abort()``. In the latter case, the test code
also needs to detect whether LAMMPS was compiled with the OpenMPI
library, as OpenMPI is **only** compatible the death test options of the
GoogleTest library when C++ exceptions are enabled; otherwise those
"death tests" must be skipped to avoid reporting bogus failures. The
specifics of this step are implemented in the ``TEST_FAILURE()``
macro. These tests operate by capturing the screen output when executing
the failing command and then comparing that with a provided regular
expression string pattern. Example:
The specifics of so-called "death tests", i.e. conditions where LAMMPS
should fail and throw an exception, are implemented in the
``TEST_FAILURE()`` macro. These tests operate by capturing the screen
output when executing the failing command and then comparing that with a
provided regular expression string pattern. Example:
.. code-block:: c++

15
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@ -3038,14 +3038,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
This function can be used to query if an error inside of LAMMPS
has thrown a :ref:`C++ exception <exceptions>`.
.. note::
This function will always report "no error" when the LAMMPS library
has been compiled without ``-DLAMMPS_EXCEPTIONS``, which turns fatal
errors aborting LAMMPS into C++ exceptions. You can use the library
function :cpp:func:`lammps_config_has_exceptions` to check if this is
the case.
:to: :cpp:func:`lammps_has_error`
:r has_error: ``.TRUE.`` if there is an error.
:rtype has_error: logical
@ -3068,13 +3060,6 @@ Procedures Bound to the :f:type:`lammps` Derived Type
would happen only in a single MPI rank and thus may not be recoverable, as
other MPI ranks may be waiting on the failing MPI rank(s) to send messages.
.. note::
This function will do nothing when the LAMMPS library has been
compiled without ``-DLAMMPS_EXCEPTIONS``, which turns errors aborting
LAMMPS into C++ exceptions. You can use the function
:f:func:`config_has_exceptions` to check whether this is the case.
:p character(len=\*) buffer: string buffer to copy the error message into
:o integer(c_int) status [optional]: 1 when all ranks had the error,
2 on a single-rank error.

1
doc/src/Howto.rst
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@ -101,6 +101,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_lammps_gui
Howto_moltemplate
Howto_pylammps
Howto_wsl

2
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@ -335,7 +335,7 @@ faces are listed, so that M = 6 + 3\*N + 1.
The integer line has three values: number of vertices (N), number of
edges (E) and number of faces (F). The floating point line(s) list 6
moments of inertia followed by the coordinates of the N vertices (x1
to zN) as 3N values, followed by 2N vertex indices corresponding to
to zN) as 3N values, followed by 2E vertex indices corresponding to
the end points of the E edges, then 4\*F vertex indices defining F
faces. The last value is the diameter value = the rounded diameter of
the sphere that surrounds each vertex. The diameter value can be

371
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@ -0,0 +1,371 @@
Moltemplate Tutorial
====================
In this tutorial, we are going to use the tool :ref:`Moltemplate
<moltemplate>` to set up a classical molecular dynamic simulation using
the :ref:`OPLS-AA force field <OPLSAA96>`. The first
task is to describe an organic compound and create a complete input deck
for LAMMPS. The second task is to map the OPLS-AA force field to a
molecular sample created with an external tool, e.g. PACKMOL, and
exported as a PDB file. The files used in this tutorial can be found
in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
source code distribution.
Simulating an organic solvent
"""""""""""""""""""""""""""""
This example aims to create a cubic box of the organic solvent
formamide.
The first step is to create a molecular topology in the
LAMMPS-template (LT) file format representing a single molecule, which
will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
This command states that the object ``_FAM`` is based on an existing
object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
definitions, partial charges, masses and bond-angle rules for many organic
and biological compounds.
The atomic structure is the starting point to populate the command
``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
therefore, this column format is used:
``# atomID molID atomType charge coordX coordY coordZ``.
The ``atomID``\ s are replaced with Moltemplate ``$``-type variables, which
are then substituted with unique numerical IDs. The same logic is applied
to the ``molID``, except that the same variable is used for the whole
molecule. The atom types are assigned using ``@``-type variables. The
assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
the OPLS-AA atom types defined in the "In Charges" section of the file
``oplsaa.lt``, looking for a reasonable match with the description of the atom.
The resulting file (``formamide.lt``) follows:
.. code-block:: bash
_FAM inherits OPLSAA {
# atomID molID atomType charge coordX coordY coordZ
write('Data Atoms') {
$atom:C00 $mol @atom:177 0.00 0.100 0.490 0.0
$atom:O01 $mol @atom:178 0.00 1.091 -0.250 0.0
$atom:N02 $mol @atom:179 0.00 -1.121 -0.181 0.0
$atom:H03 $mol @atom:182 0.00 -2.013 0.272 0.0
$atom:H04 $mol @atom:182 0.00 -1.056 -1.190 0.0
$atom:H05 $mol @atom:221 0.00 0.144 1.570 0.0
}
# A list of the bonds in the molecule:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:C1 $atom:C00 $atom:O01
$bond:C2 $atom:C00 $atom:H05
$bond:C3 $atom:C00 $atom:N02
$bond:C4 $atom:N02 $atom:H03
$bond:C5 $atom:N02 $atom:H04
}
}
You don't have to specify the charge in this example because they will
be assigned according to the atom type. Analogously, only a
"Data Bond List" section is needed as the atom type will determine the
bond type. The other bonded interactions (e.g. angles,
dihedrals, and impropers) will be automatically generated by
Moltemplate.
If the simulation is non-neutral, or Moltemplate complains that you have
missing bond, angle, or dihedral types, this means at least one of your
atom types is incorrect.
The second step is to create a master file with instructions to build a
starting structure and the LAMMPS commands to run an NPT simulation. The
master file (``solv_01.lt``) follows:
.. code-block:: bash
# Import the force field.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import formamide.lt # after oplsaa.lt, as it depends on it.
# Create the input sample.
solv = new _FAM [5].move( 4.6, 0, 0)
[5].move( 0, 4.6, 0)
[5].move( 0, 0, 4.6)
solv[*][*][*].move(-11.5, -11.5, -11.5)
# Set the simulation box.
write_once("Data Boundary") {
-11.5 11.5 xlo xhi
-11.5 11.5 ylo yhi
-11.5 11.5 zlo zhi
}
# Create an input deck for LAMMPS.
write_once("In Init"){
# Input variables.
variable run string solv_01 # output name
variable ts equal 1 # timestep
variable temp equal 300 # equilibrium temperature
variable p equal 1. # equilibrium pressure
variable d equal 1000 # output frequency
variable equi equal 5000 # Equilibration steps
variable prod equal 30000 # Production steps
# PBC (set them before the creation of the box).
boundary p p p
}
# Run an NPT simulation.
write_once("In Run"){
# Derived variables.
variable tcouple equal \$\{ts\}*100
variable pcouple equal \$\{ts\}*1000
# Output.
thermo \$d
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
edihed eimp ke pe temp press vol density cpu
thermo_modify flush yes
# Trajectory.
dump TRJ all dcd \$d \$\{run\}.dcd
dump_modify TRJ unwrap yes
# Thermalisation and relaxation, NPT ensemble.
timestep \$\{ts\}
fix NPT all npt temp \$\{temp\} \$\{temp\} \$\{tcouple\} iso \$p \$p \$\{pcouple\}
velocity all create \$\{temp\} 858096 dist gaussian
# Short runs to update the PPPM settings as the box shinks.
run \$\{equi\} post no
run \$\{equi\} post no
run \$\{equi\} post no
run \$\{equi\}
# From now on, the density shouldn't change too much.
run \$\{prod\}
unfix NPT
}
The first two commands insert the content of files ``oplsaa.lt`` and
``formamide.lt`` into the master file. At this point, we can use the
command ``solv = new _FAM [N]`` to create N copies of a molecule of type
``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
grid using the coordinate transformation command ``.move( 4.6, 0, 0)``.
See the Moltemplate documentation to learn more about the syntax. As
the sample was created from scratch, we also specify the simulation box
size in the "Data Boundary" section.
The LAMMPS setting for the force field are specified in the file
``oplsaa.lt`` and are written automatically in the input deck. We also
specify the boundary conditions and a set of variables in
the "In Init" section. The remaining commands to run an NPT simulation
are written in the "In Run" section. Note that in this script, LAMMPS
variables are protected with the escape character ``\`` to distinguish
them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
variable that is written in the input deck as ``${run}``.
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all solv_01.lt
And execute the simulation with the following:
.. code-block:: bash
mpirun -np 4 lmp -in solv_01.in -l solv_01.log
.. figure:: JPG/solv_01.png
:figwidth: 80%
:figclass: align-center
Snapshot of the sample at the beginning and end of the simulation.
Rendered with Ovito.
Mapping an existing structure
"""""""""""""""""""""""""""""
Another helpful way to use Moltemplate is mapping an existing molecular
sample to a force field. This is useful when a complex sample is
assembled from different simulations or created with specialized
software (e.g. PACKMOL). As in the previous example, all molecular
species in the sample must be defined using single-molecule Moltemplate
objects. For this example, we use a short polymer in a box containing
water molecules and ions in the PDB file ``model.pdb``.
It is essential to understand that the order of atoms in the PDB file
and in the Moltemplate master script must match, as we are using the
coordinates from the PDB file in the order they appear. The order of
atoms and molecules in the PDB file provided is as follows:
- 500 water molecules, with atoms ordered in this sequence:
.. parsed-literal::
ATOM 1 O MOL D 1 5.901 7.384 1.103 0.00 0.00 DUM
ATOM 2 H MOL D 1 6.047 8.238 0.581 0.00 0.00 DUM
ATOM 3 H MOL D 1 6.188 7.533 2.057 0.00 0.00 DUM
- 1 polymer molecule.
- 1 Ca\ :sup:`2+` ion.
- 2 Cl\ :sup:`-` ions.
In the master LT file, this sequence of molecules is matched with the
following commands:
.. code-block:: bash
# Create the sample.
wat=new SPC[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
Note that the first command would create 500 water molecules in the
same position in space, and the other commands will use the coordinates
specified in the corresponding molecular topology block. However, the
coordinates will be overwritten by rendering an external atomic
structure file. Note that if the same molecule species are scattered in
the input structure, it is recommended to reorder and group together
for molecule types to facilitate the creation of the input sample.
The molecular topology for the polymer is created as in the previous
example, with the atom types assigned as in the following schema:
.. figure:: JPG/PolyNIPAM.jpg
:scale: 30%
:align: center
Atom types assigned to the polymer's repeating unit.
The molecular topology of the water and ions is stated directly into
the master file for the sake of space, but they could also be written
in a separate file(s) and imported before the sample is created.
The resulting master LT file defining short annealing at a fixed volume
(NVT) follows:
.. code-block:: bash
# Use the OPLS-AA force field for all species.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import PolyNIPAM.lt
# Define the SPC water and ions as in the OPLS-AA
Ca inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
}
}
Cl inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
}
}
SPC inherits OPLSAA {
write("Data Atoms"){
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
}
write("Data Bond List") {
$bond:OH1 $atom:O $atom:H1
$bond:OH2 $atom:O $atom:H2
}
}
# Create the sample.
wat=new SPC[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]
# Periodic boundary conditions:
write_once("Data Boundary"){
0 26 xlo xhi
0 26 ylo yhi
0 26 zlo zhi
}
# Define the input variables.
write_once("In Init"){
# Input variables.
variable run string sample01 # output name
variable ts equal 2 # timestep
variable temp equal 298.15 # equilibrium temperature
variable p equal 1. # equilibrium pressure
variable equi equal 30000 # equilibration steps
# PBC (set them before the creation of the box).
boundary p p p
neighbor 3 bin
}
# Run an NVT simulation.
write_once("In Run"){
# Set the output.
thermo 1000
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
edihed eimp pe ke temp press atoms vol density cpu
thermo_modify flush yes
compute pe1 all pe/atom pair
dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1
# Minimise the input structure, just in case.
minimize .01 .001 1000 100000
write_data \$\{run\}.min
# Set the constrains.
group watergroup type @atom:76 @atom:77
fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
# Short annealing.
timestep \$\{ts\}
fix 1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
velocity all create \$\{temp\} 315443
run \$\{equi\}
unfix 1
}
In this example, the water model is SPC and it is defined in the
``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``. For
water we also use the ``group`` and ``fix shake`` commands with
Moltemplate ``@``-type variables, to ensure consistency with the
numerical values assigned during compilation. To identify the bond and
angle types, look for the extended ``@atom`` IDs, which in this case
are:
.. code-block:: bash
replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
From which we can identify the following "Data Bonds By Type":
``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
And execute the simulation with the following:
.. code-block:: bash
mpirun -np 4 lmp -in sample01.in -l sample01.log
.. figure:: JPG/sample01.png
:figwidth: 50%
:figclass: align-center
Sample visualized with Ovito loading the trajectory into the DATA
file written after minimization.
------------
.. _OPLSAA96:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
118(45), 11225-11236 (1996).

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@ -80,13 +80,15 @@ run LAMMPS in serial mode.
:class: note
If the LAMMPS executable encounters an error condition, it will abort
after printing an error message. For a library interface this is
usually not desirable. Thus LAMMPS can be compiled to to :ref:`throw
a C++ exception <exceptions>` instead. If enabled, the library
functions will catch those exceptions and return. The error status
:cpp:func:`can be queried <lammps_has_error>` and an :cpp:func:`error
message retrieved <lammps_get_last_error_message>`. We thus
recommend enabling C++ exceptions when using the library interface,
after printing an error message. It does so by catching the
exceptions that LAMMPS could throw. For a C library interface this
is usually not desirable since the calling code might lack the
ability to catch such exceptions. Thus, the library functions will
catch those exceptions and return from the affected functions. The
error status :cpp:func:`can be queried <lammps_has_error>` and an
:cpp:func:`error message retrieved <lammps_get_last_error_message>`.
This is, for example used by the :doc:`LAMMPS python module
<Python_module>` and then a suitable Python exception is thrown.
.. admonition:: Using the C library interface as a plugin
:class: note

4
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@ -15,9 +15,7 @@ Python exception handling mechanism.
try:
# LAMMPS will normally terminate itself and the running process if an error
# occurs. This would kill the Python interpreter. To avoid this, make sure to
# compile with LAMMPS_EXCEPTIONS enabled. This ensures the library API calls
# will not terminate the parent process. Instead, the library wrapper will
# occurs. This would kill the Python interpreter. The library wrapper will
# detect that an error has occured and throw a Python exception
lmp.command('unknown')

3
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@ -5,8 +5,7 @@ The LAMMPS Python module enables calling the :ref:`LAMMPS C library API
<lammps_c_api>` from Python by dynamically loading functions in the
LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`. It is also recommended to
compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
compiled in :ref:`"shared" mode <exe>`.
Two components are necessary for Python to be able to invoke LAMMPS code:

2
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
@ -279,6 +280,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
* :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

2
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@ -36,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 21Nov2023
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,

9
doc/src/compute_contact_atom.rst
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@ -36,6 +36,9 @@ sum of the radii of the two particles.
The value of the contact number will be 0.0 for atoms not in the
specified compute group.
The optional *group2-ID* argument allows to specify from which group atoms
contribute to the coordination number. Default setting is group 'all'.
Output info
"""""""""""
@ -47,9 +50,6 @@ overview of LAMMPS output options.
The per-atom vector values will be a number :math:`\ge 0.0`, as explained
above.
The optional *group2-ID* argument allows to specify from which group atoms
contribute to the coordination number. Default setting is group 'all.'
Restrictions
""""""""""""
@ -69,6 +69,3 @@ Default
"""""""
*group2-ID* = all
none

251
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@ -0,0 +1,251 @@
.. 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 hyperparameters, 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
a highly generalizable atomic descriptor, 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>`. et. al, 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 hyperparameters 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).

6
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@ -128,9 +128,9 @@ Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these attributes. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
which are the "name" portion of these attributes. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
The additional quantities only accessible via this command, and not
directly via the :doc:`dump custom <dump>` command, are as follows.

2
doc/src/compute_property_grid.rst
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@ -61,7 +61,7 @@ varying fastest, then Y, then Z slowest. For 2d grids (in 2d
simulations), the grid IDs range from 1 to Nx*Ny, with X varying
fastest and Y slowest.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *proc* attribute is the ID of the processor which owns the grid
cell. Processor IDs range from 0 to Nprocs - 1, where Nprocs is the

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@ -0,0 +1,92 @@
.. index:: compute rattlers/atom
compute rattlers/atom command
========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID rattlers/atom cutoff zmin ntries
* ID, group-ID are documented in :doc:`compute <compute>` command
* rattlers/atom = style name of this compute command
* cutoff = *type* or *radius*
.. parsed-literal::
*type* = cutoffs determined based on atom types
*radius* = cutoffs determined based on atom diameters (atom style sphere)
* zmin = minimum coordination for a non-rattler atom
* ntries = maximum number of iterations to remove rattlers
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all rattlers/atom type 4 10
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
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
helpful for excluding them from analysis or providing extra damping forces
to accelerate relaxation processes.
Rattlers are identified using an interactive approach. The coordination
number of all atoms is first calculated. The *type* and *radius* settings
are used to select whether interaction cutoffs are determined by atom
types or by the sum of atomic radii (atom style sphere), respectively.
Rattlers are then identified as atoms with a coordination number less
than *zmin* and are removed from consideration. Atomic coordination
numbers are then recalculated, excluding previously identified rattlers,
to identify a new set of rattlers. This process is iterated up to a maximum
of *ntries* or until no new rattlers are identified and the remaining
atoms form a stable network of contacts.
In dense homogeneous systems where the average atom coordination number
is expected to be larger than *zmin*, this process usually only takes a few
iterations and a value of *ntries* around ten may be sufficient. In systems
with significant heterogeneity or average coordination numbers less than
*zmin*, an appropriate value of *ntries* depends heavily on the specific
system. For instance, a linear chain of N rattler atoms with a *zmin* of 2
would take N/2 iterations to identify that all the atoms are rattlers.
Output info
"""""""""""
This compute calculates a per-atom vector and a global scalar. The vector
designates which atoms are rattlers, indicated by a value 1. Non-rattlers
have a value of 0. The global scalar returns the total number of rattlers
in the system. 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.
The *radius* cutoff option requires that atoms store a radius as defined by the
:doc:`atom_style sphere <atom_style>` or similar commands.
Related commands
""""""""""""""""
:doc:`compute coord/atom <compute_coord_atom>`
:doc:`compute contact/atom <compute_contact_atom>`
Default
"""""""
none

2
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@ -201,7 +201,7 @@ information in this context, the *replace* keywords will extract the
atom IDs for the two atoms in the bond of maximum stretch. These atom
IDs and the bond stretch will be printed with thermodynamic output.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *inputs* keyword allows selection of whether all the inputs are
per-atom or local quantities. As noted above, all the inputs must be

2
doc/src/compute_voronoi_atom.rst
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@ -190,7 +190,7 @@ Voro++ software in the src/VORONOI/README file.
Output info
"""""""""""
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The *peratom* keyword was removed as it is no longer required.

29
doc/src/compute_xrd.rst
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@ -62,28 +62,29 @@ equations:
\frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
:math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering
factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
scattering angle of diffraction. The Lorentz-polarization factor can be turned
off using the optional *LP* keyword.
:math:`r_j` is the position of each atom, :math:`f_j` are atomic
scattering factors, *Lp* is the Lorentz-polarization factor, and
:math:`\theta` is the scattering angle of diffraction. The
Lorentz-polarization factor can be turned off using the optional *LP*
keyword.
Diffraction intensities are calculated on a three-dimensional mesh of
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.
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/xrd_mesh.jpg
.. image:: img/xrd_mesh.png
:scale: 75%
:align: center
For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
axis, where :math:`A` is a matrix containing the vectors corresponding to the
edges of the simulation cell. If one or two directions has non-periodic
boundary conditions, then the spacing in these directions is defined from the
average of the (inversed) box lengths with periodic boundary conditions.
Meshes defined by the simulation domain must contain at least one periodic
boundary.
axis, where :math:`A` is a matrix containing the vectors corresponding
to the edges of the simulation cell. If one or two directions has
non-periodic boundary conditions, then the spacing in these directions
is defined from the average of the (inversed) box lengths with periodic
boundary conditions. Meshes defined by the simulation domain must
contain at least one periodic boundary.
If the *manual* flag is included, the mesh of reciprocal lattice nodes
will be defined using the *c* values for the spacing along each

22
doc/src/dump.rst
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@ -613,7 +613,7 @@ when running on large numbers of processors.
Note that using the "\*" and "%" characters together can produce a
large number of small dump files!
.. deprecated:: TBD
.. deprecated:: 21Nov2023
The MPIIO package and the the corresponding "/mpiio" dump styles, except
for the unrelated "netcdf/mpiio" style were removed from LAMMPS.
@ -805,16 +805,16 @@ computes, fixes, or variables when they are evaluated, so this is a very
general means of creating quantities to output to a dump file.
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
in the range from 1 to :math:`M`, where :math:`M` is the number of
columns in the custom array). See the discussion above for how :math:`i`
can be specified with a wildcard asterisk to effectively specify
multiple values.
custom per-atom integer and floating-point vectors or arrays that have
been added via the :doc:`fix property/atom <fix_property_atom>`
command. When that command is used specific names are given to each
attribute which are the "name" portion of these keywords. For arrays
*i2_name* and *d2_name*, the column of the array must also be included
following the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where
:math:`i` is in the range from 1 to :math:`M`, where :math:`M` is the
number of columns in the custom array). See the discussion above for
how :math:`i` can be specified with a wildcard asterisk to effectively
specify multiple values.
See the :doc:`Modify <Modify>` page for information on how to add
new compute and fix styles to LAMMPS to calculate per-atom quantities

2
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@ -599,7 +599,7 @@ image will appear. The *sfactor* value must be a value 0.0 <=
*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface
and *sfactor* = 0 is a rough non-shiny surface.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *fsaa* keyword can be used with the dump image command to improve
the image quality by enabling full scene anti-aliasing. Internally the

1
doc/src/fix.rst
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@ -287,6 +287,7 @@ accelerated styles exist.
* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
* :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
* :doc:`nph/body <fix_nph_body>` - NPH for body particles

26
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@ -205,6 +205,8 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`quip <pair_quip>` | scale | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`snap <pair_snap>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
@ -315,21 +317,21 @@ Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+------------------------------------+-------+-----------------+
+------------------------------------+------------+------------+
----------
@ -353,11 +355,11 @@ Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
+------------------------------------+----------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+-------+-----------------+
+------------------------------------+----------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+-------+-----------------+
+------------------------------------+----------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.
@ -482,7 +484,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute ti <compute_ti>`
:doc:`compute ti <compute_ti>`, :doc:`fix adapt/fep <fix_adapt_fep>`
Default
"""""""

4
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@ -307,7 +307,9 @@ the :doc:`run <run>` command. This fix is not invoked during
Restrictions
""""""""""""
none
The keyword "scale yes" is not supported for scaling per-atom parameters
diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
Related commands
""""""""""""""""

6
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@ -181,6 +181,12 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
This fix cannot be used with systems that do not have per-type masses
(e.g. atom style sphere) since the implemented algorithm pre-computes
velocity rescaling factors from per-type masses and ignores any per-atom
masses, if present. In case both, per-type and per-atom masses are
present, a warning is printed.
Related commands
""""""""""""""""

2
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@ -220,7 +220,7 @@ rotated configuration of the molecule.
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
The *var* and *set* keywords can be used together to provide a criterion
for accepting or rejecting the addition of an individual atom, based on its

4
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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

133
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@ -0,0 +1,133 @@
.. index:: fix nonaffine/displacement
fix nonaffine/displacement command
==================================
Syntax
""""""
.. parsed-literal::
fix ID group nonaffine/displacement style args reference/style nstep
* ID, group are documented in :doc:`fix <fix>` command
* nonaffine/displacement = style name of this fix command
* nevery = calculate nonaffine displacement every this many timesteps
* style = *d2min* or *integrated*
.. parsed-literal::
*d2min* args = cutoff args
cutoff = *type* or *radius* or *custom*
*type* args = none, cutoffs determined by atom types
*radius* args = none, cutoffs determined based on atom diameters (atom style sphere)
*custom* args = *rmax*, cutoff set by a constant numeric value *rmax* (distance units)
*integrated* args = none
* reference/style = *fixed* or *update* or *offset*
.. parsed-literal::
*fixed* = use a fixed reference frame at *nstep*
*update* = update the reference frame every *nstep* timesteps
*offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all nonaffine/displacement 100 integrated update 100
fix 1 all nonaffine/displacement 1000 d2min type fixed 0
fix 1 all nonaffine/displacement 1000 d2min custom 2.0 offset 100
Description
"""""""""""
.. versionadded:: TBD
This fix computes different metrics of the nonaffine displacement of
particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`
nonaffine displacement by Falk and Langer in :ref:`(Falk) <d2min-Falk>`.
For each atom, the fix computes the two tensors
.. math::
X = \sum_{\mathrm{neighbors}} \vec{r} \left(\vec{r}_{0} \right)^T
and
.. math::
Y = \sum_{\mathrm{neighbors}} \vec{r}_0 \left(\vec{r}_{0} \right)^T
where the neighbors include all other atoms within the distance criterion
set by the cutoff option, discussed below, :math:`\vec{r}` is the current
displacement between particles, and :math:`\vec{r}_0` is the reference
displacement. A deformation gradient tensor is then calculated as
:math:`F = X Y^{-1}` from which
.. math::
D^2_\mathrm{min} = \sum_{\mathrm{neighbors}} \left| \vec{r} - F \vec{r}_0 \right|^2
and a strain tensor is calculated :math:`E = F F^{T} - I` where :math:`I`
is the identity tensor. This calculation is only performed on timesteps that
are a multiple of *nevery* (including timestep zero). Data accessed before
this occurs will simply be zeroed.
The *integrated* style simply integrates the velocity of particles
every timestep to calculate a displacement. This style only works if
used in conjunction with another fix that deforms the box and displaces
atom positions such as :doc:`fix deform <fix_deform>` with remap x,
:doc:`fix press/berendsen <fix_press_berendsen>`, or :doc:`fix nh <fix_nh>`.
Both of these methods require defining a reference state. With the *fixed* reference
style, the user picks a specific timestep *nstep* at which particle positions are saved.
If peratom data is accessed from this compute prior to this timestep, it will simply be
zeroed. The *update* reference style implies the reference state will be updated every
*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The reference state is saved to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.
This fix computes a peratom array with 3 columns, which can be accessed
by indices 1-3 using any command that uses per-atom values from a fix
as input.
For the *integrated* style, the three columns are the nonaffine
displacements in the x, y, and z directions. For the *d2min* style,
the three columns are the calculated :math:`\sqrt{D^2_\mathrm{min}}`, the
volumetric strain, and the deviatoric strain.
Restrictions
""""""""""""
This compute is part of the EXTRA-FIX 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
""""""""""""""""
none
Default
"""""""
none
----------
.. _d2min-Falk:
**(Falk)** Falk and Langer PRE, 57, 7192 (1998).

2
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@ -149,7 +149,7 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
only the k > 0 modes are thermostatted, not the centroid degrees of
freedom.
.. versionadded:: TBD
.. versionadded:: 21Nov2023
Mode *pimd* added to fix pimd/langevin.

4
doc/src/fix_rigid.rst
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@ -80,7 +80,7 @@ Syntax
groupID1, groupID2, ... = list of N group IDs
* zero or more keyword/value pairs may be appended
* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
* keyword = *langevin* or *reinit* or *temp* or *mol* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
.. parsed-literal::
@ -92,6 +92,8 @@ Syntax
*temp* values = Tstart Tstop Tdamp
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
*mol* value = template-ID
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
*iso* or *aniso* values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)

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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@ -154,21 +154,25 @@ These are the recognized header keywords. Header lines can come in
any order. The numeric value(s) are read from the beginning of the
line. The keyword should appear at the end of the line. All these
settings have default values, as explained below. A line need only
appear if the value(s) are different than the default.
appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values in body
particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consists of a set of point particles or finite-size particles (with a
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
@ -188,6 +192,7 @@ These are the allowed section keywords for the body of the file.
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
* *Body Integers, Body Doubles* = body-property sections
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
atom/bond/angle/etc type can be specified either as a number (numeric
@ -515,6 +520,67 @@ of SHAKE clusters.
----------
*Body Integers* section:
* one line
* line syntax: N E F
* N = number of sub-particles or number or vertices
* E,F = number of edges and faces
This section is only needed when the molecule is a body particle. the other
Body section must also appear in the file.
The total number of values that must appear is determined by the body style, and
must be equal to the Ninteger value given in the *body* header.
For *nparticle* and *rounded/polygon*, only the number of sub-particles or
vertices N is required, and Ninteger should have a value of 1.
For *rounded/polyhedron*, the number of edges E and faces F is required, and
Ninteger should have a value of 3.
See the :doc:`Howto body <Howto_body>` page for a further description of
the file format.
----------
*Body Doubles* section:
* first line
* line syntax: Ixx Iyy Izz Ixy Ixz Iyz
* Ixx Iyy Izz Ixy Ixz Iyz = 6 components of inertia tensor of body particle
* one line per sub-particle or vertex
* line syntax: x y z
* x, y, z = coordinates of sub-particle or vertex
* one line per edge
* line syntax: N1 N2
* N1, N2 = vertex indices
* one line per face
* line syntax: N1 N2 N3 N4
* N1, N2, N3, N4 = vertex indices
* last line
* line syntax: diam
* diam = rounded diameter that surrounds each vertex
This section is only needed when the molecule is a body particle. the other
Body section must also appear in the file.
The total number of values that must appear is determined by the body style, and
must be equal to the Ndouble value given in the *body* header. The 6 moments of
inertia and the 3N coordinates of the sub-particles or vertices are required
for all body styles.
For *rounded/polygon*, the E = 6 + 3*N + 1 edges are automatically determined
from the vertices.
For *rounded/polyhedron*, the 2E vertex indices for the end points of the edges
and 4F vertex indices defining the faces are required.
See the :doc:`Howto body <Howto_body>` page for a further description of
the file format.
----------
Restrictions
""""""""""""

6
doc/src/pair_beck.rst
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@ -30,11 +30,11 @@ Description
Style *beck* computes interactions based on the potential by
:ref:`(Beck) <Beck>`, originally designed for simulation of Helium. It
includes truncation at a cutoff distance Rc.
includes truncation at a cutoff distance :math:`r_c`.
.. math::
E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\
E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < r_c \\
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -50,7 +50,7 @@ commands.
* cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff
:math:`R_c` is used.
:math:`r_c` is used.
----------

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
=========================================

62
doc/src/pair_lj_cut_tip4p.rst
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@ -58,6 +58,40 @@ Examples
Description
"""""""""""
The *lj/cut/tip4p* styles implement the TIP4P water model of
:ref:`(Jorgensen) <Jorgensen2>` and similar models, which introduce a
massless site M located a short distance away from the oxygen atom along
the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as pair_style
arguments and are used to identify the TIP4P-like molecules and
determine the position of the M site from the positions of the hydrogen
and oxygen atoms of the water molecules. The M site location is used
for all Coulomb interactions instead of the oxygen atom location, also
with all other atom types, while the location of the oxygen atom is used
for the Lennard-Jones interactions. Style *lj/cut/tip4p/cut* uses a
cutoff for Coulomb interactions; style *lj/cut/tip4p/long* is for use
with a long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
given by
@ -91,34 +125,6 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
The *lj/cut/tip4p* styles implement the TIP4P
water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
site located a short distance away from the oxygen atom along the
bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style *lj/cut/tip4p/cut* uses a cutoff for
Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
long-range Coulombic solver (Ewald or PPPM).
.. note::
For each TIP4P water molecule in your system, the atom IDs for
the O and 2 H atoms must be consecutive, with the O atom first. This
is to enable LAMMPS to "find" the 2 H atoms associated with each O
atom. For example, if the atom ID of an O atom in a TIP4P water
molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
on how to use the TIP4P pair styles and lists of parameters to set.
Note that the neighbor list cutoff for Coulomb interactions is
effectively extended by a distance 2\*qdist when using the TIP4P pair
style, to account for the offset distance of the fictitious charges on
O atoms in water molecules. Thus it is typically best in an
efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
shrink the size of the neighbor list. This leads to slightly larger
cost for the long-range calculation, so you can test the trade-off for
your model.
Coefficients
""""""""""""

9
doc/src/pair_lj_smooth_linear.rst
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@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
interaction (aka Shifted Force Lennard-Jones) that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term based
on the cutoff distance, so that both, the potential and the force, go
continuously to zero at the cutoff Rc :ref:`(Toxvaerd) <Toxvaerd>`:
continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) <Toxvaerd>`:
.. math::
\phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style writes its information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands do not need to be specified
in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the

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
==============================

2
doc/src/pair_mie.rst
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@ -35,7 +35,7 @@ The *mie/cut* style computes the Mie potential, given by
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
\qquad r < r_c
Rc is the cutoff and C is a function that depends on the repulsive and
:math:`r_c` is the cutoff and C is a function that depends on the repulsive and
attractive exponents, given by:
.. math::

4
doc/src/pair_morse.rst
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@ -53,7 +53,7 @@ Style *morse* computes pairwise interactions with the formula
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
\qquad r < r_c
Rc is the cutoff.
:math:`r_c` is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -78,7 +78,7 @@ so that both, potential energy and force, go to zero at the cut-off:
.. math::
\phi\left(r\right) & = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\
E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The syntax of the pair_style and pair_coeff commands are the same for
the *morse* and *morse/smooth/linear* styles.

21
doc/src/pair_pace.rst
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@ -40,6 +40,9 @@ Examples
pair_style pace product chunksize 2048
pair_coeff * * Cu-PBE-core-rep.ace Cu
pair_style pace
pair_coeff * * Cu.yaml Cu
pair_style pace/extrapolation
pair_coeff * * Cu.yaml Cu.asi Cu
@ -64,7 +67,7 @@ specifies an ACE coefficient file followed by N additional arguments
specifying the mapping of ACE elements to LAMMPS atom types, where N is
the number of LAMMPS atom types:
* ACE coefficient file
* ACE coefficient file (.yaml or .yace/.ace format)
* N element names = mapping of ACE elements to atom types
Only a single pair_coeff command is used with the *pace* style which
@ -136,6 +139,22 @@ product B-basis evaluator is always used and only *linear* ASI is supported.
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
to specify the path for the ACE coefficient file.
Core repulsion
"""""""""""""""""""
The ACE potential can be configured to initiate core-repulsion from an inner cutoff,
seamlessly transitioning from ACE to ZBL. The core repulsion factor can be accessed
as a per-atom quantity, as demonstrated in the example below:
.. code-block:: LAMMPS
pair_style pace
pair_coeff * * CuNi.yaml Cu Ni
fix pace_corerep all pair 1 pace corerep 1
In this case, per-atom `f_pace_corerep` quantities represent the fraction of ZBL
core-repulsion for each atom.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

5
doc/src/pair_soft.rst
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@ -44,8 +44,9 @@ It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a prefactor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart
overlapping atoms.
interactions over time. :math:`r_c` is the cutoff.
See the :doc:`fix nve/limit <fix_nve_limit>` command for another way
to push apart overlapping atoms.
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,

3
doc/src/pair_sph_heatconduction.rst
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@ -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
""""""

2
doc/src/pair_spica.rst
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@ -81,7 +81,7 @@ given by
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
:math:`r_c` is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/spica/coul/long* computes the adds Coulombic interactions

94
doc/src/variable.rst
View File

@ -53,7 +53,7 @@ Syntax
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
@ -71,6 +71,7 @@ Syntax
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j]
compute references = c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]
fix references = f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]
variable references = v_name, v_name[i]
@ -514,38 +515,40 @@ is a valid (though strange) variable formula:
Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
functions, special functions, feature functions, atom values, atom
vectors, compute references, fix references, and references to other
vectors, custom atom properties, compute references, fix references, and references to other
variables.
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Constant | PI, version, on, off, true, false, yes, no |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Thermo keywords | vol, pe, ebond, etc |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math operators | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Group functions | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Custom atom properties | i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d_name[i][j] |
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Compute references | c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Fix references | f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Other variables | v_name, v_name[i] |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
Most of the formula elements produce a scalar value. Some produce a
global or per-atom vector of values. Global vectors can be produced
@ -703,6 +706,13 @@ library. Ceil() is the smallest integer not less than its argument.
Floor() if the largest integer not greater than its argument. Round()
is the nearest integer to its argument.
.. versionadded:: TBD
The ternary(x,y,z) function is the equivalent of the ternary operator
(? and :) in C or C++. It takes 3 arguments. The first argument is a
conditional. The result of the function is y if x evaluates to true
(non-zero). The result is z if x evaluates to false (zero).
The ramp(x,y) function uses the current timestep to generate a value
linearly interpolated between the specified x,y values over the course
of a run, according to this formula:
@ -1034,10 +1044,9 @@ to built-in commands. For all of these styles except *command*,
appending of active suffixes is also tried before reporting failure.
The *feature* category checks the availability of the following
compile-time enabled features: GZIP support, PNG support, JPEG
support, FFMPEG support, and C++ exceptions for error
handling. Corresponding names are *gzip*, *png*, *jpeg*, *ffmpeg* and
*exceptions*\ .
compile-time enabled features: GZIP support, PNG support, JPEG support,
FFMPEG support, and C++ exceptions for error handling. Corresponding
names are *gzip*, *png*, *jpeg*, *ffmpeg* and *exceptions*\ .
Example: Only dump in a given format if the compiled binary supports it.
@ -1139,8 +1148,45 @@ defines molecule IDs.
Note that many other atom attributes can be used as inputs to a
variable by using the :doc:`compute property/atom
<compute_property_atom>` command and then specifying a quantity from
that compute.
<compute_property_atom>` command and then referencing that compute.
----------
Custom atom properties
----------------------
.. versionadded:: TBD
Custom atom properties refer to per-atom integer and floating point
vectors or arrays that have been added via the :doc:`fix property/atom
<fix_property_atom>` command. When that command is used specific
names are given to each attribute which are the "name" portion of
these references. References beginning with *i* and *d* refer to
integer and floating point properties respectively. Per-atom vectors
are referenced by *i_name* and *d_name*; per-atom arrays are
referenced by *i2_name* and *d2_name*.
The various allowed references to integer custom atom properties in
the variable formulas for equal-, vector-, and atom-style variables
are listed in the following table. References to floating point
custom atom properties are the same; just replace the leading "i" with
"d".
+--------+---------------+------------------------------------------+
| equal | i_name[I] | element of per-atom vector (I = atom ID) |
| equal | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| vector | i_name[I] | element of per-atom vector (I = atom ID) |
| vector | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
| atom | i_name | per-atom vector |
| atom | i2_name[I] | column of per-atom array |
+--------+---------------+------------------------------------------+
The I and J indices in these custom atom property references can be
integers or can be a variable name, specified as v_name, where name is
the name of the variable. The rules for this syntax are the same as
for indices in the "Atom Values and Vectors" discussion above.
----------

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -1074,6 +1074,7 @@ facesets
factorizable
factorizations
Fahrenberger
Falk
Faken
Farago
Fasolino
@ -1173,6 +1174,7 @@ Foiles
fopenmp
forceclear
forestgreen
formamide
formatarg
formulae
Forschungszentrum
@ -1821,6 +1823,7 @@ Lanczos
Lande
Landron
Landsgesell
Langer
langevin
Langevin
Langston
@ -1969,6 +1972,7 @@ lps
lpsapi
lrt
lsfftw
lt
ltbbmalloc
Lua
lubricateU
@ -2497,6 +2501,7 @@ noforce
noguess
Noid
nolib
nonaffine
nonequilibrium
nongauss
nonGaussian
@ -2569,6 +2574,7 @@ nthreads
ntimestep
Ntptask
Ntriples
ntries
ntris
Ntype
ntypes
@ -3373,6 +3379,7 @@ Sodani
Soderlind
Solaris
Solida
solv
solvated
solvation
someuser
@ -3619,6 +3626,7 @@ timestepping
timesteps
TiN
TiO
Tirado
Tirrell
Titer
Tji

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

9
examples/PACKAGES/pace/README.md Normal file
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@ -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]}
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- {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]}
- {mu0: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 1], 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: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 1, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 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]}
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 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: 1, 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: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 1], 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 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]}
- {mu0: 2, 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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 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: 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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 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: [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: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 1], 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: [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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 1], 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: 9, mus: [0, 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: 9, mus: [0, 0, 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: 9, mus: [0, 0, 1], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
- {mu0: 2, 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: 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]}
- {mu0: 2, 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]}
- {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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 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]}
- {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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 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]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 1], 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: 9, mus: [1, 1, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
- {mu0: 2, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 1, 1], 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: 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
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@ -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
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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"
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81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1 Normal file
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@ -0,0 +1,81 @@
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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@ -0,0 +1,81 @@
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

2
examples/PACKAGES/phonon/2-1D-diatomic/in.Ana
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@ -7,7 +7,7 @@ atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
communicate single cutoff 2.0
comm_modify cutoff 2.0
# geometry
read_data data.pos

33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst Normal file
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@ -0,0 +1,33 @@
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
#restart 1000 restart
run 500

280
examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.1 Normal file
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@ -0,0 +1,280 @@
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
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 5 ${y_rep} ${z_rep}
replicate 5 5 ${z_rep}
replicate 5 5 10
Replication is creating a 5x5x10 = 250 times larger system...
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
1 by 1 by 1 MPI processor grid
1250 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 500 #500 fs
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 4 4 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 201.3 | 201.3 | 201.3 Mbytes
Step Temp Press TotEng Volume
0 110 -15717.706 -110869.31 15741.751
20 133.92166 8773.5364 -110569.51 15741.751
40 184.43244 -12136.835 -110378.92 15741.751
60 203.58164 6527.2188 -110190.9 15741.751
80 183.0518 -9667.6163 -110095.24 15741.751
100 236.07378 4393.5089 -109905.8 15741.751
120 226.94599 -5612.6845 -109708.46 15741.751
140 249.34156 988.50573 -109631.88 15741.751
160 255.08331 -1397.98 -109469.09 15741.751
180 281.64743 -1682.598 -109285.53 15741.751
200 303.76929 2594.8345 -109206.84 15741.751
220 311.6547 -4566.4307 -109053.21 15741.751
240 350.68316 5132.0272 -108918.26 15741.751
260 347.11102 -6078.5078 -108828.31 15741.751
280 366.56298 6373.2426 -108694.64 15741.751
300 393.62524 -6438.9321 -108521.5 15741.751
320 403.64821 5946.6873 -108487.83 15741.751
340 406.12883 -5053.5592 -108331.25 15741.751
360 450.60139 4323.0942 -108185.06 15741.751
380 429.46056 -3317.8604 -108146.84 15741.751
400 448.11876 3264.6165 -108048.01 15741.751
420 485.98657 -3047.3542 -107882.88 15741.751
440 463.23761 3088.3325 -107853.09 15741.751
460 504.27223 -1966.5888 -107689.56 15741.751
480 515.66783 2915.6322 -107550.83 15741.751
500 516.26369 -1733.2701 -107498.06 15741.751
Loop time of 41.4818 on 1 procs for 500 steps with 1250 atoms
Performance: 0.260 ns/day, 92.182 hours/ns, 12.053 timesteps/s, 15.067 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 | 30.707 | 30.707 | 30.707 | 0.0 | 74.03
Neigh | 2.2815 | 2.2815 | 2.2815 | 0.0 | 5.50
Comm | 0.023963 | 0.023963 | 0.023963 | 0.0 | 0.06
Output | 0.00073327 | 0.00073327 | 0.00073327 | 0.0 | 0.00
Modify | 8.4653 | 8.4653 | 8.4653 | 0.0 | 20.41
Other | | 0.00334 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8444 ave 8444 max 8444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 601915 ave 601915 max 601915 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 601915
Ave neighs/atom = 481.532
Neighbor list builds = 50
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
QBMSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
Shock velocity = 1.22000e-01
Artificial viscosity (units of mass/length/time) = 9.00000e-01
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
timestep 0.25
#restart 1000 restart
run 500
Fix QBMSST v0 = 1.57418e+04
Fix QBMSST p0 = -3.03801e+03
Fix QBMSST e0 = to be -1.07498e+05
Fix QBMSST initial strain rate of -1.02043e-04 established by reducing temperature by factor of 1.00000e-02
Per MPI rank memory allocation (min/avg/max) = 201.4 | 201.4 | 201.4 Mbytes
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
0 110 -1789.091 -107498.06 15741.751 19.891812 19.891812 39.783624 -3095.1546 1.9543098e-12 -57.148468 0 0
20 110 313.41128 -107231.57 15733.908 19.891812 19.891812 39.763803 1026.815 -35.805172 3755.1834 6.0783853e-05 -0.60983919
40 110 1248.5771 -107106.23 15726.494 19.891812 19.891812 39.745066 -277.53233 -52.672766 2158.1479 0.00011824041 -1.219383
60 110 -944.55947 -107017.75 15719.482 19.891812 19.891812 39.727345 1006.8843 -64.550247 3165.7346 0.00017258388 -1.8286479
80 110 2164.646 -107053.82 15712.848 19.891812 19.891812 39.710579 686.99949 -59.728513 2583.9345 0.00022399951 -2.4376489
100 110 -332.40946 -106996.04 15706.579 19.891812 19.891812 39.694734 1555.274 -67.472889 3204.6947 0.00027258815 -3.0464001
120 110 2556.8172 -106828.33 15700.655 19.891812 19.891812 39.679765 -1406.2492 -90.123866 9.330762 0.00031849257 -3.6549157
140 110 -649.1633 -106851.95 15695.029 19.891812 19.891812 39.665545 3704.8784 -86.742267 4898.3193 0.00036209988 -4.2632077
160 110 2301.4774 -106787.04 15689.738 19.891812 19.891812 39.652174 -893.31294 -95.690383 91.247096 0.00040310452 -4.8712886
180 110 -701.59672 -106639.61 15684.711 19.891812 19.891812 39.63947 3211.2065 -115.27944 3997.3199 0.00044206086 -5.47917
200 110 3857.6228 -106696.51 15679.975 19.891812 19.891812 39.627501 -1722.9124 -107.93584 -1123.778 0.00047876602 -6.0868625
220 110 -1057.1346 -106590.95 15675.462 19.891812 19.891812 39.616094 3285.0876 -121.80821 3706.0326 0.00051374575 -6.6943761
240 110 2748.5299 -106428.9 15671.216 19.891812 19.891812 39.605364 172.15717 -143.78629 425.48974 0.00054664912 -7.3017201
260 110 64.99143 -106442.23 15667.188 19.891812 19.891812 39.595183 981.21139 -141.94851 1075.4979 0.00057787086 -7.9089043
280 110 1612.9607 -106412.77 15663.362 19.891812 19.891812 39.585514 662.48897 -145.93658 605.73218 0.00060752164 -8.5159364
300 110 1435.9566 -106307.06 15659.725 19.891812 19.891812 39.576323 759.46794 -160.13403 559.12791 0.00063570794 -9.1228243
320 110 -890.72712 -106332.6 15656.258 19.891812 19.891812 39.56756 234.14376 -156.75496 -103.07714 0.00066257852 -9.7295747
340 110 4270.0983 -106252.72 15652.976 19.891812 19.891812 39.559265 5411.2268 -167.0427 4944.423 0.00068801647 -10.336194
360 110 -2801.0763 -106105.96 15649.905 19.891812 19.891812 39.551504 -3276.3824 -187.5258 -3864.4213 0.00071181569 -10.942691
380 110 5566.9116 -106139.88 15646.926 19.891812 19.891812 39.543977 2737.1121 -182.43141 2031.4929 0.00073489745 -11.549071
400 110 -4432.9416 -106074.79 15644.09 19.891812 19.891812 39.536808 -4946.1908 -191.90759 -5763.8068 0.00075688314 -12.155339
420 52.599535 5582.8126 -105959.96 15641.311 19.891812 19.891812 39.529786 7869.5301 -206.09135 6942.2136 0.00077841805 -12.761497
440 52.599535 -2861.6332 -106017.66 15638.758 19.891812 19.891812 39.523335 -1820.4742 -199.30721 -2848.5648 0.00079820063 -13.367553
460 52.599535 3942.7505 -105984.45 15636.294 19.891812 19.891812 39.517106 3327.0393 -203.24794 2201.6559 0.00081729985 -13.973511
480 52.599535 419.18442 -105827.32 15633.955 19.891812 19.891812 39.511194 -1910.6109 -224.9021 -3128.3482 0.00083542949 -14.579377
500 52.599535 117.60016 -105904.83 15631.655 19.891812 19.891812 39.505383 -603.40365 -214.36236 -1911.9203 0.00085325005 -15.185153
Loop time of 41.8312 on 1 procs for 500 steps with 1250 atoms
Performance: 0.258 ns/day, 92.958 hours/ns, 11.953 timesteps/s, 14.941 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 | 31.016 | 31.016 | 31.016 | 0.0 | 74.15
Neigh | 2.2849 | 2.2849 | 2.2849 | 0.0 | 5.46
Comm | 0.020391 | 0.020391 | 0.020391 | 0.0 | 0.05
Output | 0.0019403 | 0.0019403 | 0.0019403 | 0.0 | 0.00
Modify | 8.505 | 8.505 | 8.505 | 0.0 | 20.33
Other | | 0.003238 | | | 0.01
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8489 ave 8489 max 8489 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 606382 ave 606382 max 606382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 606382
Ave neighs/atom = 485.1056
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:01:23

280
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@ -0,0 +1,280 @@
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
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 5 ${y_rep} ${z_rep}
replicate 5 5 ${z_rep}
replicate 5 5 10
Replication is creating a 5x5x10 = 250 times larger system...
orthogonal box = (0 0 0) to (19.891812 19.891812 39.783624)
1 by 1 by 4 MPI processor grid
1250 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 500 #500 fs
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 4 4 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 125.2 | 125.3 | 125.4 Mbytes
Step Temp Press TotEng Volume
0 110 -15717.706 -110869.31 15741.751
20 133.92621 9503.0083 -110548.47 15741.751
40 188.1524 -13687.131 -110344.93 15741.751
60 205.85747 8421.3906 -110165.58 15741.751
80 185.08989 -11337.006 -110026.24 15741.751
100 245.36524 5805.0694 -109841.66 15741.751
120 218.83661 -7740.8838 -109674.15 15741.751
140 254.6075 3396.3936 -109589.89 15741.751
160 262.20963 -3574.2575 -109413.81 15741.751
180 297.89271 917.40867 -109204.79 15741.751
200 315.54026 -371.17448 -109129.45 15741.751
220 323.90745 -2811.4367 -108988.12 15741.751
240 358.28478 3972.8358 -108848.95 15741.751
260 359.12673 -6289.689 -108788.08 15741.751
280 376.47656 6851.3186 -108664.07 15741.751
300 404.30975 -7805.7238 -108482.75 15741.751
320 410.9097 7696.2518 -108421.87 15741.751
340 406.19092 -8175.1703 -108311.84 15741.751
360 460.37085 7630.6182 -108139.6 15741.751
380 413.96355 -7515.2307 -108150.73 15741.751
400 452.17428 7148.0954 -108027.39 15741.751
420 467.1725 -6662.4113 -107842.71 15741.751
440 481.03775 6117.6862 -107759.03 15741.751
460 509.03937 -4095.0215 -107648.46 15741.751
480 533.22373 2211.9169 -107481.89 15741.751
500 517.71195 -214.23969 -107489.48 15741.751
Loop time of 22.2711 on 4 procs for 500 steps with 1250 atoms
Performance: 0.485 ns/day, 49.491 hours/ns, 22.451 timesteps/s, 28.063 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.689 | 15.195 | 16.732 | 27.7 | 68.23
Neigh | 1.5325 | 1.5496 | 1.5658 | 1.0 | 6.96
Comm | 0.073366 | 1.6105 | 3.116 | 85.1 | 7.23
Output | 0.00052192 | 0.00057642 | 0.00073657 | 0.0 | 0.00
Modify | 3.896 | 3.9129 | 3.9306 | 0.6 | 17.57
Other | | 0.00241 | | | 0.01
Nlocal: 312.5 ave 317 max 308 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 4982 ave 4995 max 4967 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 172509 ave 174182 max 170676 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 690037
Ave neighs/atom = 552.0296
Neighbor list builds = 50
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init ${temperature}
fix shock all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 f_max 0.3 N_f 50 seed 35082 eta 1 beta 400 T_init 110
QBMSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.50000e+01
Shock velocity = 1.22000e-01
Artificial viscosity (units of mass/length/time) = 9.00000e-01
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 20
timestep ${delta_t}
timestep 0.25
#restart 1000 restart
run 500
Fix QBMSST v0 = 1.57418e+04
Fix QBMSST p0 = -5.88788e+01
Fix QBMSST e0 = to be -1.07489e+05
Fix QBMSST initial strain rate of -1.02186e-04 established by reducing temperature by factor of 1.00000e-02
Per MPI rank memory allocation (min/avg/max) = 126.1 | 126.1 | 126.1 Mbytes
Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos
0 110 -270.21489 -107489.48 15741.751 19.891812 19.891812 39.783624 -118.93551 0 -60.056661 0 0
20 110 -2180.5877 -107208.2 15733.847 19.891812 19.891812 39.763648 223.47326 -37.773571 -29.703539 6.1258507e-05 -0.60983836
40 110 5004.864 -107109.95 15726.306 19.891812 19.891812 39.744592 3335.6341 -50.920246 2784.77 0.00011969641 -1.2193771
60 110 -4549.1199 -106949.22 15719.136 19.891812 19.891812 39.72647 -4461.4212 -72.656651 -5295.3675 0.00017526726 -1.8286321
80 110 6695.6833 -106942.12 15712.214 19.891812 19.891812 39.708976 5333.2741 -73.356417 4226.043 0.00022891479 -2.4376137
100 110 -5337.7671 -106930.78 15705.644 19.891812 19.891812 39.692373 -2682.4224 -75.129348 -4049.0157 0.00027982924 -3.0463347
120 110 6526.5587 -106736.15 15699.334 19.891812 19.891812 39.676424 7038.2375 -100.8809 5422.5046 0.00032873694 -3.6548061
140 110 -3284.0472 -106761.36 15693.36 19.891812 19.891812 39.661329 -3999.8116 -97.977739 -5851.3636 0.00037502973 -4.2630401
160 110 4792.0537 -106662.24 15687.56 19.891812 19.891812 39.64667 4484.6905 -110.86184 2404.1579 0.00041998006 -4.8710464
180 110 -1253.5849 -106532.38 15682.037 19.891812 19.891812 39.632711 -723.78287 -128.58314 -3022.3825 0.00046278801 -5.4788331
200 110 3276.2225 -106488.13 15676.725 19.891812 19.891812 39.619286 5117.4749 -134.15782 2609.1518 0.00050395806 -6.0864105
220 110 -553.17982 -106421.17 15671.675 19.891812 19.891812 39.606524 -1360.8796 -143.56979 -4068.5641 0.00054309397 -6.6937871
240 110 1329.8793 -106309.56 15666.794 19.891812 19.891812 39.594187 775.35326 -158.40869 -2125.0508 0.00058092605 -7.300972
260 110 1809.8974 -106360.42 15662.075 19.891812 19.891812 39.582262 3075.2725 -151.39659 -11.4097 0.00061749364 -7.9079706
280 110 24.534819 -106310.46 15657.56 19.891812 19.891812 39.570852 1043.8352 -158.25965 -2221.0935 0.00065248454 -8.5147908
300 110 2854.2862 -106150.2 15653.217 19.891812 19.891812 39.559874 3727.6844 -179.54521 291.27132 0.00068614803 -9.1214393
320 110 -776.61228 -106199.04 15649.041 19.891812 19.891812 39.549322 -1285.3999 -173.42703 -4886.655 0.00071850756 -9.7279234
340 110 3778.2238 -106201.03 15644.958 19.891812 19.891812 39.539001 3694.462 -172.6926 -68.017561 0.00075015694 -10.334247
360 110 -1505.9413 -106025.15 15641.031 19.891812 19.891812 39.529078 -1491.3768 -196.81063 -5408.8787 0.00078058882 -10.940416
380 110 3414.9599 -106071.49 15637.176 19.891812 19.891812 39.519335 4956.6752 -189.93327 886.98409 0.00081046454 -11.546435
400 110 -947.2273 -106003.34 15633.49 19.891812 19.891812 39.510021 726.91825 -199.51619 -3488.2795 0.0008390284 -12.152307
420 46.681884 1610.2414 -105884.37 15629.905 19.891812 19.891812 39.500961 -1377.8364 -215.72223 -5734.5653 0.00086681188 -12.758039
440 46.681884 2290.4653 -105923.83 15626.371 19.891812 19.891812 39.492029 6296.7177 -209.55961 1800.4591 0.00089420243 -13.363632
460 46.681884 -2068.0472 -105879.44 15622.969 19.891812 19.891812 39.483432 -5629.8405 -216.88862 -10260.4 0.00092056659 -13.969092
480 46.681884 5011.06 -105748.92 15619.556 19.891812 19.891812 39.474805 8649.5097 -232.72756 3884.1859 0.00094702163 -14.574419
500 46.681884 -3314.8335 -105829.23 15616.305 19.891812 19.891812 39.46659 -5120.4784 -223.60669 -10014.132 0.00097221364 -15.179618
Loop time of 26.5748 on 4 procs for 500 steps with 1250 atoms
Performance: 0.406 ns/day, 59.055 hours/ns, 18.815 timesteps/s, 23.519 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.259 | 18.109 | 19.999 | 31.1 | 68.14
Neigh | 1.8265 | 1.8477 | 1.8638 | 1.0 | 6.95
Comm | 0.045073 | 1.9349 | 3.7845 | 95.1 | 7.28
Output | 0.0019058 | 0.0019666 | 0.0021202 | 0.2 | 0.01
Modify | 4.6619 | 4.6782 | 4.699 | 0.6 | 17.60
Other | | 0.002774 | | | 0.01
Nlocal: 312.5 ave 318 max 307 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 5059 ave 5080 max 5039 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 173854 ave 176807 max 170839 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 695414
Ave neighs/atom = 556.3312
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:49

33
examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in
View File

@ -1,33 +0,0 @@
## This script first uses fix qtb to equilibrate liquid methane to an initial state with quantum nuclear correction and then simulate shock induced chemical reactions through the quantum thermal bath multi-scale shock technique
#The default system size may take a while to run you can change to a smaller size
variable x_rep equal 5 #x-direction replication number
variable y_rep equal 5 #y-direction replication number
variable z_rep equal 10 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
variable v_msst equal 0.122 #Shock velocity (Angstrom/fs in metal units)
variable q_msst equal 25.0 #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in real units)
variable mu_msst equal 0.9 #Artificial viscosity in the MSST (mass/length/time, where mass=grams/mole, length=Angstrom and time=fs in real units)
variable tscale_msst equal 0.01 #Temperature reduction parameter in the MSST (unitless)
variable eta_qbmsst equal 1.0 #Coupling constant between the shock and the quantum thermal bath (unitless constant)
##The included part first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
include methane_qtb.mod
##Shock compression with quantum nuclear corrections
reset_timestep 0
fix shock all qbmsst z ${v_msst} q ${q_msst} mu ${mu_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 0.3 N_f 50 seed 35082 eta ${eta_qbmsst} beta 400 T_init ${temperature}
fix_modify shock energy yes
variable dhug equal f_shock[1]
variable dray equal f_shock[2]
variable lgr_vel equal f_shock[3]
variable lgr_pos equal f_shock[4]
variable T_qm equal f_shock[5] #Temperature with quantum nuclear correction
thermo_style custom step v_T_qm press etotal vol lx ly lz pzz v_dhug v_dray v_lgr_vel v_lgr_pos
thermo 100
timestep ${delta_t}
restart 1000 restart
run 5000

8
examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
View File

@ -38,9 +38,9 @@ mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reax/c NULL
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
@ -53,12 +53,12 @@ velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
thermo 20
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 2000 #500 fs
run 500 #500 fs
unfix methane_qtb
unfix scapegoat_qtb

70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb Normal file
View File

@ -0,0 +1,70 @@
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 1000
unfix methane_qtb
unfix scapegoat_qtb

174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1 Normal file
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@ -0,0 +1,174 @@
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
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 1 by 1 MPI processor grid
40 atoms
replicate CPU = 0.001 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 82.45 | 82.45 | 82.45 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 191.27715 -7523.7503 -3530.4179 503.73603
100 214.09982 12016.892 -3517.4544 503.73603
150 317.38272 3098.2254 -3499.5793 503.73603
200 338.76362 -4484.9241 -3490.3649 503.73603
250 402.05826 3973.0488 -3474.81 503.73603
300 340.80076 11193.4 -3470.8029 503.73603
350 556.19747 8086.3266 -3451.5937 503.73603
400 566.8737 5499.5505 -3439.2335 503.73603
450 643.2883 -8270.5736 -3426.0767 503.73603
500 613.09742 -12406.229 -3419.8547 503.73603
550 669.28891 -9757.601 -3410.7281 503.73603
600 600.66922 10407.403 -3408.3776 503.73603
650 573.1485 30971.977 -3405.0744 503.73603
700 726.22146 29573.798 -3386.3167 503.73603
750 777.22659 13265.88 -3378.8462 503.73603
800 652.46476 -9231.9331 -3388.7229 503.73603
850 679.18414 -19802.254 -3384.6321 503.73603
900 711.60594 -18792.396 -3373.2944 503.73603
950 865.79013 -2837.6042 -3363.2971 503.73603
1000 884.14995 6160.4875 -3360.6295 503.73603
Loop time of 7.87 on 1 procs for 1000 steps with 40 atoms
Performance: 2.745 ns/day, 8.744 hours/ns, 127.065 timesteps/s, 5.083 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3662 | 6.3662 | 6.3662 | 0.0 | 80.89
Neigh | 0.97757 | 0.97757 | 0.97757 | 0.0 | 12.42
Comm | 0.013653 | 0.013653 | 0.013653 | 0.0 | 0.17
Output | 0.00042319 | 0.00042319 | 0.00042319 | 0.0 | 0.01
Modify | 0.50971 | 0.50971 | 0.50971 | 0.0 | 6.48
Other | | 0.00248 | | | 0.03
Nlocal: 40 ave 40 max 40 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2552 ave 2552 max 2552 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25110 ave 25110 max 25110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 25110
Ave neighs/atom = 627.75
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:07

174
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@ -0,0 +1,174 @@
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
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 a1 3.9783624 0 0 a2 0 3.9783624 0 a3 0 0 3.9783624 basis 0.5 0.5 0.5 basis 0.663 0.663 0.663 basis 0.337 0.337 0.663 basis 0.663 0.337 0.337 basis 0.337 0.663 0.337
Lattice spacing in x,y,z = 3.9783624 3.9783624 3.9783624
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
Created orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 1 1 basis 2 2 basis 3 2 basis 4 2 basis 5 2
Created 5 atoms
using lattice units in orthogonal box = (0 0 0) to (3.9783624 3.9783624 3.9783624)
create_atoms CPU = 0.000 seconds
replicate ${x_rep} ${y_rep} ${z_rep}
replicate 2 ${y_rep} ${z_rep}
replicate 2 2 ${z_rep}
replicate 2 2 2
Replication is creating a 2x2x2 = 8 times larger system...
orthogonal box = (0 0 0) to (7.9567248 7.9567248 7.9567248)
1 by 2 by 2 MPI processor grid
40 atoms
replicate CPU = 0.000 seconds
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reaxff NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reaxff
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
velocity all create 110 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 50
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
fix methane_qtb all qtb temp 110 damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50
fix methane_qtb all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 50
timestep ${delta_t}
timestep 0.25
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 72.47 | 72.47 | 72.47 Mbytes
Step Temp Press TotEng Volume
0 110 -15746.508 -3548.1354 503.73603
50 183.74482 -917.59204 -3534.8518 503.73603
100 200.96363 16464.403 -3517.1456 503.73603
150 255.33305 14801.963 -3507.7299 503.73603
200 328.11626 5119.3618 -3498.0388 503.73603
250 356.88626 -11306.151 -3485.1746 503.73603
300 284.7363 -25276.091 -3479.4732 503.73603
350 434.79382 -23326.29 -3471.7491 503.73603
400 414.69602 2800.9047 -3465.7225 503.73603
450 464.61242 20775.398 -3449.1675 503.73603
500 671.43369 15272.581 -3433.9453 503.73603
550 534.01157 -8545.4173 -3427.6672 503.73603
600 512.69648 -15904.052 -3417.8071 503.73603
650 604.62051 -1777.9242 -3419.4324 503.73603
700 650.2196 20108.199 -3415.8902 503.73603
750 677.45644 21721.335 -3409.1253 503.73603
800 707.98295 171.53756 -3413.4048 503.73603
850 740.68522 -23846.627 -3384.7024 503.73603
900 739.55514 -22742.841 -3377.091 503.73603
950 769.44821 -7060.9388 -3389.817 503.73603
1000 987.6246 -0.47618437 -3373.9263 503.73603
Loop time of 6.80367 on 4 procs for 1000 steps with 40 atoms
Performance: 3.175 ns/day, 7.560 hours/ns, 146.980 timesteps/s, 5.879 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.1801 | 5.3491 | 5.5417 | 6.1 | 78.62
Neigh | 0.76934 | 0.77281 | 0.77567 | 0.3 | 11.36
Comm | 0.072213 | 0.26492 | 0.4339 | 27.2 | 3.89
Output | 0.00032365 | 0.00035547 | 0.00044739 | 0.0 | 0.01
Modify | 0.41139 | 0.41424 | 0.4179 | 0.4 | 6.09
Other | | 0.00226 | | | 0.03
Nlocal: 10 ave 10 max 10 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1950 ave 1950 max 1950 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 6434.5 ave 6447 max 6427 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 25738
Ave neighs/atom = 643.45
Neighbor list builds = 100
Dangerous builds not checked
unfix methane_qtb
unfix scapegoat_qtb
Total wall time: 0:00:06

70
examples/PACKAGES/qtb/methane_qtb/methane_qtb.in
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@ -1,70 +0,0 @@
## This script first constructs a liquid methane structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable temperature equal 110.0 #Target quantum temperature (K in real units)
variable delta_t equal 0.25 #MD timestep length (fs in real units)
variable damp_qtb equal 200 #1/gamma where gamma is the friction coefficient in quantum thermal bath (fs in real units)
## This part defines units, methane structure, and atomic information
#General
units real
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 3.9783624 0 0 &
a2 0 3.9783624 0 &
a3 0 0 3.9783624 &
&
basis 0.5 0.5 0.5 &
basis 0.663 0.663 0.663 &
basis 0.337 0.337 0.663 &
basis 0.663 0.337 0.337 &
basis 0.337 0.663 0.337
#Computational Cell
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
create_box 2 simbox
create_atoms 1 box &
basis 1 1 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 12.011150
mass 2 1.007970
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
#Pair Potentials
pair_style reax/c NULL
pair_coeff * * ffield.reax C H
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
#Neighbor Style
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
thermo_style custom step temp press etotal vol
thermo 100
#Colored thermal bath
fix scapegoat_qtb all nve #NVE does the time integration
fix methane_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 0.3 N_f 50 #Change f_max if your Debye frequency is higher
timestep ${delta_t}
run 3000 #750 fs
unfix methane_qtb
unfix scapegoat_qtb

5
examples/amoeba/amoeba_ubiquitin.key
View File

@ -12,7 +12,8 @@ ewald
ewald-alpha 0.4
pewald-alpha 0.5
ewald-cutoff 7.0
#pme-grid 60 45 45
pme-grid 60 48 48
pme-order 5
polar-eps 0.00001
#pme-grid 15 12 12
#polar-eps 0.0002
pme-order 5

8
examples/qeq/in.qeq.reaxc → examples/qeq/in.qeq.reaxff
View File

@ -1,19 +1,19 @@
# This example demonstrates the use of various fix qeq variants with pair reax/c
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
pair_style reax/c NULL checkqeq no
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
neighbor 1 bin

116
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@ -1,116 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
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 = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
2 -10223.656 0.095669731 -0.15666714 -0.091175264 -6.4392935e-15
3 -10220.276 0.095691257 -0.15671597 -0.091178813 2.6645353e-15
4 -10215.894 0.095714363 -0.15676887 -0.091182006 -3.1086245e-15
5 -10210.804 0.095733863 -0.15681398 -0.09118412 6.6613381e-16
6 -10205.342 0.095751253 -0.15685427 -0.091185918 -1.110223e-15
7 -10199.848 0.095762028 -0.1568795 -0.091186707 8.8817842e-15
8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms
Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/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 | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16
Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85
Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57
Other | | 2.694e-05 | | | 0.08
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.5429
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

116
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@ -1,116 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
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 = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
2 -10223.656 0.095669684 -0.15666698 -0.091175327 1.110223e-15
3 -10220.276 0.095691296 -0.15671615 -0.091178696 0
4 -10215.894 0.09571384 -0.15676787 -0.091181678 8.8817842e-16
5 -10210.804 0.095734178 -0.15681468 -0.09118418 1.3322676e-15
6 -10205.342 0.095751126 -0.15685409 -0.091185769 4.4408921e-16
7 -10199.848 0.095762403 -0.15688037 -0.091186751 0
8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms
Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s
92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45
Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50
Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27
Other | | 0.0002902 | | | 1.57
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.0571
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

146
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@ -0,0 +1,146 @@
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
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.54 | 14.54 | 14.54 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633909 -0.15658753 -0.091167311 -2.8865799e-15
1 -10225.799 0.095650157 -0.15662321 -0.091171465 5.3290705e-15
2 -10223.656 0.095669727 -0.15666713 -0.091175264 -2.8865799e-15
3 -10220.276 0.095691262 -0.15671593 -0.09117887 4.6629367e-15
4 -10215.894 0.095714037 -0.15676816 -0.091181914 4.4408921e-16
5 -10210.804 0.095733939 -0.15681378 -0.091184589 -3.9968029e-15
6 -10205.342 0.09575102 -0.15685378 -0.091185835 -3.5527137e-15
7 -10199.848 0.095762356 -0.1568802 -0.091186815 2.220446e-15
8 -10194.646 0.095766731 -0.15689071 -0.091186805 -3.9968029e-15
9 -10190.016 0.095761083 -0.15687817 -0.091185537 -2.6645353e-15
10 -10186.168 0.095747444 -0.15684695 -0.091183644 -1.5543122e-15
Loop time of 0.013327 on 1 procs for 10 steps with 105 atoms
Performance: 16.208 ns/day, 1.481 hours/ns, 750.359 timesteps/s, 78.788 katom-step/s
97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010565 | 0.010565 | 0.010565 | 0.0 | 79.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.3272e-05 | 2.3272e-05 | 2.3272e-05 | 0.0 | 0.17
Output | 0.00023198 | 0.00023198 | 0.00023198 | 0.0 | 1.74
Modify | 0.0024913 | 0.0024913 | 0.0024913 | 0.0 | 18.69
Other | | 1.529e-05 | | | 0.11
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.542857
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

146
examples/qeq/log.30Nov23.reaxff.g++.4 Normal file
View File

@ -0,0 +1,146 @@
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
# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.000 seconds
pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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 = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.845 | 10.57 | 11.28 Mbytes
Step PotEng c_q1 c_q2 c_q3 v_qtot
0 -10226.557 0.095633904 -0.15658758 -0.091167237 -8.8817842e-16
1 -10225.799 0.095650278 -0.1566235 -0.091171458 -1.7763568e-15
2 -10223.656 0.095669806 -0.15666728 -0.091175321 0
3 -10220.276 0.095691215 -0.15671588 -0.091178792 1.7763568e-15
4 -10215.894 0.09571392 -0.15676795 -0.091181826 1.7763568e-15
5 -10210.804 0.095734058 -0.15681436 -0.091184227 1.3322676e-15
6 -10205.342 0.095751113 -0.15685409 -0.091185731 -4.4408921e-16
7 -10199.848 0.095762524 -0.15688062 -0.091186803 -1.3322676e-15
8 -10194.646 0.095766647 -0.15689045 -0.091186875 2.8865799e-15
9 -10190.016 0.095760978 -0.15687772 -0.09118579 -4.4408921e-16
10 -10186.168 0.095747037 -0.15684594 -0.091183687 -1.5543122e-15
Loop time of 0.00732332 on 4 procs for 10 steps with 105 atoms
Performance: 29.495 ns/day, 0.814 hours/ns, 1365.500 timesteps/s, 143.378 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0033186 | 0.0038166 | 0.0041063 | 0.5 | 52.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0002671 | 0.00057126 | 0.0010608 | 0.0 | 7.80
Output | 0.00019157 | 0.0002237 | 0.00028058 | 0.0 | 3.05
Modify | 0.0026446 | 0.0026528 | 0.0026604 | 0.0 | 36.22
Other | | 5.9e-05 | | | 0.81
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.057143
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

6
examples/reaxff/AB/in.AB
View File

@ -6,7 +6,7 @@ units real
atom_style charge
read_data data.AB
pair_style reax/c lmp_control
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
neighbor 2 bin
@ -17,7 +17,7 @@ fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
run 3000
run 2000

9
examples/reaxff/AB/lmp_control
View File

@ -1,17 +1,8 @@
simulation_name AB_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title AB ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file

131
examples/reaxff/AB/log.30Nov23.AB.g++.1 Normal file
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@ -0,0 +1,131 @@
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
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
104 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.54 | 16.54 | 16.54 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
100 83.873108 -8497.003 0 -8471.252 -609.71138
200 125.22992 -8479.8879 0 -8441.4394 -1069.4072
300 202.34273 -8479.1321 0 -8417.0081 -707.7946
400 260.53055 -8476.7914 0 -8396.8025 221.10403
500 282.47043 -8466.8576 0 -8380.1326 -223.61988
600 288.72043 -8452.9503 0 -8364.3064 681.87761
700 379.03381 -8467.4869 0 -8351.1146 921.82426
800 382.0856 -8458.717 0 -8341.4078 253.69164
900 380.10802 -8449.5745 0 -8332.8725 1199.5539
1000 377.60669 -8440.3419 0 -8324.4078 -365.02585
1100 372.89451 -8428.8743 0 -8314.387 -1401.9593
1200 392.77958 -8426.3492 0 -8305.7567 -572.78319
1300 429.04209 -8430.6839 0 -8298.958 -409.55236
1400 471.52489 -8438.2785 0 -8293.5093 -16.649651
1500 404.49399 -8411.1192 0 -8286.93 338.99191
1600 443.77567 -8418.1237 0 -8281.8741 -774.22575
1700 479.8234 -8424.6901 0 -8277.3731 65.260334
1800 386.73299 -8390.8969 0 -8272.1608 70.076616
1900 431.57275 -8401.0671 0 -8268.5641 30.882406
2000 454.96043 -8406.0467 0 -8266.3632 728.1499
Loop time of 2.35094 on 1 procs for 2000 steps with 104 atoms
Performance: 18.376 ns/day, 1.306 hours/ns, 850.725 timesteps/s, 88.475 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9254 | 1.9254 | 1.9254 | 0.0 | 81.90
Neigh | 0.10479 | 0.10479 | 0.10479 | 0.0 | 4.46
Comm | 0.0067523 | 0.0067523 | 0.0067523 | 0.0 | 0.29
Output | 0.0005375 | 0.0005375 | 0.0005375 | 0.0 | 0.02
Modify | 0.31152 | 0.31152 | 0.31152 | 0.0 | 13.25
Other | | 0.001934 | | | 0.08
Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 710 ave 710 max 710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3076 ave 3076 max 3076 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3076
Ave neighs/atom = 29.576923
Neighbor list builds = 200
Dangerous builds not checked
Total wall time: 0:00:02

131
examples/reaxff/AB/log.30Nov23.AB.g++.4 Normal file
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@ -0,0 +1,131 @@
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
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.ab
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.06 | 11.68 | 11.96 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
100 83.873123 -8497.0031 0 -8471.252 -609.71119
200 125.23001 -8479.8879 0 -8441.4394 -1069.4122
300 202.34219 -8479.1319 0 -8417.0081 -707.82246
400 260.52726 -8476.7906 0 -8396.8026 221.14446
500 282.4624 -8466.8556 0 -8380.133 -223.17501
600 288.8059 -8452.9729 0 -8364.3028 679.38441
700 378.87007 -8467.429 0 -8351.107 920.99401
800 382.10004 -8458.7194 0 -8341.4058 256.06383
900 379.69698 -8449.4416 0 -8332.8657 1266.1715
1000 379.63496 -8440.9584 0 -8324.4015 -604.987
1100 372.82256 -8428.7507 0 -8314.2854 -1236.8451
1200 397.12809 -8427.4286 0 -8305.501 -356.42394
1300 413.36951 -8425.3861 0 -8298.472 -47.619729
1400 428.68835 -8424.4328 0 -8292.8154 -812.52975
1500 403.59408 -8411.0829 0 -8287.1701 71.054401
1600 448.76276 -8419.8186 0 -8282.0379 -339.19148
1700 450.87444 -8416.1981 0 -8277.769 -44.043208
1800 485.33509 -8421.3776 0 -8272.3684 -848.94941
1900 481.36374 -8416.1719 0 -8268.382 -282.62675
2000 437.25967 -8398.9233 0 -8264.6743 -217.40762
Loop time of 1.44368 on 4 procs for 2000 steps with 104 atoms
Performance: 29.924 ns/day, 0.802 hours/ns, 1385.350 timesteps/s, 144.076 katom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77999 | 0.87212 | 0.96576 | 8.1 | 60.41
Neigh | 0.054058 | 0.059726 | 0.06287 | 1.4 | 4.14
Comm | 0.031767 | 0.12609 | 0.21802 | 21.3 | 8.73
Output | 0.00041377 | 0.00045661 | 0.00058001 | 0.0 | 0.03
Modify | 0.3805 | 0.38348 | 0.3894 | 0.6 | 26.56
Other | | 0.001808 | | | 0.13
Nlocal: 26 ave 34 max 14 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 429.25 ave 457 max 386 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 922.5 ave 1238 max 496 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3690
Ave neighs/atom = 35.480769
Neighbor list builds = 200
Dangerous builds not checked
Total wall time: 0:00:01

81
examples/reaxff/AB/log.8Mar18.AB.g++.1
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 478.18595 -8398.4168 0 -8251.6025 1452.6935
Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms
Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s
96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52
Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56
Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16
Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00
Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72
Other | | 0.006263 | | | 0.04
Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 694 ave 694 max 694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2866 ave 2866 max 2866 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2866
Ave neighs/atom = 27.5577
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:14

81
examples/reaxff/AB/log.8Mar18.AB.g++.4
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
units real
atom_style charge
read_data data.AB
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
104 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.AB H B N
Reading potential file ffield.reax.AB with DATE: 2011-02-18
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.ab
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
3000 555.17702 -8426.5541 0 -8256.1017 219.26856
Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms
Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20
Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29
Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27
Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00
Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17
Other | | 0.005646 | | | 0.06
Nlocal: 26 ave 35 max 13 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 420.25 ave 454 max 370 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 862.5 ave 1178 max 444 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 3450
Ave neighs/atom = 33.1731
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

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