Merge branch 'develop' into snann_slcsa
This commit is contained in:
Axel Kohlmeyer
@ -971,33 +971,53 @@ if(PKG_KOKKOS)
|
|||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
if(PKG_KSPACE)
|
if(PKG_KSPACE)
|
||||||
message(STATUS "<<< FFT settings >>>
|
if (LMP_HEFFTE)
|
||||||
-- Primary FFT lib: ${FFT}")
|
message(STATUS "<<< FFT settings >>>
|
||||||
if(FFT_SINGLE)
|
-- Primary FFT lib: heFFTe")
|
||||||
message(STATUS "Using single precision FFTs")
|
if (HEFFTE_BACKEND)
|
||||||
else()
|
message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
|
||||||
message(STATUS "Using double precision FFTs")
|
|
||||||
endif()
|
|
||||||
if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
|
|
||||||
message(STATUS "Using threaded FFTs")
|
|
||||||
else()
|
|
||||||
message(STATUS "Using non-threaded FFTs")
|
|
||||||
endif()
|
|
||||||
if(PKG_KOKKOS)
|
|
||||||
if(Kokkos_ENABLE_CUDA)
|
|
||||||
if(FFT STREQUAL "KISS")
|
|
||||||
message(STATUS "Kokkos FFT: KISS")
|
|
||||||
else()
|
|
||||||
message(STATUS "Kokkos FFT: cuFFT")
|
|
||||||
endif()
|
|
||||||
elseif(Kokkos_ENABLE_HIP)
|
|
||||||
if(FFT STREQUAL "KISS")
|
|
||||||
message(STATUS "Kokkos FFT: KISS")
|
|
||||||
else()
|
|
||||||
message(STATUS "Kokkos FFT: hipFFT")
|
|
||||||
endif()
|
|
||||||
else()
|
else()
|
||||||
message(STATUS "Kokkos FFT: ${FFT}")
|
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)
|
||||||
|
message(STATUS "Using single precision FFTs")
|
||||||
|
else()
|
||||||
|
message(STATUS "Using double precision FFTs")
|
||||||
|
endif()
|
||||||
|
if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
|
||||||
|
message(STATUS "Using threaded FFTs")
|
||||||
|
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")
|
||||||
|
message(STATUS "Kokkos FFT: KISS")
|
||||||
|
else()
|
||||||
|
message(STATUS "Kokkos FFT: cuFFT")
|
||||||
|
endif()
|
||||||
|
elseif(Kokkos_ENABLE_HIP)
|
||||||
|
if(FFT STREQUAL "KISS")
|
||||||
|
message(STATUS "Kokkos FFT: KISS")
|
||||||
|
else()
|
||||||
|
message(STATUS "Kokkos FFT: hipFFT")
|
||||||
|
endif()
|
||||||
|
else()
|
||||||
|
message(STATUS "Kokkos FFT: ${FFT}")
|
||||||
|
endif()
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -46,6 +46,42 @@ else()
|
|||||||
target_compile_definitions(lammps PRIVATE -DFFT_KISS)
|
target_compile_definitions(lammps PRIVATE -DFFT_KISS)
|
||||||
endif()
|
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 "array" CACHE STRING "Optimization for FFT")
|
||||||
set(FFT_PACK_VALUES array pointer memcpy)
|
set(FFT_PACK_VALUES array pointer memcpy)
|
||||||
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
|
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
|
||||||
|
|||||||
@ -1,33 +1,40 @@
|
|||||||
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_URL)
|
||||||
mark_as_advanced(PACELIB_MD5)
|
mark_as_advanced(PACELIB_MD5)
|
||||||
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
|
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
|
||||||
|
|
||||||
# download library sources to build folder
|
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
|
||||||
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
|
# to make it easier to check local build without going through the public github releases
|
||||||
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
|
if(LOCAL_ML-PACE)
|
||||||
endif()
|
set(lib-pace "${LOCAL_ML-PACE}")
|
||||||
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 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
|
|
||||||
if((NOT DL_STATUS EQUAL 0) OR (NOT "${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")
|
# download library sources to build folder
|
||||||
endif()
|
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}")
|
||||||
|
message(STATUS "Downloading ${PACELIB_URL}")
|
||||||
|
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
|
||||||
|
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
|
||||||
|
if((NOT DL_STATUS EQUAL 0) OR (NOT "${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()
|
||||||
|
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
|
||||||
|
endif()
|
||||||
|
|
||||||
# uncompress downloaded sources
|
|
||||||
execute_process(
|
# uncompress downloaded sources
|
||||||
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
|
execute_process(
|
||||||
COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
|
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
|
||||||
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
|
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)
|
add_subdirectory(${lib-pace} build-pace)
|
||||||
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
|
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
|
||||||
|
|||||||
@ -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
|
require use of an FFT library to compute 1d FFTs. The KISS FFT
|
||||||
library is included with LAMMPS, but other libraries can be faster.
|
library is included with LAMMPS, but other libraries can be faster.
|
||||||
LAMMPS can use them if they are available on your system.
|
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::
|
.. 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=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_SINGLE=value # yes or no (default), no = double precision
|
||||||
-D FFT_PACK=value # array (default) or pointer or memcpy
|
-D FFT_PACK=value # array (default) or pointer or memcpy
|
||||||
|
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
|
||||||
|
|
||||||
.. note::
|
.. 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 MKL_INCLUDE_DIR=path # ditto for Intel MKL library
|
||||||
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
|
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
|
||||||
-D MKL_LIBRARY=path # path to 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
|
.. 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``
|
files in its default search path. You must specify ``FFT_LIB``
|
||||||
with the appropriate FFT libraries to include in the link.
|
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
|
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
|
||||||
included in the LAMMPS distribution. It is portable across all
|
included in the LAMMPS distribution. It is portable across all
|
||||||
platforms. Depending on the size of the FFTs and the number of
|
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
|
processors used, one option may be slightly faster. The default is
|
||||||
ARRAY mode.
|
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:
|
.. _size:
|
||||||
|
|||||||
@ -100,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
|
|||||||
* :doc:`nbond/atom <compute_nbond_atom>`
|
* :doc:`nbond/atom <compute_nbond_atom>`
|
||||||
* :doc:`omega/chunk <compute_omega_chunk>`
|
* :doc:`omega/chunk <compute_omega_chunk>`
|
||||||
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
|
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
|
||||||
|
* :doc:`pace <compute_pace>`
|
||||||
* :doc:`pair <compute_pair>`
|
* :doc:`pair <compute_pair>`
|
||||||
* :doc:`pair/local <compute_pair_local>`
|
* :doc:`pair/local <compute_pair_local>`
|
||||||
* :doc:`pe <compute_pe>`
|
* :doc:`pe <compute_pe>`
|
||||||
@ -115,6 +116,7 @@ KOKKOS, o = OPENMP, t = OPT.
|
|||||||
* :doc:`property/grid <compute_property_grid>`
|
* :doc:`property/grid <compute_property_grid>`
|
||||||
* :doc:`property/local <compute_property_local>`
|
* :doc:`property/local <compute_property_local>`
|
||||||
* :doc:`ptm/atom <compute_ptm_atom>`
|
* :doc:`ptm/atom <compute_ptm_atom>`
|
||||||
|
* :doc:`rattlers/atom <compute_rattlers_atom>`
|
||||||
* :doc:`rdf <compute_rdf>`
|
* :doc:`rdf <compute_rdf>`
|
||||||
* :doc:`reduce <compute_reduce>`
|
* :doc:`reduce <compute_reduce>`
|
||||||
* :doc:`reduce/chunk <compute_reduce_chunk>`
|
* :doc:`reduce/chunk <compute_reduce_chunk>`
|
||||||
|
|||||||
@ -122,6 +122,7 @@ OPT.
|
|||||||
* :doc:`mvv/tdpd <fix_mvv_dpd>`
|
* :doc:`mvv/tdpd <fix_mvv_dpd>`
|
||||||
* :doc:`neb <fix_neb>`
|
* :doc:`neb <fix_neb>`
|
||||||
* :doc:`neb/spin <fix_neb_spin>`
|
* :doc:`neb/spin <fix_neb_spin>`
|
||||||
|
* :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
|
||||||
* :doc:`nph (ko) <fix_nh>`
|
* :doc:`nph (ko) <fix_nh>`
|
||||||
* :doc:`nph/asphere (o) <fix_nph_asphere>`
|
* :doc:`nph/asphere (o) <fix_nph_asphere>`
|
||||||
* :doc:`nph/body <fix_nph_body>`
|
* :doc:`nph/body <fix_nph_body>`
|
||||||
@ -238,10 +239,10 @@ OPT.
|
|||||||
* :doc:`store/force <fix_store_force>`
|
* :doc:`store/force <fix_store_force>`
|
||||||
* :doc:`store/state <fix_store_state>`
|
* :doc:`store/state <fix_store_state>`
|
||||||
* :doc:`tdpd/source <fix_dpd_source>`
|
* :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/csld <fix_temp_csvr>`
|
||||||
* :doc:`temp/csvr <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:`temp/rescale/eff <fix_temp_rescale_eff>`
|
||||||
* :doc:`tfmc <fix_tfmc>`
|
* :doc:`tfmc <fix_tfmc>`
|
||||||
* :doc:`tgnpt/drude <fix_tgnh_drude>`
|
* :doc:`tgnpt/drude <fix_tgnh_drude>`
|
||||||
|
|||||||
@ -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
|
have to be adapted. The REAXFF package was originally called
|
||||||
USER-REAXC.
|
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
|
USER-CUDA package
|
||||||
-----------------
|
-----------------
|
||||||
|
|
||||||
|
|||||||
@ -101,6 +101,7 @@ Tutorials howto
|
|||||||
Howto_cmake
|
Howto_cmake
|
||||||
Howto_github
|
Howto_github
|
||||||
Howto_lammps_gui
|
Howto_lammps_gui
|
||||||
|
Howto_moltemplate
|
||||||
Howto_pylammps
|
Howto_pylammps
|
||||||
Howto_wsl
|
Howto_wsl
|
||||||
|
|
||||||
|
|||||||
@ -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
|
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
|
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
|
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
|
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
|
faces. The last value is the diameter value = the rounded diameter of
|
||||||
the sphere that surrounds each vertex. The diameter value can be
|
the sphere that surrounds each vertex. The diameter value can be
|
||||||
|
|||||||
371
doc/src/Howto_moltemplate.rst
Normal file
371
doc/src/Howto_moltemplate.rst
Normal file
@ -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).
|
||||||
BIN
doc/src/JPG/PolyNIPAM.jpg
Normal file
BIN
doc/src/JPG/PolyNIPAM.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 40 KiB |
BIN
doc/src/JPG/sample01.png
Normal file
BIN
doc/src/JPG/sample01.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 808 KiB |
BIN
doc/src/JPG/solv_01.png
Normal file
BIN
doc/src/JPG/solv_01.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 86 KiB |
@ -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:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
|
||||||
* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
|
* :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
|
||||||
* :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
|
* :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 <compute_pair>` - values computed by a pair style
|
||||||
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
|
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
|
||||||
* :doc:`pe <compute_pe>` - potential energy
|
* :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/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:`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:`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:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
|
||||||
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
|
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
|
||||||
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
|
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
|
||||||
|
|||||||
@ -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
|
The value of the contact number will be 0.0 for atoms not in the
|
||||||
specified compute group.
|
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
|
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
|
The per-atom vector values will be a number :math:`\ge 0.0`, as explained
|
||||||
above.
|
above.
|
||||||
|
|
||||||
The optional *group2-ID* argument allows to specify from which group atoms
|
|
||||||
contribute to the coordination number. Default setting is group 'all.'
|
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
@ -69,6 +69,3 @@ Default
|
|||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
*group2-ID* = all
|
*group2-ID* = all
|
||||||
|
|
||||||
|
|
||||||
none
|
|
||||||
|
|||||||
251
doc/src/compute_pace.rst
Normal file
251
doc/src/compute_pace.rst
Normal file
@ -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).
|
||||||
92
doc/src/compute_rattlers_atom.rst
Normal file
92
doc/src/compute_rattlers_atom.rst
Normal file
@ -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
|
||||||
@ -62,28 +62,29 @@ equations:
|
|||||||
\frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
|
\frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
|
||||||
|
|
||||||
Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
|
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
|
:math:`r_j` is the position of each atom, :math:`f_j` are atomic
|
||||||
factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
|
scattering factors, *Lp* is the Lorentz-polarization factor, and
|
||||||
scattering angle of diffraction. The Lorentz-polarization factor can be turned
|
:math:`\theta` is the scattering angle of diffraction. The
|
||||||
off using the optional *LP* keyword.
|
Lorentz-polarization factor can be turned off using the optional *LP*
|
||||||
|
keyword.
|
||||||
|
|
||||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||||
reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
|
reciprocal lattice nodes. The mesh spacing is defined either (a) by the
|
||||||
simulation domain or (b) manually using selected values as
|
entire simulation domain or (b) manually using selected values as shown
|
||||||
shown in the 2D diagram below.
|
in the 2D diagram below.
|
||||||
|
|
||||||
.. image:: img/xrd_mesh.jpg
|
.. image:: img/xrd_mesh.png
|
||||||
:scale: 75%
|
:scale: 75%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
For a mesh defined by the simulation domain, a rectilinear grid is
|
For a mesh defined by the simulation domain, a rectilinear grid is
|
||||||
constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
|
constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
|
||||||
axis, where :math:`A` is a matrix containing the vectors corresponding to the
|
axis, where :math:`A` is a matrix containing the vectors corresponding
|
||||||
edges of the simulation cell. If one or two directions has non-periodic
|
to the edges of the simulation cell. If one or two directions has
|
||||||
boundary conditions, then the spacing in these directions is defined from the
|
non-periodic boundary conditions, then the spacing in these directions
|
||||||
average of the (inversed) box lengths with periodic boundary conditions.
|
is defined from the average of the (inversed) box lengths with periodic
|
||||||
Meshes defined by the simulation domain must contain at least one periodic
|
boundary conditions. Meshes defined by the simulation domain must
|
||||||
boundary.
|
contain at least one periodic boundary.
|
||||||
|
|
||||||
If the *manual* flag is included, the mesh of reciprocal lattice nodes
|
If the *manual* flag is included, the mesh of reciprocal lattice nodes
|
||||||
will be defined using the *c* values for the spacing along each
|
will be defined using the *c* values for the spacing along each
|
||||||
|
|||||||
@ -287,6 +287,7 @@ accelerated styles exist.
|
|||||||
* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
|
* :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 <fix_neb>` - nudged elastic band (NEB) spring forces
|
||||||
* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
|
* :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 <fix_nh>` - constant NPH time integration via Nose/Hoover
|
||||||
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
|
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
|
||||||
* :doc:`nph/body <fix_nph_body>` - NPH for body particles
|
* :doc:`nph/body <fix_nph_body>` - NPH for body particles
|
||||||
|
|||||||
@ -205,6 +205,8 @@ formulas for the meaning of these parameters:
|
|||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
|
| :doc:`pace, pace/extrapolation <pair_pace>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
|
| :doc:`quip <pair_quip>` | scale | type global |
|
||||||
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`snap <pair_snap>` | scale | type pairs |
|
| :doc:`snap <pair_snap>` | scale | type pairs |
|
||||||
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
|
||||||
| :doc:`spin/dmi <pair_spin_dmi>` | coulombic_cutoff | type global |
|
| :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
|
hybrid/overlay as bond styles. The bond styles that currently work
|
||||||
with fix_adapt are
|
with fix_adapt are
|
||||||
|
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`class2 <bond_class2>` | r0 | type bonds |
|
| :doc:`class2 <bond_class2>` | r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
|
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
|
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
|
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
|
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`morse <bond_morse>` | r0 | type bonds |
|
| :doc:`morse <bond_morse>` | r0 | type bonds |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+------------+------------+
|
||||||
| :doc:`nonlinear <bond_nonlinear>` | epsilon,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
|
hybrid/overlay as angle styles. The angle styles that currently work
|
||||||
with fix_adapt are
|
with fix_adapt are
|
||||||
|
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+----------+-------------+
|
||||||
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
|
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+----------+-------------+
|
||||||
| :doc:`cosine <angle_cosine>` | k | type angles |
|
| :doc:`cosine <angle_cosine>` | k | type angles |
|
||||||
+------------------------------------+-------+-----------------+
|
+------------------------------------+----------+-------------+
|
||||||
|
|
||||||
Note that internally, theta0 is stored in radians, so the variable
|
Note that internally, theta0 is stored in radians, so the variable
|
||||||
this fix uses to reset theta0 needs to generate values in radians.
|
this fix uses to reset theta0 needs to generate values in radians.
|
||||||
@ -482,7 +484,7 @@ Restrictions
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`compute ti <compute_ti>`
|
:doc:`compute ti <compute_ti>`, :doc:`fix adapt/fep <fix_adapt_fep>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -23,7 +23,7 @@ Syntax
|
|||||||
.. parsed-literal::
|
.. 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*
|
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
|
*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
|
sets the external dimensions used to calculate the scalar pressure
|
||||||
*strain* values = e_x e_y = initial strain
|
*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>`
|
<fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
|
||||||
commands.
|
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
|
*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
|
directions. It is implicitly assumed that the flow field is
|
||||||
traceless, and therefore the strain rate in the zz direction is eqal
|
traceless, and therefore the strain rate in the zz direction is eqal
|
||||||
|
|||||||
133
doc/src/fix_nonaffine_displacement.rst
Normal file
133
doc/src/fix_nonaffine_displacement.rst
Normal file
@ -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).
|
||||||
@ -80,7 +80,7 @@ Syntax
|
|||||||
groupID1, groupID2, ... = list of N group IDs
|
groupID1, groupID2, ... = list of N group IDs
|
||||||
|
|
||||||
* zero or more keyword/value pairs may be appended
|
* 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::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -92,6 +92,8 @@ Syntax
|
|||||||
*temp* values = Tstart Tstop Tdamp
|
*temp* values = Tstart Tstop Tdamp
|
||||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||||
Tdamp = temperature damping parameter (time 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
|
*iso* or *aniso* values = Pstart Pstop Pdamp
|
||||||
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
|
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
|
||||||
Pdamp = pressure damping parameter (time units)
|
Pdamp = pressure damping parameter (time units)
|
||||||
|
|||||||
@ -1,8 +1,11 @@
|
|||||||
.. index:: fix temp/berendsen
|
.. index:: fix temp/berendsen
|
||||||
|
.. index:: fix temp/berendsen/kk
|
||||||
|
|
||||||
fix temp/berendsen command
|
fix temp/berendsen command
|
||||||
==========================
|
==========================
|
||||||
|
|
||||||
|
Accelerator Variants: *temp/berendsen/kk*
|
||||||
|
|
||||||
Syntax
|
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
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -1,8 +1,11 @@
|
|||||||
.. index:: fix temp/rescale
|
.. index:: fix temp/rescale
|
||||||
|
.. index:: fix temp/rescale/kk
|
||||||
|
|
||||||
fix temp/rescale command
|
fix temp/rescale command
|
||||||
========================
|
========================
|
||||||
|
|
||||||
|
Accelerator Variants: *temp/rescale/kk*
|
||||||
|
|
||||||
Syntax
|
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
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
Binary file not shown.
|
Before Width: | Height: | Size: 118 KiB |
BIN
doc/src/img/xrd_mesh.png
Normal file
BIN
doc/src/img/xrd_mesh.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 101 KiB |
@ -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
|
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
|
line. The keyword should appear at the end of the line. All these
|
||||||
settings have default values, as explained below. A line need only
|
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
|
* N *atoms* = # of atoms N in molecule, default = 0
|
||||||
* Nb *bonds* = # of bonds Nb in molecule, default = 0
|
* Nb *bonds* = # of bonds Nb in molecule, default = 0
|
||||||
* Na *angles* = # of angles Na in molecule, default = 0
|
* Na *angles* = # of angles Na in molecule, default = 0
|
||||||
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
|
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
|
||||||
* Ni *impropers* = # of impropers Ni 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
|
* Mtotal *mass* = total mass of molecule
|
||||||
* Xc Yc Zc *com* = coordinates of center-of-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
|
* 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
|
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
|
||||||
calculate this quantity itself if needed, assuming the molecules
|
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
|
non-zero diameter) that do not overlap. If finite-size particles in
|
||||||
the molecule do overlap, LAMMPS will not account for the overlap
|
the molecule do overlap, LAMMPS will not account for the overlap
|
||||||
effects when calculating any of these 3 quantities, so you should
|
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
|
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
|
||||||
* *Special Bond Counts, Special Bonds* = special neighbor info
|
* *Special Bond Counts, Special Bonds* = special neighbor info
|
||||||
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE 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
|
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
|
||||||
atom/bond/angle/etc type can be specified either as a number (numeric
|
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
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -30,11 +30,11 @@ Description
|
|||||||
|
|
||||||
Style *beck* computes interactions based on the potential by
|
Style *beck* computes interactions based on the potential by
|
||||||
:ref:`(Beck) <Beck>`, originally designed for simulation of Helium. It
|
: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::
|
.. 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
|
The following coefficients must be defined for each pair of atoms
|
||||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||||
@ -50,7 +50,7 @@ commands.
|
|||||||
* cutoff (distance units)
|
* cutoff (distance units)
|
||||||
|
|
||||||
The last coefficient is optional. If not specified, the global cutoff
|
The last coefficient is optional. If not specified, the global cutoff
|
||||||
:math:`R_c` is used.
|
:math:`r_c` is used.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -58,6 +58,40 @@ Examples
|
|||||||
Description
|
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,
|
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
|
||||||
given by
|
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
|
distance are computed directly; interactions outside that distance are
|
||||||
computed in reciprocal space.
|
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
|
Coefficients
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|||||||
@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
|
|||||||
interaction (aka Shifted Force Lennard-Jones) that combines the
|
interaction (aka Shifted Force Lennard-Jones) that combines the
|
||||||
standard 12/6 Lennard-Jones function and subtracts a linear term based
|
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
|
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::
|
.. math::
|
||||||
|
|
||||||
\phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
\phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||||
\left(\frac{\sigma}{r}\right)^6 \right] \\
|
\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
|
The following coefficients must be defined for each pair of atoms
|
||||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
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
|
pressure, since the energy of the pair interaction is smoothed to 0.0
|
||||||
at the cutoff.
|
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
|
This pair style writes its information to :doc:`binary restart files <restart>`,
|
||||||
to be specified in an input script that reads a restart file.
|
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
|
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
|
:doc:`run_style respa <run_style>` command. It does not support the
|
||||||
|
|||||||
@ -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]
|
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
|
||||||
\qquad r < r_c
|
\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:
|
attractive exponents, given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|||||||
@ -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]
|
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
|
||||||
\qquad r < r_c
|
\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
|
The following coefficients must be defined for each pair of atoms
|
||||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
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::
|
.. 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 \\
|
\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 syntax of the pair_style and pair_coeff commands are the same for
|
||||||
the *morse* and *morse/smooth/linear* styles.
|
the *morse* and *morse/smooth/linear* styles.
|
||||||
|
|||||||
@ -40,6 +40,9 @@ Examples
|
|||||||
pair_style pace product chunksize 2048
|
pair_style pace product chunksize 2048
|
||||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||||
|
|
||||||
|
pair_style pace
|
||||||
|
pair_coeff * * Cu.yaml Cu
|
||||||
|
|
||||||
pair_style pace/extrapolation
|
pair_style pace/extrapolation
|
||||||
pair_coeff * * Cu.yaml Cu.asi Cu
|
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
|
specifying the mapping of ACE elements to LAMMPS atom types, where N is
|
||||||
the number of LAMMPS atom types:
|
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
|
* N element names = mapping of ACE elements to atom types
|
||||||
|
|
||||||
Only a single pair_coeff command is used with the *pace* style which
|
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
|
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
|
||||||
to specify the path for the ACE coefficient file.
|
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
|
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -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
|
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),
|
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
|
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
|
interactions over time. :math:`r_c` is the cutoff.
|
||||||
overlapping atoms.
|
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
|
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,
|
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
|
||||||
|
|||||||
@ -81,7 +81,7 @@ given by
|
|||||||
|
|
||||||
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
|
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>`.
|
: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
|
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
|
Style *lj/spica/coul/long* computes the adds Coulombic interactions
|
||||||
|
|||||||
@ -1077,6 +1077,7 @@ facesets
|
|||||||
factorizable
|
factorizable
|
||||||
factorizations
|
factorizations
|
||||||
Fahrenberger
|
Fahrenberger
|
||||||
|
Falk
|
||||||
Faken
|
Faken
|
||||||
Farago
|
Farago
|
||||||
Fasolino
|
Fasolino
|
||||||
@ -1176,6 +1177,7 @@ Foiles
|
|||||||
fopenmp
|
fopenmp
|
||||||
forceclear
|
forceclear
|
||||||
forestgreen
|
forestgreen
|
||||||
|
formamide
|
||||||
formatarg
|
formatarg
|
||||||
formulae
|
formulae
|
||||||
Forschungszentrum
|
Forschungszentrum
|
||||||
@ -1826,6 +1828,7 @@ Lanczos
|
|||||||
Lande
|
Lande
|
||||||
Landron
|
Landron
|
||||||
Landsgesell
|
Landsgesell
|
||||||
|
Langer
|
||||||
langevin
|
langevin
|
||||||
Langevin
|
Langevin
|
||||||
Langston
|
Langston
|
||||||
@ -1976,6 +1979,7 @@ lpsapi
|
|||||||
lr
|
lr
|
||||||
lrt
|
lrt
|
||||||
lsfftw
|
lsfftw
|
||||||
|
lt
|
||||||
ltbbmalloc
|
ltbbmalloc
|
||||||
Lua
|
Lua
|
||||||
lubricateU
|
lubricateU
|
||||||
@ -2510,6 +2514,7 @@ noforce
|
|||||||
noguess
|
noguess
|
||||||
Noid
|
Noid
|
||||||
nolib
|
nolib
|
||||||
|
nonaffine
|
||||||
nonequilibrium
|
nonequilibrium
|
||||||
nongauss
|
nongauss
|
||||||
nonGaussian
|
nonGaussian
|
||||||
@ -2582,6 +2587,7 @@ nthreads
|
|||||||
ntimestep
|
ntimestep
|
||||||
Ntptask
|
Ntptask
|
||||||
Ntriples
|
Ntriples
|
||||||
|
ntries
|
||||||
ntris
|
ntris
|
||||||
Ntype
|
Ntype
|
||||||
ntypes
|
ntypes
|
||||||
@ -3387,6 +3393,7 @@ Sodani
|
|||||||
Soderlind
|
Soderlind
|
||||||
Solaris
|
Solaris
|
||||||
Solida
|
Solida
|
||||||
|
solv
|
||||||
solvated
|
solvated
|
||||||
solvation
|
solvation
|
||||||
someuser
|
someuser
|
||||||
@ -3633,6 +3640,7 @@ timestepping
|
|||||||
timesteps
|
timesteps
|
||||||
TiN
|
TiN
|
||||||
TiO
|
TiO
|
||||||
|
Tirado
|
||||||
Tirrell
|
Tirrell
|
||||||
Titer
|
Titer
|
||||||
Tji
|
Tji
|
||||||
|
|||||||
9
examples/PACKAGES/pace/README.md
Normal file
9
examples/PACKAGES/pace/README.md
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
# This folder contains examples for pace in LAMMPS
|
||||||
|
|
||||||
|
|
||||||
|
## Compute pace usage
|
||||||
|
compute/latte_cell_0.data # lammps data file with C-H-O structure
|
||||||
|
compute/latte_cell_0.xyz # xyz file with C-H-O structure
|
||||||
|
compute/coupling_coefficients.yace # .yace file containing coupling coefficients (or ACE potential parameters)
|
||||||
|
compute/in.compute # input file for calling `compute pace`
|
||||||
|
|
||||||
294
examples/PACKAGES/pace/compute/coupling_coefficients.yace
Normal file
294
examples/PACKAGES/pace/compute/coupling_coefficients.yace
Normal file
@ -0,0 +1,294 @@
|
|||||||
|
elements: [H, N, O]
|
||||||
|
E0: [0.000000, 0.000000, 0.000000]
|
||||||
|
deltaSplineBins: 0.001000
|
||||||
|
embeddings:
|
||||||
|
0: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
|
||||||
|
1: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
|
||||||
|
2: {ndensity: 1, FS_parameters: [1.0, 1.0], npoti: FinnisSinclair, rho_core_cutoff: 100000, drho_core_cutoff: 250}
|
||||||
|
bonds:
|
||||||
|
[0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.0, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[0, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[0, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[1, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[1, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 4.4, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[1, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[2, 0]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[2, 1]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.7, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
[2, 2]: {nradmax: 2, lmax: 2, nradbasemax: 2, radbasename: ChebExpCos, radparameters: [3.3], radcoefficients: [[[1, 0], [1, 0], [1, 0]], [[0, 1], [0, 1], [0, 1]]], prehc: 0, lambdahc: 3.3, rcut: 5.5, dcut: 0.01, rcut_in: 0.1, dcut_in: 0.01, inner_cutoff_type: distance}
|
||||||
|
functions:
|
||||||
|
0:
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, 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: 0, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 0], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 0, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 0, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [0, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 1], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
- {mu0: 0, rank: 4, ndensity: 1, num_ms_combs: 19, mus: [2, 2, 2, 2], ns: [1, 1, 1, 1], ls: [1, 1, 1, 1], ms_combs: [-1, -1, 1, 1, -1, 0, 0, 1, -1, 0, 1, 0, -1, 1, -1, 1, -1, 1, 0, 0, -1, 1, 1, -1, 0, -1, 0, 1, 0, -1, 1, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 1, -1, 0, 1, -1, 0, 0, 1, 0, -1, 1, -1, -1, 1, 1, -1, 0, 0, 1, -1, 1, -1, 1, 0, -1, 0, 1, 0, 0, -1, 1, 1, -1, -1], ctildes: [0.0, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, -0.3333333333333333, 0.3333333333333333, -0.3333333333333333, 0.0, 0.0, 0.3333333333333333, -0.3333333333333333, 0.3333333333333333, 0.0, 0.0, 0.0]}
|
||||||
|
1:
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [1], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [2], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 1, ndensity: 1, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [1.0]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 1], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {mu0: 1, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
|
||||||
|
- {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]}
|
||||||
|
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 0, 0], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
|
||||||
|
- {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]}
|
||||||
|
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 1], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
|
||||||
|
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 1, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
|
||||||
|
- {mu0: 1, 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: 1, 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: 1, rank: 3, ndensity: 1, num_ms_combs: 19, mus: [1, 2, 2], ns: [1, 1, 1], ls: [2, 2, 2], ms_combs: [-2, 0, 2, -2, 1, 1, -2, 2, 0, -1, -1, 2, -1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -2, 2, 0, -1, 1, 0, 0, 0, 0, 1, -1, 0, 2, -2, 1, -2, 1, 1, -1, 0, 1, 0, -1, 1, 1, -2, 2, -2, 0, 2, -1, -1, 2, 0, -2], ctildes: [0.10690449676496976, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, 0.05345224838248488, -0.10690449676496976, 0.05345224838248488, 0.10690449676496976, -0.1309307341415954, 0.05345224838248488, 0.05345224838248488, -0.1309307341415954, 0.10690449676496976, -0.1309307341415954, 0.10690449676496976]}
|
||||||
|
- {mu0: 1, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [0, 1, 2], ns: [1, 1, 1], ls: [1, 1, 2], ms_combs: [-1, -1, 2, -1, 0, 1, -1, 1, 0, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -1, 0, 1, 0, -1, 1, 1, -2], ctildes: [0.19999999999999998, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.16329931618554522, -0.1414213562373095, 0.08164965809277261, -0.1414213562373095, 0.19999999999999998]}
|
||||||
|
- {mu0: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 1, 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: 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
22
examples/PACKAGES/pace/compute/in.compute
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
#info all out log
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
boundary p p p
|
||||||
|
atom_modify map hash
|
||||||
|
boundary p p p
|
||||||
|
read_data latte_cell_0.data
|
||||||
|
mass 1 1.00
|
||||||
|
mass 2 14.00
|
||||||
|
mass 3 15.999
|
||||||
|
|
||||||
|
# potential settings
|
||||||
|
|
||||||
|
pair_style zero 5.7
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
compute pace all pace coupling_coefficients.yace 1 0
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
thermo_style custom step temp c_pace[1][183]
|
||||||
|
|
||||||
|
run 0
|
||||||
172
examples/PACKAGES/pace/compute/latte_cell_0.data
Normal file
172
examples/PACKAGES/pace/compute/latte_cell_0.data
Normal file
@ -0,0 +1,172 @@
|
|||||||
|
latte_cell_0.data (written by ASE)
|
||||||
|
|
||||||
|
161 atoms
|
||||||
|
3 atom types
|
||||||
|
0.0 12 xlo xhi
|
||||||
|
0.0 12 ylo yhi
|
||||||
|
0.0 12 zlo zhi
|
||||||
|
|
||||||
|
|
||||||
|
Atoms
|
||||||
|
|
||||||
|
1 3 1.2688096799999999 2.0079938400000001 2.7446829899999998
|
||||||
|
2 1 1.5343068200000001 2.0638766500000001 3.7105626900000002
|
||||||
|
3 1 1.7848279600000001 2.6755003400000001 2.2268847200000002
|
||||||
|
4 1 1.56251195 1.1089126899999999 2.3978115199999999
|
||||||
|
5 1 11.61728216 5.71881094 2.4732045999999999
|
||||||
|
6 2 6.5501865600000002 4.7439566800000001 3.6526025500000001
|
||||||
|
7 1 6.4564895299999998 4.1571673000000002 2.6975267999999999
|
||||||
|
8 2 2.0835561 1.59406078 8.5498047600000007
|
||||||
|
9 1 1.1041162499999999 1.4971771599999999 8.1507879200000009
|
||||||
|
10 1 2.60115534 2.2945960400000001 7.95374187
|
||||||
|
11 1 1.9817723300000001 2.0194066400000001 9.5128239400000005
|
||||||
|
12 1 0.99333338000000004 3.6983907299999998 8.1903947899999991
|
||||||
|
13 3 4.9484070999999998 5.3645501400000004 9.16152503
|
||||||
|
14 1 9.0716170599999995 9.3748453999999999 4.2276462400000003
|
||||||
|
15 2 0.30864418999999998 7.7136657499999997 2.9274995599999998
|
||||||
|
16 1 0.47661671 10.1807211 3.71160091
|
||||||
|
17 1 1.07465334 7.8226921999999997 3.5771466900000002
|
||||||
|
18 1 0.38402249999999999 8.3770493300000002 2.1748437100000002
|
||||||
|
19 1 11.435413410000001 7.7903735999999997 3.4040245499999999
|
||||||
|
20 3 6.1570384599999999 10.25988474 3.50899568
|
||||||
|
21 1 5.5932224399999999 9.5632944700000007 3.1446559000000001
|
||||||
|
22 2 1.7785569000000001 7.6312579300000003 9.1488452299999992
|
||||||
|
23 1 2.5594048599999999 6.96832838 9.3069700199999996
|
||||||
|
24 1 2.12441551 8.4547986999999996 8.6428622900000001
|
||||||
|
25 1 1.04552782 7.1697722800000001 8.5894244999999998
|
||||||
|
26 1 0.34824445999999998 10.17844028 9.1629463799999993
|
||||||
|
27 3 5.9638830399999998 10.723709400000001 9.4568803900000002
|
||||||
|
28 1 6.5890835699999997 10.926486110000001 8.7981925800000003
|
||||||
|
29 2 7.1065890400000002 1.83029753 3.3452543600000002
|
||||||
|
30 1 6.9229304999999997 1.8465022099999999 4.3089037100000001
|
||||||
|
31 1 8.0780433600000006 1.9303052199999999 3.2089521400000001
|
||||||
|
32 1 5.6795373600000003 10.471831630000001 4.3244390499999996
|
||||||
|
33 1 6.82999417 0.95850113000000003 2.9815288199999999
|
||||||
|
34 2 11.383805349999999 4.6301225199999996 2.5393688399999998
|
||||||
|
35 1 0.37927047000000003 4.1943216300000001 2.59073807
|
||||||
|
36 3 5.2376410099999999 1.91523463 9.7240636400000007
|
||||||
|
37 1 4.7887202499999999 2.7036936499999999 9.5698142300000004
|
||||||
|
38 1 9.8129906699999996 9.2075140700000002 4.08265499
|
||||||
|
39 1 4.7980879500000002 1.1403494700000001 9.6739962800000008
|
||||||
|
40 1 5.4455845600000004 2.0102099999999998 10.620773509999999
|
||||||
|
41 3 0.90954338999999995 4.6240093199999999 8.3108110600000007
|
||||||
|
42 1 11.909735319999999 4.7483814000000004 8.2500624600000005
|
||||||
|
43 2 7.3223424499999998 7.5866457 3.0245226500000002
|
||||||
|
44 1 7.4470362200000002 8.3169646700000008 3.7148003300000001
|
||||||
|
45 1 6.9073805300000002 7.9385021 2.1723768699999999
|
||||||
|
46 1 5.5542868500000004 5.1176065800000003 3.7655251999999999
|
||||||
|
47 1 6.8124309500000004 6.7778811599999997 3.3973232499999999
|
||||||
|
48 2 0.29575823000000001 11.04303794 3.1016142499999999
|
||||||
|
49 1 0.86490721999999998 11.83879228 3.6389974500000002
|
||||||
|
50 3 6.85201686 8.0846369300000003 8.8762878799999996
|
||||||
|
51 1 7.3351430100000004 7.4263498700000001 9.3821674799999997
|
||||||
|
52 1 6.7919613300000004 7.7595477199999996 7.9716174799999999
|
||||||
|
53 1 3.8990487699999998 6.4283490399999996 8.8832409600000002
|
||||||
|
54 1 5.95997296 9.9329723199999993 9.4746654699999997
|
||||||
|
55 3 11.403658979999999 10.371960359999999 9.2766092199999992
|
||||||
|
56 1 10.983666360000001 9.5157199800000001 9.1478757300000009
|
||||||
|
57 3 1.5223279700000001 5.3327331100000004 0.57537605999999997
|
||||||
|
58 1 2.3815113999999999 5.7251991200000001 0.77945295999999997
|
||||||
|
59 1 0.92079957000000001 6.0931282299999996 0.62203253000000003
|
||||||
|
60 3 11.23490924 2.9153355200000002 6.7585064099999999
|
||||||
|
61 1 10.792340190000001 2.9755225099999998 5.9000018399999998
|
||||||
|
62 1 10.751242059999999 2.1896156000000002 7.1807401500000001
|
||||||
|
63 3 11.39027944 7.3462855600000001 6.7258299499999996
|
||||||
|
64 1 10.92025679 6.69831954 7.2776696599999999
|
||||||
|
65 1 11.12238028 7.0632020999999998 5.8394107799999997
|
||||||
|
66 3 8.4684319499999994 10.71736286 10.60018556
|
||||||
|
67 1 8.5672201599999998 11.420466080000001 11.25794033
|
||||||
|
68 1 9.0803109800000001 10.04804949 10.9406517
|
||||||
|
69 3 6.5851757299999996 9.9940623399999993 6.5574614899999997
|
||||||
|
70 1 7.0276325799999997 10.76096604 6.1723333699999996
|
||||||
|
71 1 5.7419327400000002 10.384583920000001 6.8228822999999998
|
||||||
|
72 3 1.7600546399999999 1.01771919 5.4926787700000004
|
||||||
|
73 1 1.9704209100000001 1.01748419 6.4429703700000003
|
||||||
|
74 1 1.42973007 0.11076352 5.3470644900000002
|
||||||
|
75 1 2.61130613 9.7034123700000006 10.450306830000001
|
||||||
|
76 3 3.05086908 10.48131334 10.085189310000001
|
||||||
|
77 1 3.0032693199999998 10.93357295 9.3652121000000008
|
||||||
|
78 3 6.4631532199999997 8.7652058299999993 11.967847969999999
|
||||||
|
79 1 6.4506808400000004 9.6596595300000008 11.588956019999999
|
||||||
|
80 1 5.6611629700000003 8.3535737700000006 11.638443329999999
|
||||||
|
81 3 1.1745999300000001 5.2420690800000003 5.1001449699999997
|
||||||
|
82 1 1.31932881 5.5236392399999996 6.0128966300000002
|
||||||
|
83 1 0.58053834999999998 4.4898134599999997 5.2325565000000003
|
||||||
|
84 3 6.7275549699999999 0.78840874999999999 7.3817280900000002
|
||||||
|
85 1 6.3887965600000003 1.54670982 6.8634520400000003
|
||||||
|
86 1 7.6791783999999996 0.94039024000000004 7.2649461000000004
|
||||||
|
87 3 8.5476657199999995 0.0064750299999999997 5.0450514100000001
|
||||||
|
88 1 8.8736290899999997 11.10484108 4.8601807900000003
|
||||||
|
89 1 8.0477597599999999 0.20198361000000001 4.2357399400000002
|
||||||
|
90 3 1.2895030000000001 8.4280097900000008 11.82038504
|
||||||
|
91 1 1.4766666399999999 8.1087866399999999 10.87290333
|
||||||
|
92 1 2.10220669 8.1947620200000006 0.29510553
|
||||||
|
93 3 9.6797907599999995 6.4207335499999996 4.3469150599999997
|
||||||
|
94 1 8.9271530099999996 6.72940235 3.7974122399999999
|
||||||
|
95 1 10.20024126 5.9167739199999998 3.66976111
|
||||||
|
96 3 3.57411616 6.7041021699999996 3.8825478499999999
|
||||||
|
97 1 2.8894899500000002 6.1560529800000001 4.2980848099999998
|
||||||
|
98 1 4.3613707699999997 6.4304732400000004 4.3804965400000002
|
||||||
|
99 3 4.7506556 11.441853350000001 1.12537088
|
||||||
|
100 1 4.0861192800000001 10.748523670000001 1.1923347099999999
|
||||||
|
101 1 5.5035301600000004 10.965688249999999 0.73651277000000004
|
||||||
|
102 3 9.5254526399999992 4.8994443900000002 8.3732284099999994
|
||||||
|
103 1 8.7885959800000002 4.3508043900000004 8.6632831400000008
|
||||||
|
104 1 9.6149067499999994 4.6084911499999999 7.4540068699999997
|
||||||
|
105 3 4.1970746700000001 1.34592128 3.67401439
|
||||||
|
106 1 4.9437011999999996 0.74406280999999996 3.514068
|
||||||
|
107 1 4.1905534900000001 1.7730376000000001 2.7963049400000002
|
||||||
|
108 3 1.88232618 11.95451227 0.60024434000000004
|
||||||
|
109 1 2.0464587299999999 11.02454723 0.38329541
|
||||||
|
110 1 1.1518493700000001 0.17494340999999999 11.99928285
|
||||||
|
111 3 3.7593842199999998 11.01685511 6.4562050800000002
|
||||||
|
112 1 3.2125414299999999 10.4553747 5.8894917099999997
|
||||||
|
113 1 3.4166026899999999 10.821557670000001 7.3296563900000002
|
||||||
|
114 3 9.7039841399999993 3.95001545 11.894743249999999
|
||||||
|
115 1 10.461666060000001 3.9163117999999999 11.285435229999999
|
||||||
|
116 1 10.09834695 4.4026997400000001 0.68193007999999999
|
||||||
|
117 3 8.5639596400000002 3.5169507499999999 5.6224104199999996
|
||||||
|
118 1 8.3966650299999994 2.6262214699999999 5.2638164300000003
|
||||||
|
119 1 7.9695371399999999 4.0825059799999996 5.0049407400000003
|
||||||
|
120 3 9.6736245000000007 0.48030482000000002 7.9257577799999996
|
||||||
|
121 1 9.6131980400000003 11.883419180000001 7.1680923999999999
|
||||||
|
122 1 9.9784050299999993 11.90238635 8.63894187
|
||||||
|
123 3 3.9424153099999999 6.9650296699999998 11.60258943
|
||||||
|
124 1 4.2767152700000004 6.8460048999999996 10.670225220000001
|
||||||
|
125 1 4.6570638500000001 6.5129461500000003 0.091159879999999999
|
||||||
|
126 3 3.0570173199999999 9.6631958499999993 3.6611250599999998
|
||||||
|
127 1 2.5400490100000002 9.5743355000000001 2.8444047600000002
|
||||||
|
128 1 2.9314874400000002 8.7809807200000005 4.0425234200000002
|
||||||
|
129 3 7.4549612700000001 5.8430850799999998 11.011384720000001
|
||||||
|
130 1 8.1675884100000005 5.4639182799999997 10.47644287
|
||||||
|
131 1 6.7135573700000002 5.8393818399999997 10.361099749999999
|
||||||
|
132 3 9.8029139300000008 7.9578901699999998 10.21404942
|
||||||
|
133 1 10.38910242 8.3400641400000008 10.87949429
|
||||||
|
134 1 9.0637612000000001 7.6392374099999998 10.756928869999999
|
||||||
|
135 3 4.4963435599999997 4.1067935799999997 11.73387805
|
||||||
|
136 1 4.5473727899999998 4.9577970899999997 11.19223377
|
||||||
|
137 1 5.3588818399999996 4.1756111699999998 0.20355936999999999
|
||||||
|
138 3 9.5923448100000002 7.3418014600000001 1.34856172
|
||||||
|
139 1 8.8715593300000002 7.4776837199999999 2.05040471
|
||||||
|
140 1 9.0443221699999992 7.2732200799999998 0.54011714
|
||||||
|
141 3 7.0350963100000001 3.22348773 0.7070824
|
||||||
|
142 1 7.1784470499999999 4.1340314300000003 1.0184109699999999
|
||||||
|
143 1 7.7787854400000001 2.7888888399999998 1.15838887
|
||||||
|
144 3 9.2124107800000008 0.48085899999999998 1.21751966
|
||||||
|
145 1 9.6620436499999993 11.657271079999999 1.45318397
|
||||||
|
146 1 9.9404883900000005 1.11619136 1.18684594
|
||||||
|
147 3 1.19704207 9.5859959200000002 6.6190888899999996
|
||||||
|
148 1 0.25606413 9.6737366500000004 6.8319340899999998
|
||||||
|
149 1 1.2690051899999999 8.6249354900000004 6.5480112500000001
|
||||||
|
150 3 0.78256133999999999 2.6040609300000002 11.453408359999999
|
||||||
|
151 1 0.61502181 3.5607405999999999 11.40300991
|
||||||
|
152 1 1.55655312 2.5457368800000002 10.866733030000001
|
||||||
|
153 3 5.8627936099999998 7.1217054800000001 5.89173203
|
||||||
|
154 1 6.3432410700000004 7.9400136699999999 6.0855840299999997
|
||||||
|
155 1 5.5077296699999998 6.8468306800000001 6.7436875799999996
|
||||||
|
156 3 10.887828150000001 9.9637482500000001 0.51092815999999996
|
||||||
|
157 1 11.78841776 10.322043069999999 0.44704989000000001
|
||||||
|
158 1 11.02688182 9.2051906700000004 1.0976661299999999
|
||||||
|
159 3 3.93073389 4.1645674499999998 5.7137877000000001
|
||||||
|
160 1 4.6884062999999996 3.5788913299999998 5.5644605800000004
|
||||||
|
161 1 4.2956948500000003 4.7644888099999996 6.3801669700000003
|
||||||
163
examples/PACKAGES/pace/compute/latte_cell_0.xyz
Normal file
163
examples/PACKAGES/pace/compute/latte_cell_0.xyz
Normal file
@ -0,0 +1,163 @@
|
|||||||
|
161
|
||||||
|
Lattice="12.0 0.0 0.0 0.0 12.0 0.0 0.0 0.0 12.0" Properties=species:S:1:pos:R:3 pbc="T T T"
|
||||||
|
O 1.26880968 2.00799384 2.74468299
|
||||||
|
H 1.53430682 2.06387665 3.71056269
|
||||||
|
H 1.78482796 2.67550034 2.22688472
|
||||||
|
H 1.56251195 1.10891269 2.39781152
|
||||||
|
H 11.61728216 5.71881094 2.47320460
|
||||||
|
N 6.55018656 4.74395668 3.65260255
|
||||||
|
H 6.45648953 4.15716730 2.69752680
|
||||||
|
N 2.08355610 1.59406078 8.54980476
|
||||||
|
H 1.10411625 1.49717716 8.15078792
|
||||||
|
H 2.60115534 2.29459604 7.95374187
|
||||||
|
H 1.98177233 2.01940664 9.51282394
|
||||||
|
H 0.99333338 3.69839073 8.19039479
|
||||||
|
O 4.94840710 5.36455014 9.16152503
|
||||||
|
H 9.07161706 9.37484540 4.22764624
|
||||||
|
N 0.30864419 7.71366575 2.92749956
|
||||||
|
H 0.47661671 10.18072110 3.71160091
|
||||||
|
H 1.07465334 7.82269220 3.57714669
|
||||||
|
H 0.38402250 8.37704933 2.17484371
|
||||||
|
H 11.43541341 7.79037360 3.40402455
|
||||||
|
O 6.15703846 10.25988474 3.50899568
|
||||||
|
H 5.59322244 9.56329447 3.14465590
|
||||||
|
N 1.77855690 7.63125793 9.14884523
|
||||||
|
H 2.55940486 6.96832838 9.30697002
|
||||||
|
H 2.12441551 8.45479870 8.64286229
|
||||||
|
H 1.04552782 7.16977228 8.58942450
|
||||||
|
H 0.34824446 10.17844028 9.16294638
|
||||||
|
O 5.96388304 10.72370940 9.45688039
|
||||||
|
H 6.58908357 10.92648611 8.79819258
|
||||||
|
N 7.10658904 1.83029753 3.34525436
|
||||||
|
H 6.92293050 1.84650221 4.30890371
|
||||||
|
H 8.07804336 1.93030522 3.20895214
|
||||||
|
H 5.67953736 10.47183163 4.32443905
|
||||||
|
H 6.82999417 0.95850113 2.98152882
|
||||||
|
N 11.38380535 4.63012252 2.53936884
|
||||||
|
H 0.37927047 4.19432163 2.59073807
|
||||||
|
O 5.23764101 1.91523463 9.72406364
|
||||||
|
H 4.78872025 2.70369365 9.56981423
|
||||||
|
H 9.81299067 9.20751407 4.08265499
|
||||||
|
H 4.79808795 1.14034947 9.67399628
|
||||||
|
H 5.44558456 2.01021000 10.62077351
|
||||||
|
O 0.90954339 4.62400932 8.31081106
|
||||||
|
H 11.90973532 4.74838140 8.25006246
|
||||||
|
N 7.32234245 7.58664570 3.02452265
|
||||||
|
H 7.44703622 8.31696467 3.71480033
|
||||||
|
H 6.90738053 7.93850210 2.17237687
|
||||||
|
H 5.55428685 5.11760658 3.76552520
|
||||||
|
H 6.81243095 6.77788116 3.39732325
|
||||||
|
N 0.29575823 11.04303794 3.10161425
|
||||||
|
H 0.86490722 11.83879228 3.63899745
|
||||||
|
O 6.85201686 8.08463693 8.87628788
|
||||||
|
H 7.33514301 7.42634987 9.38216748
|
||||||
|
H 6.79196133 7.75954772 7.97161748
|
||||||
|
H 3.89904877 6.42834904 8.88324096
|
||||||
|
H 5.95997296 9.93297232 9.47466547
|
||||||
|
O 11.40365898 10.37196036 9.27660922
|
||||||
|
H 10.98366636 9.51571998 9.14787573
|
||||||
|
O 1.52232797 5.33273311 0.57537606
|
||||||
|
H 2.38151140 5.72519912 0.77945296
|
||||||
|
H 0.92079957 6.09312823 0.62203253
|
||||||
|
O 11.23490924 2.91533552 6.75850641
|
||||||
|
H 10.79234019 2.97552251 5.90000184
|
||||||
|
H 10.75124206 2.18961560 7.18074015
|
||||||
|
O 11.39027944 7.34628556 6.72582995
|
||||||
|
H 10.92025679 6.69831954 7.27766966
|
||||||
|
H 11.12238028 7.06320210 5.83941078
|
||||||
|
O 8.46843195 10.71736286 10.60018556
|
||||||
|
H 8.56722016 11.42046608 11.25794033
|
||||||
|
H 9.08031098 10.04804949 10.94065170
|
||||||
|
O 6.58517573 9.99406234 6.55746149
|
||||||
|
H 7.02763258 10.76096604 6.17233337
|
||||||
|
H 5.74193274 10.38458392 6.82288230
|
||||||
|
O 1.76005464 1.01771919 5.49267877
|
||||||
|
H 1.97042091 1.01748419 6.44297037
|
||||||
|
H 1.42973007 0.11076352 5.34706449
|
||||||
|
H 2.61130613 9.70341237 10.45030683
|
||||||
|
O 3.05086908 10.48131334 10.08518931
|
||||||
|
H 3.00326932 10.93357295 9.36521210
|
||||||
|
O 6.46315322 8.76520583 11.96784797
|
||||||
|
H 6.45068084 9.65965953 11.58895602
|
||||||
|
H 5.66116297 8.35357377 11.63844333
|
||||||
|
O 1.17459993 5.24206908 5.10014497
|
||||||
|
H 1.31932881 5.52363924 6.01289663
|
||||||
|
H 0.58053835 4.48981346 5.23255650
|
||||||
|
O 6.72755497 0.78840875 7.38172809
|
||||||
|
H 6.38879656 1.54670982 6.86345204
|
||||||
|
H 7.67917840 0.94039024 7.26494610
|
||||||
|
O 8.54766572 0.00647503 5.04505141
|
||||||
|
H 8.87362909 11.10484108 4.86018079
|
||||||
|
H 8.04775976 0.20198361 4.23573994
|
||||||
|
O 1.28950300 8.42800979 11.82038504
|
||||||
|
H 1.47666664 8.10878664 10.87290333
|
||||||
|
H 2.10220669 8.19476202 0.29510553
|
||||||
|
O 9.67979076 6.42073355 4.34691506
|
||||||
|
H 8.92715301 6.72940235 3.79741224
|
||||||
|
H 10.20024126 5.91677392 3.66976111
|
||||||
|
O 3.57411616 6.70410217 3.88254785
|
||||||
|
H 2.88948995 6.15605298 4.29808481
|
||||||
|
H 4.36137077 6.43047324 4.38049654
|
||||||
|
O 4.75065560 11.44185335 1.12537088
|
||||||
|
H 4.08611928 10.74852367 1.19233471
|
||||||
|
H 5.50353016 10.96568825 0.73651277
|
||||||
|
O 9.52545264 4.89944439 8.37322841
|
||||||
|
H 8.78859598 4.35080439 8.66328314
|
||||||
|
H 9.61490675 4.60849115 7.45400687
|
||||||
|
O 4.19707467 1.34592128 3.67401439
|
||||||
|
H 4.94370120 0.74406281 3.51406800
|
||||||
|
H 4.19055349 1.77303760 2.79630494
|
||||||
|
O 1.88232618 11.95451227 0.60024434
|
||||||
|
H 2.04645873 11.02454723 0.38329541
|
||||||
|
H 1.15184937 0.17494341 11.99928285
|
||||||
|
O 3.75938422 11.01685511 6.45620508
|
||||||
|
H 3.21254143 10.45537470 5.88949171
|
||||||
|
H 3.41660269 10.82155767 7.32965639
|
||||||
|
O 9.70398414 3.95001545 11.89474325
|
||||||
|
H 10.46166606 3.91631180 11.28543523
|
||||||
|
H 10.09834695 4.40269974 0.68193008
|
||||||
|
O 8.56395964 3.51695075 5.62241042
|
||||||
|
H 8.39666503 2.62622147 5.26381643
|
||||||
|
H 7.96953714 4.08250598 5.00494074
|
||||||
|
O 9.67362450 0.48030482 7.92575778
|
||||||
|
H 9.61319804 11.88341918 7.16809240
|
||||||
|
H 9.97840503 11.90238635 8.63894187
|
||||||
|
O 3.94241531 6.96502967 11.60258943
|
||||||
|
H 4.27671527 6.84600490 10.67022522
|
||||||
|
H 4.65706385 6.51294615 0.09115988
|
||||||
|
O 3.05701732 9.66319585 3.66112506
|
||||||
|
H 2.54004901 9.57433550 2.84440476
|
||||||
|
H 2.93148744 8.78098072 4.04252342
|
||||||
|
O 7.45496127 5.84308508 11.01138472
|
||||||
|
H 8.16758841 5.46391828 10.47644287
|
||||||
|
H 6.71355737 5.83938184 10.36109975
|
||||||
|
O 9.80291393 7.95789017 10.21404942
|
||||||
|
H 10.38910242 8.34006414 10.87949429
|
||||||
|
H 9.06376120 7.63923741 10.75692887
|
||||||
|
O 4.49634356 4.10679358 11.73387805
|
||||||
|
H 4.54737279 4.95779709 11.19223377
|
||||||
|
H 5.35888184 4.17561117 0.20355937
|
||||||
|
O 9.59234481 7.34180146 1.34856172
|
||||||
|
H 8.87155933 7.47768372 2.05040471
|
||||||
|
H 9.04432217 7.27322008 0.54011714
|
||||||
|
O 7.03509631 3.22348773 0.70708240
|
||||||
|
H 7.17844705 4.13403143 1.01841097
|
||||||
|
H 7.77878544 2.78888884 1.15838887
|
||||||
|
O 9.21241078 0.48085900 1.21751966
|
||||||
|
H 9.66204365 11.65727108 1.45318397
|
||||||
|
H 9.94048839 1.11619136 1.18684594
|
||||||
|
O 1.19704207 9.58599592 6.61908889
|
||||||
|
H 0.25606413 9.67373665 6.83193409
|
||||||
|
H 1.26900519 8.62493549 6.54801125
|
||||||
|
O 0.78256134 2.60406093 11.45340836
|
||||||
|
H 0.61502181 3.56074060 11.40300991
|
||||||
|
H 1.55655312 2.54573688 10.86673303
|
||||||
|
O 5.86279361 7.12170548 5.89173203
|
||||||
|
H 6.34324107 7.94001367 6.08558403
|
||||||
|
H 5.50772967 6.84683068 6.74368758
|
||||||
|
O 10.88782815 9.96374825 0.51092816
|
||||||
|
H 11.78841776 10.32204307 0.44704989
|
||||||
|
H 11.02688182 9.20519067 1.09766613
|
||||||
|
O 3.93073389 4.16456745 5.71378770
|
||||||
|
H 4.68840630 3.57889133 5.56446058
|
||||||
|
H 4.29569485 4.76448881 6.38016697
|
||||||
81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1
Normal file
81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1
Normal file
@ -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
81
examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.4
Normal file
@ -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
|
||||||
@ -2,15 +2,15 @@
|
|||||||
dimension 2
|
dimension 2
|
||||||
boundary p f p
|
boundary p f p
|
||||||
|
|
||||||
units lj
|
units lj
|
||||||
atom_style bond
|
atom_style bond
|
||||||
atom_modify sort 0 1.
|
atom_modify sort 0 1.
|
||||||
bond_style harmonic
|
bond_style harmonic
|
||||||
pair_style none
|
pair_style none
|
||||||
communicate single cutoff 2.0
|
comm_modify cutoff 2.0
|
||||||
|
|
||||||
# geometry
|
# geometry
|
||||||
read_data data.pos
|
read_data data.pos
|
||||||
|
|
||||||
#
|
#
|
||||||
neighbor 1.0 nsq
|
neighbor 1.0 nsq
|
||||||
@ -43,4 +43,4 @@ thermo_modify temp MyTemp
|
|||||||
thermo 100
|
thermo 100
|
||||||
|
|
||||||
#
|
#
|
||||||
run 2000000
|
run 2000000
|
||||||
|
|||||||
33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
Normal file
33
examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
Normal file
@ -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
|
||||||
@ -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
|
||||||
@ -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
|
||||||
@ -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
|
|
||||||
@ -3,62 +3,62 @@
|
|||||||
|
|
||||||
## This part defines units, methane structure, and atomic information
|
## This part defines units, methane structure, and atomic information
|
||||||
#General
|
#General
|
||||||
units real
|
units real
|
||||||
dimension 3
|
dimension 3
|
||||||
boundary p p p
|
boundary p p p
|
||||||
atom_style charge
|
atom_style charge
|
||||||
|
|
||||||
#Lattice
|
#Lattice
|
||||||
lattice custom 1.0 &
|
lattice custom 1.0 &
|
||||||
a1 3.9783624 0 0 &
|
a1 3.9783624 0 0 &
|
||||||
a2 0 3.9783624 0 &
|
a2 0 3.9783624 0 &
|
||||||
a3 0 0 3.9783624 &
|
a3 0 0 3.9783624 &
|
||||||
&
|
&
|
||||||
basis 0.5 0.5 0.5 &
|
basis 0.5 0.5 0.5 &
|
||||||
basis 0.663 0.663 0.663 &
|
basis 0.663 0.663 0.663 &
|
||||||
basis 0.337 0.337 0.663 &
|
basis 0.337 0.337 0.663 &
|
||||||
basis 0.663 0.337 0.337 &
|
basis 0.663 0.337 0.337 &
|
||||||
basis 0.337 0.663 0.337
|
basis 0.337 0.663 0.337
|
||||||
|
|
||||||
#Computational Cell
|
#Computational Cell
|
||||||
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
region simbox block 0 3.9783624 0 3.9783624 0 3.9783624 units box
|
||||||
create_box 2 simbox
|
create_box 2 simbox
|
||||||
create_atoms 1 box &
|
create_atoms 1 box &
|
||||||
basis 1 1 &
|
basis 1 1 &
|
||||||
basis 2 2 &
|
basis 2 2 &
|
||||||
basis 3 2 &
|
basis 3 2 &
|
||||||
basis 4 2 &
|
basis 4 2 &
|
||||||
basis 5 2
|
basis 5 2
|
||||||
replicate ${x_rep} ${y_rep} ${z_rep}
|
replicate ${x_rep} ${y_rep} ${z_rep}
|
||||||
|
|
||||||
#Atomic Information
|
#Atomic Information
|
||||||
mass 1 12.011150
|
mass 1 12.011150
|
||||||
mass 2 1.007970
|
mass 2 1.007970
|
||||||
|
|
||||||
|
|
||||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||||
#Pair Potentials
|
#Pair Potentials
|
||||||
pair_style reax/c NULL
|
pair_style reaxff NULL
|
||||||
pair_coeff * * ffield.reax C H
|
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 Style
|
||||||
neighbor 2.5 bin
|
neighbor 2.5 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
|
|
||||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||||
#Initialization
|
#Initialization
|
||||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||||
|
|
||||||
#Setup output
|
#Setup output
|
||||||
thermo_style custom step temp press etotal vol
|
thermo_style custom step temp press etotal vol
|
||||||
thermo 100
|
thermo 20
|
||||||
|
|
||||||
#Colored thermal bath
|
#Colored thermal bath
|
||||||
fix scapegoat_qtb all nve #NVE does the time integration
|
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 ${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}
|
timestep ${delta_t}
|
||||||
run 2000 #500 fs
|
run 500 #500 fs
|
||||||
unfix methane_qtb
|
unfix methane_qtb
|
||||||
unfix scapegoat_qtb
|
unfix scapegoat_qtb
|
||||||
|
|||||||
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal file
70
examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
Normal 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
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
Normal file
@ -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
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
174
examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
Normal file
@ -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
|
||||||
@ -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
|
|
||||||
@ -12,7 +12,8 @@ ewald
|
|||||||
ewald-alpha 0.4
|
ewald-alpha 0.4
|
||||||
pewald-alpha 0.5
|
pewald-alpha 0.5
|
||||||
ewald-cutoff 7.0
|
ewald-cutoff 7.0
|
||||||
#pme-grid 60 45 45
|
|
||||||
pme-grid 60 48 48
|
pme-grid 60 48 48
|
||||||
pme-order 5
|
|
||||||
polar-eps 0.00001
|
polar-eps 0.00001
|
||||||
|
#pme-grid 15 12 12
|
||||||
|
#polar-eps 0.0002
|
||||||
|
pme-order 5
|
||||||
|
|||||||
@ -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
|
# You can comment in/out various versions below
|
||||||
#
|
#
|
||||||
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
# 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
|
# 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
|
# the QEq parameters are the same. These two styles can also be used with
|
||||||
# pair_style reax/c.
|
# pair_style reaxff.
|
||||||
|
|
||||||
units real
|
units real
|
||||||
atom_style charge
|
atom_style charge
|
||||||
|
|
||||||
read_data data.CHO
|
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
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
|
||||||
neighbor 1 bin
|
neighbor 1 bin
|
||||||
@ -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
|
|
||||||
@ -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
examples/qeq/log.30Nov23.reaxff.g++.1
Normal file
146
examples/qeq/log.30Nov23.reaxff.g++.1
Normal 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 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
146
examples/qeq/log.30Nov23.reaxff.g++.4
Normal 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
|
||||||
@ -1,23 +1,23 @@
|
|||||||
# REAX potential for Nitroamines system
|
# REAX potential for Nitroamines system
|
||||||
# .....
|
# .....
|
||||||
|
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.AB
|
read_data data.AB
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
pair_style reaxff lmp_control
|
||||||
pair_coeff * * ffield.reax.AB H B N
|
pair_coeff * * ffield.reax.AB H B N
|
||||||
|
|
||||||
neighbor 2 bin
|
neighbor 2 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
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
|
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||||
|
|
||||||
timestep 0.25
|
timestep 0.25
|
||||||
|
thermo 100
|
||||||
|
#dump 1 all atom 30 dump.reax.ab
|
||||||
|
|
||||||
#dump 1 all atom 30 dump.reax.ab
|
run 2000
|
||||||
|
|
||||||
run 3000
|
|
||||||
|
|||||||
@ -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
|
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
|
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
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
131
examples/reaxff/AB/log.30Nov23.AB.g++.1
Normal file
@ -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
131
examples/reaxff/AB/log.30Nov23.AB.g++.4
Normal file
@ -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
|
||||||
@ -1,81 +0,0 @@
|
|||||||
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
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
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
|
|
||||||
@ -1,23 +1,25 @@
|
|||||||
# REAX potential for AuO system
|
# REAX potential for AuO system
|
||||||
# .....
|
# .....
|
||||||
|
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.AuO
|
read_data data.AuO
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
pair_style reaxff lmp_control
|
||||||
pair_coeff * * ffield.reax.AuO O Au
|
pair_coeff * * ffield.reax.AuO O Au
|
||||||
|
|
||||||
neighbor 2 bin
|
neighbor 2 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
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
|
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||||
|
|
||||||
timestep 0.25
|
timestep 0.25
|
||||||
|
|
||||||
#dump 1 all atom 30 dump.reax.auo
|
thermo 5
|
||||||
|
|
||||||
run 100
|
#dump 1 all atom 30 dump.reax.auo
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|||||||
@ -1,17 +1,7 @@
|
|||||||
simulation_name AuO_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
|
||||||
|
|
||||||
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
|
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||||
energy_update_freq 1
|
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
|
||||||
|
|
||||||
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 AuO ! (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
|
|
||||||
|
|||||||
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.1
Normal file
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.1
Normal file
@ -0,0 +1,132 @@
|
|||||||
|
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 AuO system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.AuO
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
960 atoms
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.AuO O Au
|
||||||
|
Reading potential file ffield.reax.AuO 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
|
||||||
|
|
||||||
|
thermo 5
|
||||||
|
|
||||||
|
#dump 1 all atom 30 dump.reax.auo
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
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 4 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) = 129.2 | 129.2 | 129.2 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -72201.743 0 -72201.743 -166.19508
|
||||||
|
5 6.5398577 -72202.679 0 -72183.984 71.658901
|
||||||
|
10 13.280881 -72204.445 0 -72166.481 515.28836
|
||||||
|
15 19.951637 -72206.24 0 -72149.206 886.438
|
||||||
|
20 26.441301 -72207.78 0 -72132.195 1549.914
|
||||||
|
25 32.580167 -72208.5 0 -72115.367 2309.8004
|
||||||
|
30 38.264935 -72208.14 0 -72098.756 3148.7379
|
||||||
|
35 43.433009 -72206.523 0 -72082.366 3853.4389
|
||||||
|
40 48.028176 -72203.472 0 -72066.178 4830.1846
|
||||||
|
45 52.019459 -72198.85 0 -72050.147 5881.5166
|
||||||
|
50 55.407353 -72192.638 0 -72034.251 6996.89
|
||||||
|
55 58.218407 -72184.89 0 -72018.467 8191.8057
|
||||||
|
60 60.499102 -72175.717 0 -72002.774 9470.0601
|
||||||
|
65 62.309031 -72165.271 0 -71987.155 10831.309
|
||||||
|
70 63.72857 -72153.749 0 -71971.575 12270.345
|
||||||
|
75 64.847533 -72141.43 0 -71956.057 13791.775
|
||||||
|
80 65.755809 -72128.548 0 -71940.579 15397.406
|
||||||
|
85 66.547696 -72115.362 0 -71925.129 17100.883
|
||||||
|
90 67.309412 -72102.119 0 -71909.708 18888.699
|
||||||
|
95 68.120206 -72089.043 0 -71894.315 20757.038
|
||||||
|
100 69.043359 -72076.31 0 -71878.942 22702.463
|
||||||
|
Loop time of 5.72003 on 1 procs for 100 steps with 960 atoms
|
||||||
|
|
||||||
|
Performance: 0.378 ns/day, 63.556 hours/ns, 17.482 timesteps/s, 16.783 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 | 4.2903 | 4.2903 | 4.2903 | 0.0 | 75.00
|
||||||
|
Neigh | 0.31194 | 0.31194 | 0.31194 | 0.0 | 5.45
|
||||||
|
Comm | 0.0034139 | 0.0034139 | 0.0034139 | 0.0 | 0.06
|
||||||
|
Output | 0.0005041 | 0.0005041 | 0.0005041 | 0.0 | 0.01
|
||||||
|
Modify | 1.1134 | 1.1134 | 1.1134 | 0.0 | 19.46
|
||||||
|
Other | | 0.0005147 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 960 ave 960 max 960 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 6708 ave 6708 max 6708 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 369128 ave 369128 max 369128 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 369128
|
||||||
|
Ave neighs/atom = 384.50833
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:05
|
||||||
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.4
Normal file
132
examples/reaxff/AuO/log.30Nov23.AuO.g++.4
Normal file
@ -0,0 +1,132 @@
|
|||||||
|
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 AuO system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.AuO
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (26.15618 21.54252 24.00246)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
960 atoms
|
||||||
|
read_data CPU = 0.002 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.AuO O Au
|
||||||
|
Reading potential file ffield.reax.AuO 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
|
||||||
|
|
||||||
|
thermo 5
|
||||||
|
|
||||||
|
#dump 1 all atom 30 dump.reax.auo
|
||||||
|
|
||||||
|
run 100
|
||||||
|
|
||||||
|
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 4 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) = 71.65 | 71.65 | 71.65 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -72201.743 0 -72201.743 -166.19214
|
||||||
|
5 6.5398578 -72202.679 0 -72183.984 71.651708
|
||||||
|
10 13.280883 -72204.445 0 -72166.481 515.29601
|
||||||
|
15 19.951639 -72206.24 0 -72149.206 886.53083
|
||||||
|
20 26.441291 -72207.78 0 -72132.195 1550.0745
|
||||||
|
25 32.580153 -72208.5 0 -72115.366 2309.9393
|
||||||
|
30 38.264928 -72208.14 0 -72098.756 3148.6036
|
||||||
|
35 43.432999 -72206.523 0 -72082.365 3853.6963
|
||||||
|
40 48.028158 -72203.472 0 -72066.179 4830.1407
|
||||||
|
45 52.019436 -72198.85 0 -72050.147 5881.1916
|
||||||
|
50 55.407331 -72192.638 0 -72034.251 6996.6661
|
||||||
|
55 58.218406 -72184.89 0 -72018.467 8191.9075
|
||||||
|
60 60.499115 -72175.716 0 -72002.774 9470.4845
|
||||||
|
65 62.309058 -72165.271 0 -71987.154 10831.926
|
||||||
|
70 63.728581 -72153.75 0 -71971.575 12269.823
|
||||||
|
75 64.847544 -72141.431 0 -71956.058 13791.586
|
||||||
|
80 65.755816 -72128.549 0 -71940.579 15396.822
|
||||||
|
85 66.547694 -72115.363 0 -71925.13 17100.27
|
||||||
|
90 67.309401 -72102.119 0 -71909.708 18888.633
|
||||||
|
95 68.120175 -72089.042 0 -71894.314 20757.565
|
||||||
|
100 69.043333 -72076.31 0 -71878.943 22701.953
|
||||||
|
Loop time of 2.52972 on 4 procs for 100 steps with 960 atoms
|
||||||
|
|
||||||
|
Performance: 0.854 ns/day, 28.108 hours/ns, 39.530 timesteps/s, 37.949 katom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.9911 | 2.0015 | 2.0084 | 0.5 | 79.12
|
||||||
|
Neigh | 0.16044 | 0.16105 | 0.16228 | 0.2 | 6.37
|
||||||
|
Comm | 0.018211 | 0.025417 | 0.03612 | 4.2 | 1.00
|
||||||
|
Output | 0.00039837 | 0.00043613 | 0.00054664 | 0.0 | 0.02
|
||||||
|
Modify | 0.34008 | 0.34101 | 0.34154 | 0.1 | 13.48
|
||||||
|
Other | | 0.0003489 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 240 ave 240 max 240 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3981 ave 3981 max 3981 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 105979 ave 105979 max 105979 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 423916
|
||||||
|
Ave neighs/atom = 441.57917
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for AuO system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.AuO
|
|
||||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
960 atoms
|
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
|
||||||
pair_coeff * * ffield.reax.AuO O Au
|
|
||||||
Reading potential file ffield.reax.AuO 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.auo
|
|
||||||
|
|
||||||
run 100
|
|
||||||
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 4 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) = 157.6 | 157.6 | 157.6 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -72201.743 0 -72201.743 -166.19482
|
|
||||||
100 69.043331 -72076.309 0 -71878.942 22702.89
|
|
||||||
Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms
|
|
||||||
|
|
||||||
Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s
|
|
||||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38
|
|
||||||
Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19
|
|
||||||
Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04
|
|
||||||
Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
|
|
||||||
Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38
|
|
||||||
Other | | 0.001366 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 960 ave 960 max 960 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 6708 ave 6708 max 6708 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 369128 ave 369128 max 369128 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 369128
|
|
||||||
Ave neighs/atom = 384.508
|
|
||||||
Neighbor list builds = 10
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:18
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for AuO system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.AuO
|
|
||||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
960 atoms
|
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
|
||||||
pair_coeff * * ffield.reax.AuO O Au
|
|
||||||
Reading potential file ffield.reax.AuO 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.auo
|
|
||||||
|
|
||||||
run 100
|
|
||||||
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 4 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) = 87.17 | 87.17 | 87.17 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -72201.743 0 -72201.743 -166.2027
|
|
||||||
100 69.043379 -72076.31 0 -71878.943 22701.771
|
|
||||||
Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms
|
|
||||||
|
|
||||||
Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s
|
|
||||||
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31
|
|
||||||
Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49
|
|
||||||
Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32
|
|
||||||
Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00
|
|
||||||
Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88
|
|
||||||
Other | | 0.0008975 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 240 ave 240 max 240 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 3981 ave 3981 max 3981 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 105979 ave 105979 max 105979 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 423916
|
|
||||||
Ave neighs/atom = 441.579
|
|
||||||
Neighbor list builds = 10
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:08
|
|
||||||
@ -1,23 +1,24 @@
|
|||||||
# REAX potential for CHO system
|
# REAX potential for CHO system
|
||||||
# .....
|
# .....
|
||||||
|
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.CHO
|
read_data data.CHO
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
pair_style reaxff lmp_control
|
||||||
pair_coeff * * ffield.reax.cho H C O
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
|
||||||
neighbor 2 bin
|
neighbor 2 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
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
|
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||||
|
|
||||||
timestep 0.25
|
timestep 0.25
|
||||||
|
|
||||||
#dump 1 all atom 30 dump.reax.cho
|
thermo 100
|
||||||
|
#dump 1 all atom 30 dump.reax.cho
|
||||||
|
|
||||||
run 3000
|
run 3000
|
||||||
|
|||||||
@ -1,17 +1,8 @@
|
|||||||
simulation_name CHO_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
|
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
|
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||||
|
|
||||||
write_freq 1 ! write trajectory after so many steps
|
|
||||||
traj_title CHO ! (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
|
|
||||||
|
|||||||
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.1
Normal file
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.1
Normal file
@ -0,0 +1,141 @@
|
|||||||
|
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 CHO system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
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 lmp_control
|
||||||
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
Reading potential file ffield.reax.cho 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
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
#dump 1 all atom 30 dump.reax.cho
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 16.04 | 16.04 | 16.04 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -10226.557 0 -10226.557 -106.09742
|
||||||
|
100 54.051992 -10207.393 0 -10190.636 -291.38729
|
||||||
|
200 134.81151 -10200.411 0 -10158.619 -1637.1719
|
||||||
|
300 140.9118 -10177.136 0 -10133.452 -1668.5701
|
||||||
|
400 254.70109 -10189.927 0 -10110.969 -2522.3829
|
||||||
|
500 228.22383 -10162.396 0 -10091.646 404.00518
|
||||||
|
600 393.48635 -10197.284 0 -10075.301 394.0729
|
||||||
|
700 305.82675 -10156.708 0 -10061.9 362.69731
|
||||||
|
800 375.9566 -10170.288 0 -10053.74 -664.01093
|
||||||
|
900 361.59639 -10155.849 0 -10043.752 458.54613
|
||||||
|
1000 445.46183 -10176.602 0 -10038.507 251.38181
|
||||||
|
1100 475.46673 -10180.119 0 -10032.723 839.6649
|
||||||
|
1200 406.78262 -10155.498 0 -10029.394 62.559824
|
||||||
|
1300 461.0773 -10167.129 0 -10024.193 266.27742
|
||||||
|
1400 408.15446 -10148.62 0 -10022.091 -1187.1776
|
||||||
|
1500 514.43707 -10178.34 0 -10018.863 -616.2329
|
||||||
|
1600 432.19202 -10151.16 0 -10017.179 -677.67834
|
||||||
|
1700 521.01474 -10175.583 0 -10014.066 97.420991
|
||||||
|
1800 409.79407 -10138.825 0 -10011.787 1883.8131
|
||||||
|
1900 481.84667 -10160.146 0 -10010.772 1059.6448
|
||||||
|
2000 423.61284 -10138.538 0 -10007.216 -434.24008
|
||||||
|
2100 521.01756 -10169.192 0 -10007.674 376.95207
|
||||||
|
2200 477.03314 -10153.033 0 -10005.151 -114.09514
|
||||||
|
2300 477.80526 -10153.294 0 -10005.172 869.97281
|
||||||
|
2400 471.49741 -10149.165 0 -10002.999 689.65295
|
||||||
|
2500 482.38958 -10152.956 0 -10003.413 352.08649
|
||||||
|
2600 505.57503 -10159.507 0 -10002.777 -812.75272
|
||||||
|
2700 498.41415 -10156.448 0 -10001.937 -458.03311
|
||||||
|
2800 534.65278 -10166.893 0 -10001.149 169.20767
|
||||||
|
2900 432.93717 -10134.759 0 -10000.546 -184.75627
|
||||||
|
3000 548.46832 -10170.375 0 -10000.347 41.765546
|
||||||
|
Loop time of 3.49376 on 1 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 18.547 ns/day, 1.294 hours/ns, 858.673 timesteps/s, 90.161 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 | 2.8082 | 2.8082 | 2.8082 | 0.0 | 80.38
|
||||||
|
Neigh | 0.15477 | 0.15477 | 0.15477 | 0.0 | 4.43
|
||||||
|
Comm | 0.0097478 | 0.0097478 | 0.0097478 | 0.0 | 0.28
|
||||||
|
Output | 0.00081006 | 0.00081006 | 0.00081006 | 0.0 | 0.02
|
||||||
|
Modify | 0.51773 | 0.51773 | 0.51773 | 0.0 | 14.82
|
||||||
|
Other | | 0.002538 | | | 0.07
|
||||||
|
|
||||||
|
Nlocal: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 643 ave 643 max 643 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4237 ave 4237 max 4237 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4237
|
||||||
|
Ave neighs/atom = 40.352381
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:03
|
||||||
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.4
Normal file
141
examples/reaxff/CHO/log.30Nov23.CHO.g++.4
Normal file
@ -0,0 +1,141 @@
|
|||||||
|
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 CHO system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
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 = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.cho H C O
|
||||||
|
Reading potential file ffield.reax.cho 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
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
#dump 1 all atom 30 dump.reax.cho
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 10.47 | 11.39 | 12.19 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -10226.557 0 -10226.557 -106.09736
|
||||||
|
100 54.051902 -10207.393 0 -10190.636 -291.39467
|
||||||
|
200 134.81172 -10200.411 0 -10158.619 -1637.1599
|
||||||
|
300 140.91215 -10177.136 0 -10133.452 -1668.5676
|
||||||
|
400 254.70123 -10189.927 0 -10110.968 -2522.3655
|
||||||
|
500 228.22204 -10162.396 0 -10091.646 403.98879
|
||||||
|
600 393.48756 -10197.284 0 -10075.301 394.11243
|
||||||
|
700 305.82625 -10156.707 0 -10061.9 362.73212
|
||||||
|
800 375.95634 -10170.288 0 -10053.74 -664.10079
|
||||||
|
900 361.59143 -10155.847 0 -10043.752 458.52018
|
||||||
|
1000 445.4582 -10176.601 0 -10038.507 251.4509
|
||||||
|
1100 475.47 -10180.12 0 -10032.722 840.09331
|
||||||
|
1200 406.77476 -10155.496 0 -10029.394 62.656622
|
||||||
|
1300 461.06079 -10167.123 0 -10024.192 265.91062
|
||||||
|
1400 408.15869 -10148.621 0 -10022.09 -1187.4869
|
||||||
|
1500 514.43021 -10178.337 0 -10018.862 -616.07216
|
||||||
|
1600 432.22013 -10151.168 0 -10017.178 -678.01121
|
||||||
|
1700 521.0846 -10175.605 0 -10014.067 98.591699
|
||||||
|
1800 409.72383 -10138.803 0 -10011.787 1884.7989
|
||||||
|
1900 481.86369 -10160.152 0 -10010.773 1058.5554
|
||||||
|
2000 423.60058 -10138.532 0 -10007.214 -437.22408
|
||||||
|
2100 520.96555 -10169.169 0 -10007.668 376.18619
|
||||||
|
2200 477.21351 -10153.089 0 -10005.15 -113.43512
|
||||||
|
2300 477.86263 -10153.309 0 -10005.17 868.89369
|
||||||
|
2400 471.46466 -10149.152 0 -10002.996 688.76379
|
||||||
|
2500 482.61616 -10153.025 0 -10003.412 350.03715
|
||||||
|
2600 505.68439 -10159.544 0 -10002.78 -810.94974
|
||||||
|
2700 498.37307 -10156.441 0 -10001.944 -460.12105
|
||||||
|
2800 535.06218 -10167.029 0 -10001.157 152.85379
|
||||||
|
2900 432.98591 -10134.778 0 -10000.55 -170.46638
|
||||||
|
3000 547.92956 -10170.199 0 -10000.339 60.201766
|
||||||
|
Loop time of 2.03179 on 4 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 31.893 ns/day, 0.753 hours/ns, 1476.533 timesteps/s, 155.036 katom-step/s
|
||||||
|
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.213 | 1.2396 | 1.2505 | 1.4 | 61.01
|
||||||
|
Neigh | 0.074765 | 0.08966 | 0.10323 | 4.3 | 4.41
|
||||||
|
Comm | 0.12894 | 0.14116 | 0.16833 | 4.2 | 6.95
|
||||||
|
Output | 0.0006079 | 0.00066664 | 0.00083802 | 0.0 | 0.03
|
||||||
|
Modify | 0.54589 | 0.55836 | 0.57217 | 1.6 | 27.48
|
||||||
|
Other | | 0.002368 | | | 0.12
|
||||||
|
|
||||||
|
Nlocal: 26.25 ave 45 max 6 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 380.75 ave 495 max 261 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Neighs: 1269.5 ave 2197 max 179 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5078
|
||||||
|
Ave neighs/atom = 48.361905
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for CHO system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.cho H C O
|
|
||||||
Reading potential file ffield.reax.cho 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.cho
|
|
||||||
|
|
||||||
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) = 18.68 | 18.68 | 18.68 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -10226.557 0 -10226.557 -106.09755
|
|
||||||
3000 548.5116 -10170.389 0 -10000.348 40.372297
|
|
||||||
Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72
|
|
||||||
Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63
|
|
||||||
Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14
|
|
||||||
Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00
|
|
||||||
Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47
|
|
||||||
Other | | 0.005059 | | | 0.04
|
|
||||||
|
|
||||||
Nlocal: 105 ave 105 max 105 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 643 ave 643 max 643 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 4237 ave 4237 max 4237 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 4237
|
|
||||||
Ave neighs/atom = 40.3524
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:12
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for CHO system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.cho H C O
|
|
||||||
Reading potential file ffield.reax.cho 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.cho
|
|
||||||
|
|
||||||
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) = 11.75 | 12.85 | 13.81 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -10226.557 0 -10226.557 -106.09745
|
|
||||||
3000 548.30567 -10170.323 0 -10000.346 47.794514
|
|
||||||
Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s
|
|
||||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86
|
|
||||||
Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41
|
|
||||||
Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24
|
|
||||||
Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00
|
|
||||||
Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44
|
|
||||||
Other | | 0.003964 | | | 0.05
|
|
||||||
|
|
||||||
Nlocal: 26.25 ave 45 max 6 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
||||||
Nghost: 380.75 ave 495 max 261 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
||||||
Neighs: 1269.5 ave 2197 max 179 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
|
||||||
|
|
||||||
Total # of neighbors = 5078
|
|
||||||
Ave neighs/atom = 48.3619
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:07
|
|
||||||
@ -3,33 +3,33 @@
|
|||||||
|
|
||||||
dimension 3
|
dimension 3
|
||||||
boundary p p p
|
boundary p p p
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.FC
|
read_data data.FC
|
||||||
|
|
||||||
pair_style reax/c NULL
|
pair_style reaxff NULL
|
||||||
pair_coeff * * ffield.reax.FC C F
|
pair_coeff * * ffield.reax.FC C F
|
||||||
neighbor 2. bin
|
neighbor 2. bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
# should equilibrate much longer in practice
|
# should equilibrate much longer in practice
|
||||||
|
|
||||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||||
timestep 0.2
|
timestep 0.2
|
||||||
thermo_style custom step temp epair etotal press
|
thermo_style custom step temp epair etotal press
|
||||||
thermo 1
|
thermo 1
|
||||||
dump 4 all xyz 5000 dumpnpt.xyz
|
dump 4 all xyz 5000 dumpnpt.xyz
|
||||||
run 10
|
run 10
|
||||||
|
|
||||||
unfix 1
|
unfix 1
|
||||||
|
|
||||||
fix 1 all nvt temp 100.0 100.0 100.0
|
fix 1 all nvt temp 100.0 100.0 100.0
|
||||||
thermo_style custom step temp epair etotal press
|
thermo_style custom step temp epair etotal press
|
||||||
timestep 0.2
|
timestep 0.2
|
||||||
|
|
||||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||||
|
|
||||||
run 10
|
run 10
|
||||||
|
|||||||
172
examples/reaxff/FC/log.30Nov23.FC.g++.1
Normal file
172
examples/reaxff/FC/log.30Nov23.FC.g++.1
Normal file
@ -0,0 +1,172 @@
|
|||||||
|
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
|
||||||
|
# .....
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.FC
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
17280 atoms
|
||||||
|
read_data CPU = 0.025 seconds
|
||||||
|
|
||||||
|
pair_style reaxff NULL
|
||||||
|
pair_coeff * * ffield.reax.FC C F
|
||||||
|
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||||
|
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 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
|
# should equilibrate much longer in practice
|
||||||
|
|
||||||
|
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||||
|
timestep 0.2
|
||||||
|
thermo_style custom step temp epair etotal press
|
||||||
|
thermo 1
|
||||||
|
dump 4 all xyz 5000 dumpnpt.xyz
|
||||||
|
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 = 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 = 28 27 17
|
||||||
|
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) = 384.3 | 384.3 | 384.3 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press
|
||||||
|
0 0 -808525.04 -808525.04 58194.694
|
||||||
|
1 4.9935726 -808803.88 -808546.69 58205.825
|
||||||
|
2 19.98696 -809640.53 -808611.1 58239.155
|
||||||
|
3 45.012616 -811035.3 -808716.9 58294.499
|
||||||
|
4 80.103613 -812988.58 -808862.81 58371.548
|
||||||
|
5 125.26228 -815500.68 -809049 58469.872
|
||||||
|
6 180.4316 -818571.56 -809278.36 58588.936
|
||||||
|
7 245.47913 -822200.73 -809557.22 58728.144
|
||||||
|
8 320.17692 -826387.19 -809896.34 58886.879
|
||||||
|
9 404.17073 -831129.38 -810312.4 59064.554
|
||||||
|
10 497.02486 -836425.06 -810825.59 59260.717
|
||||||
|
Loop time of 6.13793 on 1 procs for 10 steps with 17280 atoms
|
||||||
|
|
||||||
|
Performance: 0.028 ns/day, 852.491 hours/ns, 1.629 timesteps/s, 28.153 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 | 5.1752 | 5.1752 | 5.1752 | 0.0 | 84.31
|
||||||
|
Neigh | 0.039453 | 0.039453 | 0.039453 | 0.0 | 0.64
|
||||||
|
Comm | 0.00042596 | 0.00042596 | 0.00042596 | 0.0 | 0.01
|
||||||
|
Output | 0.00064013 | 0.00064013 | 0.00064013 | 0.0 | 0.01
|
||||||
|
Modify | 0.92205 | 0.92205 | 0.92205 | 0.0 | 15.02
|
||||||
|
Other | | 0.0002045 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 17280 ave 17280 max 17280 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5352 ave 5352 max 5352 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2621360
|
||||||
|
Ave neighs/atom = 151.69907
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds not checked
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
|
||||||
|
fix 1 all nvt temp 100.0 100.0 100.0
|
||||||
|
thermo_style custom step temp epair etotal press
|
||||||
|
timestep 0.2
|
||||||
|
|
||||||
|
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||||
|
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 386.9 | 386.9 | 386.9 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press
|
||||||
|
10 497.02486 -836425.06 -810825.59 59260.717
|
||||||
|
11 601.6514 -841814.09 -810825.78 59489.425
|
||||||
|
12 716.37597 -847724.6 -810827.35 59738.298
|
||||||
|
13 841.27959 -854161.62 -810831.16 60008.164
|
||||||
|
14 976.4666 -861131.68 -810838.36 60300.364
|
||||||
|
15 1122.0668 -868642.96 -810850.45 60616.793
|
||||||
|
16 1278.2373 -876705.43 -810869.28 60959.942
|
||||||
|
17 1445.1655 -885331.03 -810897.18 61332.932
|
||||||
|
18 1623.072 -894533.91 -810936.92 61739.541
|
||||||
|
19 1812.1864 -904337.86 -811000.45 62200.561
|
||||||
|
20 2011.5898 -915379.05 -811771.28 63361.15
|
||||||
|
Loop time of 6.11372 on 1 procs for 10 steps with 17280 atoms
|
||||||
|
|
||||||
|
Performance: 0.028 ns/day, 849.127 hours/ns, 1.636 timesteps/s, 28.264 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 | 5.0783 | 5.0783 | 5.0783 | 0.0 | 83.06
|
||||||
|
Neigh | 0.03596 | 0.03596 | 0.03596 | 0.0 | 0.59
|
||||||
|
Comm | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.01
|
||||||
|
Output | 0.00062133 | 0.00062133 | 0.00062133 | 0.0 | 0.01
|
||||||
|
Modify | 0.99825 | 0.99825 | 0.99825 | 0.0 | 16.33
|
||||||
|
Other | | 0.0002171 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 17280 ave 17280 max 17280 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5352 ave 5352 max 5352 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2621360
|
||||||
|
Ave neighs/atom = 151.69907
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:13
|
||||||
172
examples/reaxff/FC/log.30Nov23.FC.g++.4
Normal file
172
examples/reaxff/FC/log.30Nov23.FC.g++.4
Normal file
@ -0,0 +1,172 @@
|
|||||||
|
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
|
||||||
|
# .....
|
||||||
|
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.FC
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
17280 atoms
|
||||||
|
read_data CPU = 0.030 seconds
|
||||||
|
|
||||||
|
pair_style reaxff NULL
|
||||||
|
pair_coeff * * ffield.reax.FC C F
|
||||||
|
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
||||||
|
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 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
|
# should equilibrate much longer in practice
|
||||||
|
|
||||||
|
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||||
|
timestep 0.2
|
||||||
|
thermo_style custom step temp epair etotal press
|
||||||
|
thermo 1
|
||||||
|
dump 4 all xyz 5000 dumpnpt.xyz
|
||||||
|
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 = 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 = 28 27 17
|
||||||
|
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) = 121.6 | 121.6 | 121.6 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press
|
||||||
|
0 0 -808525.04 -808525.04 58194.694
|
||||||
|
1 4.9935726 -808803.88 -808546.69 58205.825
|
||||||
|
2 19.98696 -809640.53 -808611.1 58239.155
|
||||||
|
3 45.012616 -811035.3 -808716.9 58294.499
|
||||||
|
4 80.103613 -812988.58 -808862.81 58371.548
|
||||||
|
5 125.26228 -815500.68 -809049 58469.872
|
||||||
|
6 180.4316 -818571.56 -809278.36 58588.936
|
||||||
|
7 245.47913 -822200.73 -809557.22 58728.144
|
||||||
|
8 320.17692 -826387.19 -809896.34 58886.879
|
||||||
|
9 404.17073 -831129.38 -810312.4 59064.554
|
||||||
|
10 497.02486 -836425.06 -810825.59 59260.717
|
||||||
|
Loop time of 1.75962 on 4 procs for 10 steps with 17280 atoms
|
||||||
|
|
||||||
|
Performance: 0.098 ns/day, 244.392 hours/ns, 5.683 timesteps/s, 98.203 katom-step/s
|
||||||
|
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.402 | 1.4417 | 1.4815 | 3.0 | 81.93
|
||||||
|
Neigh | 0.012815 | 0.013047 | 0.01323 | 0.2 | 0.74
|
||||||
|
Comm | 0.0006609 | 0.040482 | 0.080149 | 17.9 | 2.30
|
||||||
|
Output | 0.00028041 | 0.00029538 | 0.00033093 | 0.0 | 0.02
|
||||||
|
Modify | 0.26389 | 0.26407 | 0.26425 | 0.0 | 15.01
|
||||||
|
Other | | 7.451e-05 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 4320 ave 4320 max 4320 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2856 ave 2856 max 2856 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 691892 ave 691892 max 691892 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2767568
|
||||||
|
Ave neighs/atom = 160.16019
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds not checked
|
||||||
|
|
||||||
|
unfix 1
|
||||||
|
|
||||||
|
fix 1 all nvt temp 100.0 100.0 100.0
|
||||||
|
thermo_style custom step temp epair etotal press
|
||||||
|
timestep 0.2
|
||||||
|
|
||||||
|
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||||
|
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||||
|
|
||||||
|
run 10
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 123 | 123 | 123 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press
|
||||||
|
10 497.02486 -836425.06 -810825.59 59260.717
|
||||||
|
11 601.6514 -841814.09 -810825.78 59489.425
|
||||||
|
12 716.37597 -847724.6 -810827.35 59738.298
|
||||||
|
13 841.27959 -854161.62 -810831.16 60008.164
|
||||||
|
14 976.4666 -861131.68 -810838.36 60300.364
|
||||||
|
15 1122.0668 -868642.96 -810850.45 60616.793
|
||||||
|
16 1278.2373 -876705.43 -810869.28 60959.942
|
||||||
|
17 1445.1655 -885331.03 -810897.18 61332.932
|
||||||
|
18 1623.072 -894533.91 -810936.92 61739.541
|
||||||
|
19 1812.1864 -904337.86 -811000.45 62200.561
|
||||||
|
20 2011.5898 -915379.05 -811771.28 63361.15
|
||||||
|
Loop time of 1.8322 on 4 procs for 10 steps with 17280 atoms
|
||||||
|
|
||||||
|
Performance: 0.094 ns/day, 254.473 hours/ns, 5.458 timesteps/s, 94.313 katom-step/s
|
||||||
|
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.3846 | 1.4468 | 1.524 | 4.2 | 78.96
|
||||||
|
Neigh | 0.012048 | 0.012239 | 0.012522 | 0.2 | 0.67
|
||||||
|
Comm | 0.00082283 | 0.07804 | 0.14024 | 17.9 | 4.26
|
||||||
|
Output | 0.00029695 | 0.00031243 | 0.00035323 | 0.0 | 0.02
|
||||||
|
Modify | 0.29449 | 0.29478 | 0.29497 | 0.0 | 16.09
|
||||||
|
Other | | 7.342e-05 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 4320 ave 4320 max 4320 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2856 ave 2856 max 2856 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 691892 ave 691892 max 691892 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2767568
|
||||||
|
Ave neighs/atom = 160.16019
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:04
|
||||||
@ -1,141 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for Nitroamines system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.FC
|
|
||||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
17280 atoms
|
|
||||||
|
|
||||||
pair_style reax/c NULL
|
|
||||||
pair_coeff * * ffield.reax.FC C F
|
|
||||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
|
||||||
neighbor 2. bin
|
|
||||||
neigh_modify every 10 delay 0 check no
|
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
|
||||||
|
|
||||||
# should equilibrate much longer in practice
|
|
||||||
|
|
||||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
|
||||||
timestep 0.2
|
|
||||||
thermo_style custom step temp epair etotal press
|
|
||||||
thermo 1
|
|
||||||
dump 4 all xyz 5000 dumpnpt.xyz
|
|
||||||
run 10
|
|
||||||
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 = 28 27 17
|
|
||||||
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) = 470 | 470 | 470 Mbytes
|
|
||||||
Step Temp E_pair TotEng Press
|
|
||||||
0 0 -808525.04 -808525.04 58194.694
|
|
||||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
|
||||||
2 19.98696 -809640.54 -808611.1 58239.155
|
|
||||||
3 45.012616 -811035.31 -808716.91 58294.499
|
|
||||||
4 80.103613 -812988.6 -808862.83 58371.547
|
|
||||||
5 125.26228 -815500.71 -809049.03 58469.871
|
|
||||||
6 180.4316 -818571.61 -809278.4 58588.935
|
|
||||||
7 245.47913 -822200.79 -809557.28 58728.142
|
|
||||||
8 320.17692 -826387.27 -809896.43 58886.877
|
|
||||||
9 404.17073 -831129.48 -810312.5 59064.551
|
|
||||||
10 497.02486 -836425.19 -810825.72 59260.714
|
|
||||||
Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms
|
|
||||||
|
|
||||||
Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s
|
|
||||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39
|
|
||||||
Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39
|
|
||||||
Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00
|
|
||||||
Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00
|
|
||||||
Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21
|
|
||||||
Other | | 0.0004592 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 17280 ave 17280 max 17280 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 5352 ave 5352 max 5352 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2621360
|
|
||||||
Ave neighs/atom = 151.699
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
unfix 1
|
|
||||||
|
|
||||||
fix 1 all nvt temp 100.0 100.0 100.0
|
|
||||||
thermo_style custom step temp epair etotal press
|
|
||||||
timestep 0.2
|
|
||||||
|
|
||||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
|
||||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
|
||||||
|
|
||||||
run 10
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
|
|
||||||
Step Temp E_pair TotEng Press
|
|
||||||
10 497.02486 -836425.19 -810825.72 59260.714
|
|
||||||
11 601.65141 -841814.22 -810825.91 59489.422
|
|
||||||
12 716.37599 -847724.72 -810827.48 59738.295
|
|
||||||
13 841.27961 -854161.75 -810831.29 60008.162
|
|
||||||
14 976.46663 -861131.81 -810838.49 60300.362
|
|
||||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
|
||||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
|
||||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
|
||||||
18 1623.072 -894534.04 -810937.04 61739.541
|
|
||||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
|
||||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
|
||||||
Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms
|
|
||||||
|
|
||||||
Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97
|
|
||||||
Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36
|
|
||||||
Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00
|
|
||||||
Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00
|
|
||||||
Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65
|
|
||||||
Other | | 0.0004568 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 17280 ave 17280 max 17280 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 5352 ave 5352 max 5352 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2621360
|
|
||||||
Ave neighs/atom = 151.699
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:47
|
|
||||||
@ -1,141 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for Nitroamines system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.FC
|
|
||||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
|
||||||
2 by 2 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
17280 atoms
|
|
||||||
|
|
||||||
pair_style reax/c NULL
|
|
||||||
pair_coeff * * ffield.reax.FC C F
|
|
||||||
Reading potential file ffield.reax.FC with DATE: 2013-06-28
|
|
||||||
neighbor 2. bin
|
|
||||||
neigh_modify every 10 delay 0 check no
|
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
|
||||||
|
|
||||||
# should equilibrate much longer in practice
|
|
||||||
|
|
||||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
|
||||||
timestep 0.2
|
|
||||||
thermo_style custom step temp epair etotal press
|
|
||||||
thermo 1
|
|
||||||
dump 4 all xyz 5000 dumpnpt.xyz
|
|
||||||
run 10
|
|
||||||
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 = 28 27 17
|
|
||||||
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) = 149.3 | 149.3 | 149.3 Mbytes
|
|
||||||
Step Temp E_pair TotEng Press
|
|
||||||
0 0 -808525.04 -808525.04 58194.694
|
|
||||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
|
||||||
2 19.98696 -809640.54 -808611.1 58239.155
|
|
||||||
3 45.012616 -811035.31 -808716.91 58294.499
|
|
||||||
4 80.103613 -812988.6 -808862.83 58371.547
|
|
||||||
5 125.26228 -815500.71 -809049.03 58469.871
|
|
||||||
6 180.4316 -818571.61 -809278.4 58588.935
|
|
||||||
7 245.47913 -822200.79 -809557.28 58728.142
|
|
||||||
8 320.17692 -826387.27 -809896.43 58886.877
|
|
||||||
9 404.17073 -831129.48 -810312.5 59064.551
|
|
||||||
10 497.02486 -836425.19 -810825.72 59260.714
|
|
||||||
Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms
|
|
||||||
|
|
||||||
Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 timesteps/s
|
|
||||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01
|
|
||||||
Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43
|
|
||||||
Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25
|
|
||||||
Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01
|
|
||||||
Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30
|
|
||||||
Other | | 0.0001779 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 4320 ave 4320 max 4320 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2856 ave 2856 max 2856 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 691892 ave 691892 max 691892 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2767568
|
|
||||||
Ave neighs/atom = 160.16
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
unfix 1
|
|
||||||
|
|
||||||
fix 1 all nvt temp 100.0 100.0 100.0
|
|
||||||
thermo_style custom step temp epair etotal press
|
|
||||||
timestep 0.2
|
|
||||||
|
|
||||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
|
||||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
|
||||||
|
|
||||||
run 10
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
|
|
||||||
Step Temp E_pair TotEng Press
|
|
||||||
10 497.02486 -836425.19 -810825.72 59260.714
|
|
||||||
11 601.65141 -841814.22 -810825.91 59489.422
|
|
||||||
12 716.37599 -847724.72 -810827.48 59738.295
|
|
||||||
13 841.27961 -854161.75 -810831.29 60008.162
|
|
||||||
14 976.46663 -861131.81 -810838.49 60300.362
|
|
||||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
|
||||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
|
||||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
|
||||||
18 1623.072 -894534.04 -810937.04 61739.541
|
|
||||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
|
||||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
|
||||||
Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms
|
|
||||||
|
|
||||||
Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/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 | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78
|
|
||||||
Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40
|
|
||||||
Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97
|
|
||||||
Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01
|
|
||||||
Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83
|
|
||||||
Other | | 0.0001827 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 4320 ave 4320 max 4320 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2856 ave 2856 max 2856 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 691892 ave 691892 max 691892 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2767568
|
|
||||||
Ave neighs/atom = 160.16
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:13
|
|
||||||
@ -1,23 +1,24 @@
|
|||||||
# REAX potential for Fe/O/H system
|
# REAX potential for Fe/O/H system
|
||||||
# .....
|
# .....
|
||||||
|
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.FeOH3
|
read_data data.FeOH3
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
pair_style reaxff lmp_control
|
||||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||||
|
|
||||||
neighbor 2 bin
|
neighbor 2 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
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
|
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||||
|
|
||||||
timestep 0.25
|
timestep 0.25
|
||||||
|
thermo 100
|
||||||
|
|
||||||
#dump 1 all atom 30 dump.reax.feoh
|
#dump 1 all atom 30 dump.reax.feoh
|
||||||
|
|
||||||
run 3000
|
run 3000
|
||||||
|
|||||||
@ -1,17 +1,7 @@
|
|||||||
simulation_name FeOH3_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
|
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
|
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||||
|
|
||||||
write_freq 1 ! write trajectory after so many steps
|
|
||||||
traj_title Fe_OH3 ! (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
|
|
||||||
|
|||||||
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
Normal file
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
Normal file
@ -0,0 +1,141 @@
|
|||||||
|
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 Fe/O/H system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.FeOH3
|
||||||
|
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 = 0.000 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||||
|
Reading potential file ffield.reax.Fe_O_C_H 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
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 30 dump.reax.feoh
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 15.99 | 15.99 | 15.99 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||||
|
100 127.38829 -9720.5854 0 -9681.0945 -933.74373
|
||||||
|
200 141.21008 -9696.3143 0 -9652.5386 -831.74241
|
||||||
|
300 176.81083 -9681.3376 0 -9626.5255 -520.30966
|
||||||
|
400 220.75236 -9672.6196 0 -9604.1854 -388.85436
|
||||||
|
500 301.29415 -9678.8463 0 -9585.4438 -545.22735
|
||||||
|
600 320.36877 -9670.3054 0 -9570.9897 -609.44044
|
||||||
|
700 414.53699 -9688.649 0 -9560.1408 -259.51791
|
||||||
|
800 391.93073 -9675.1212 0 -9553.621 77.352757
|
||||||
|
900 413.52476 -9673.7372 0 -9545.5428 369.71918
|
||||||
|
1000 382.03337 -9656.3848 0 -9537.9528 236.61186
|
||||||
|
1100 381.68223 -9647.4372 0 -9529.1141 -432.67374
|
||||||
|
1200 470.68889 -9671.5116 0 -9525.596 448.90781
|
||||||
|
1300 436.34973 -9659.2277 0 -9523.9574 188.12079
|
||||||
|
1400 422.25034 -9651.2639 0 -9520.3645 48.988693
|
||||||
|
1500 363.49223 -9625.6588 0 -9512.9746 -977.83513
|
||||||
|
1600 450.39155 -9646.4742 0 -9506.8509 44.80204
|
||||||
|
1700 461.44884 -9648.1215 0 -9505.0704 -29.381385
|
||||||
|
1800 457.01538 -9644.6842 0 -9503.0075 -29.157643
|
||||||
|
1900 461.56497 -9642.8457 0 -9499.7586 -608.58801
|
||||||
|
2000 491.20199 -9648.6637 0 -9496.389 -99.409356
|
||||||
|
2100 461.60295 -9636.4878 0 -9493.3889 753.00956
|
||||||
|
2200 480.92601 -9640.304 0 -9491.2149 -176.4371
|
||||||
|
2300 450.00958 -9627.8875 0 -9488.3826 -210.21397
|
||||||
|
2400 475.97134 -9634.1577 0 -9486.6046 -364.46797
|
||||||
|
2500 478.0174 -9631.5069 0 -9483.3194 557.79107
|
||||||
|
2600 500.26141 -9636.8606 0 -9481.7774 115.84535
|
||||||
|
2700 455.06433 -9620.0151 0 -9478.9433 -963.22
|
||||||
|
2800 441.50799 -9612.6546 0 -9475.7852 -177.60856
|
||||||
|
2900 471.67031 -9618.9817 0 -9472.7619 -294.38595
|
||||||
|
3000 526.94336 -9635.8664 0 -9472.5117 119.05777
|
||||||
|
Loop time of 2.33387 on 1 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 27.765 ns/day, 0.864 hours/ns, 1285.420 timesteps/s, 134.969 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 | 1.8409 | 1.8409 | 1.8409 | 0.0 | 78.88
|
||||||
|
Neigh | 0.15998 | 0.15998 | 0.15998 | 0.0 | 6.85
|
||||||
|
Comm | 0.0090909 | 0.0090909 | 0.0090909 | 0.0 | 0.39
|
||||||
|
Output | 0.00069968 | 0.00069968 | 0.00069968 | 0.0 | 0.03
|
||||||
|
Modify | 0.32099 | 0.32099 | 0.32099 | 0.0 | 13.75
|
||||||
|
Other | | 0.002244 | | | 0.10
|
||||||
|
|
||||||
|
Nlocal: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 651 ave 651 max 651 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3388 ave 3388 max 3388 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3388
|
||||||
|
Ave neighs/atom = 32.266667
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:02
|
||||||
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
Normal file
141
examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
Normal file
@ -0,0 +1,141 @@
|
|||||||
|
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 Fe/O/H system
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.FeOH3
|
||||||
|
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 = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||||
|
Reading potential file ffield.reax.Fe_O_C_H 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
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 30 dump.reax.feoh
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 10.56 | 11.55 | 12.17 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||||
|
100 127.3884 -9720.5854 0 -9681.0945 -933.74975
|
||||||
|
200 141.21023 -9696.3143 0 -9652.5385 -831.74859
|
||||||
|
300 176.81092 -9681.3376 0 -9626.5254 -520.29734
|
||||||
|
400 220.75237 -9672.6195 0 -9604.1853 -388.89122
|
||||||
|
500 301.29434 -9678.8461 0 -9585.4436 -545.24883
|
||||||
|
600 320.36921 -9670.3055 0 -9570.9897 -609.45071
|
||||||
|
700 414.5366 -9688.649 0 -9560.1409 -259.54271
|
||||||
|
800 391.93079 -9675.1212 0 -9553.621 77.314405
|
||||||
|
900 413.52641 -9673.738 0 -9545.5431 369.67477
|
||||||
|
1000 382.02987 -9656.384 0 -9537.9531 236.57634
|
||||||
|
1100 381.6811 -9647.4372 0 -9529.1144 -432.72725
|
||||||
|
1200 470.68578 -9671.511 0 -9525.5964 448.88885
|
||||||
|
1300 436.3616 -9659.2312 0 -9523.9573 188.07625
|
||||||
|
1400 422.26867 -9651.2709 0 -9520.3658 48.829055
|
||||||
|
1500 363.49419 -9625.6611 0 -9512.9764 -977.70396
|
||||||
|
1600 450.39497 -9646.4762 0 -9506.8518 45.000339
|
||||||
|
1700 461.44368 -9648.121 0 -9505.0715 -29.332359
|
||||||
|
1800 457.02327 -9644.687 0 -9503.0078 -29.48478
|
||||||
|
1900 461.60004 -9642.8571 0 -9499.7592 -608.0786
|
||||||
|
2000 491.19069 -9648.6599 0 -9496.3887 -99.479995
|
||||||
|
2100 461.50901 -9636.4581 0 -9493.3884 752.86874
|
||||||
|
2200 480.7646 -9640.2431 0 -9491.204 -175.99562
|
||||||
|
2300 450.00669 -9627.875 0 -9488.3711 -209.83065
|
||||||
|
2400 475.84946 -9634.1191 0 -9486.6038 -366.65233
|
||||||
|
2500 477.75601 -9631.4196 0 -9483.3132 558.18557
|
||||||
|
2600 500.64305 -9636.9676 0 -9481.7661 111.76394
|
||||||
|
2700 455.78826 -9620.2513 0 -9478.955 -962.65771
|
||||||
|
2800 438.72349 -9611.8395 0 -9475.8334 -180.94976
|
||||||
|
2900 471.33135 -9618.8641 0 -9472.7494 -291.14764
|
||||||
|
3000 528.64651 -9636.4232 0 -9472.5405 111.18605
|
||||||
|
Loop time of 1.42723 on 4 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 45.403 ns/day, 0.529 hours/ns, 2101.973 timesteps/s, 220.707 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 | 0.79715 | 0.88663 | 0.96735 | 7.5 | 62.12
|
||||||
|
Neigh | 0.083068 | 0.096787 | 0.10679 | 2.8 | 6.78
|
||||||
|
Comm | 0.058539 | 0.13831 | 0.22776 | 19.0 | 9.69
|
||||||
|
Output | 0.0006518 | 0.00071197 | 0.00088964 | 0.0 | 0.05
|
||||||
|
Modify | 0.29308 | 0.30291 | 0.31706 | 1.6 | 21.22
|
||||||
|
Other | | 0.001886 | | | 0.13
|
||||||
|
|
||||||
|
Nlocal: 26.25 ave 34 max 12 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||||
|
Nghost: 408 ave 462 max 347 min
|
||||||
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||||
|
Neighs: 1109 ave 1419 max 453 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 4436
|
||||||
|
Ave neighs/atom = 42.247619
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:01
|
||||||
@ -1,70 +0,0 @@
|
|||||||
LAMMPS (5 Oct 2016)
|
|
||||||
# REAX potential for Fe/O/H system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.FeOH3
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
|
||||||
Reading potential file ffield.reax.Fe_O_C_H 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.feoh
|
|
||||||
|
|
||||||
run 3000
|
|
||||||
Neighbor list info ...
|
|
||||||
2 neighbor list requests
|
|
||||||
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
|
|
||||||
Memory usage per processor = 17.7294 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
|
||||||
3000 529.72301 -9636.7144 0 -9472.498 127.52152
|
|
||||||
Loop time of 8.40814 on 1 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 7.707 ns/day, 3.114 hours/ns, 356.797 timesteps/s
|
|
||||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.3193 | 7.3193 | 7.3193 | 0.0 | 87.05
|
|
||||||
Neigh | 0.29032 | 0.29032 | 0.29032 | 0.0 | 3.45
|
|
||||||
Comm | 0.016032 | 0.016032 | 0.016032 | 0.0 | 0.19
|
|
||||||
Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00
|
|
||||||
Modify | 0.77846 | 0.77846 | 0.77846 | 0.0 | 9.26
|
|
||||||
Other | | 0.004053 | | | 0.05
|
|
||||||
|
|
||||||
Nlocal: 105 ave 105 max 105 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 651 ave 651 max 651 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 3389 ave 3389 max 3389 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 3389
|
|
||||||
Ave neighs/atom = 32.2762
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:08
|
|
||||||
@ -1,70 +0,0 @@
|
|||||||
LAMMPS (5 Oct 2016)
|
|
||||||
# REAX potential for Fe/O/H system
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.FeOH3
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
|
||||||
Reading potential file ffield.reax.Fe_O_C_H 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.feoh
|
|
||||||
|
|
||||||
run 3000
|
|
||||||
Neighbor list info ...
|
|
||||||
2 neighbor list requests
|
|
||||||
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
|
|
||||||
Memory usage per processor = 12.3695 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
|
||||||
3000 534.48882 -9638.0405 0 -9472.3467 127.47989
|
|
||||||
Loop time of 4.78344 on 4 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 13.547 ns/day, 1.772 hours/ns, 627.164 timesteps/s
|
|
||||||
99.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 3.7061 | 3.7503 | 3.7853 | 1.5 | 78.40
|
|
||||||
Neigh | 0.14361 | 0.16388 | 0.18297 | 3.4 | 3.43
|
|
||||||
Comm | 0.062001 | 0.098492 | 0.14111 | 9.0 | 2.06
|
|
||||||
Output | 2.0981e-05 | 2.2948e-05 | 2.7895e-05 | 0.1 | 0.00
|
|
||||||
Modify | 0.75012 | 0.76764 | 0.78678 | 1.5 | 16.05
|
|
||||||
Other | | 0.003105 | | | 0.06
|
|
||||||
|
|
||||||
Nlocal: 26.25 ave 35 max 12 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
|
||||||
Nghost: 408 ave 462 max 348 min
|
|
||||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
|
||||||
Neighs: 1107 ave 1428 max 453 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 4428
|
|
||||||
Ave neighs/atom = 42.1714
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:05
|
|
||||||
@ -12,16 +12,15 @@ atom_style charge
|
|||||||
atom_modify sort 100 0.0 # optional
|
atom_modify sort 100 0.0 # optional
|
||||||
dimension 3
|
dimension 3
|
||||||
boundary p p p
|
boundary p p p
|
||||||
box tilt large
|
|
||||||
|
|
||||||
read_data data.hns-equil
|
read_data data.hns-equil
|
||||||
replicate $x $y $z bbox
|
replicate $x $y $z bbox
|
||||||
|
|
||||||
|
|
||||||
pair_style reax/c NULL
|
pair_style reaxff NULL
|
||||||
pair_coeff * * ffield.reax.hns C H O N
|
pair_coeff * * ffield.reax.hns C H O N
|
||||||
|
|
||||||
compute reax all pair reax/c
|
compute reax all pair reaxff
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 20 delay 0 check no
|
neigh_modify every 20 delay 0 check no
|
||||||
@ -35,6 +34,6 @@ thermo 10
|
|||||||
velocity all create 300.0 41279 loop geom
|
velocity all create 300.0 41279 loop geom
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
run $t
|
run $t
|
||||||
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
Normal file
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
Normal file
@ -0,0 +1,149 @@
|
|||||||
|
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
|
||||||
|
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||||
|
# See README for more info
|
||||||
|
|
||||||
|
variable x index 2
|
||||||
|
variable y index 2
|
||||||
|
variable z index 2
|
||||||
|
variable t index 100
|
||||||
|
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
atom_modify sort 100 0.0 # optional
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
read_data data.hns-equil
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (22.326 11.1412 13.778966) with tilt (0 -5.02603 0)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
304 atoms
|
||||||
|
reading velocities ...
|
||||||
|
304 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
replicate $x $y $z bbox
|
||||||
|
replicate 2 $y $z bbox
|
||||||
|
replicate 2 2 $z bbox
|
||||||
|
replicate 2 2 2 bbox
|
||||||
|
Replication is creating a 2x2x2 = 8 times larger system...
|
||||||
|
triclinic box = (0 0 0) to (44.652 22.2824 27.557932) with tilt (0 -10.05206 0)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
bounding box image = (0 -1 -1) to (0 1 1)
|
||||||
|
bounding box extra memory = 0.03 MB
|
||||||
|
average # of replicas added to proc = 8.00 out of 8 (100.00%)
|
||||||
|
2432 atoms
|
||||||
|
replicate CPU = 0.001 seconds
|
||||||
|
|
||||||
|
|
||||||
|
pair_style reaxff NULL
|
||||||
|
pair_coeff * * ffield.reax.hns C H O N
|
||||||
|
|
||||||
|
compute reax all pair reaxff
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 20 delay 0 check no
|
||||||
|
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
thermo_style custom step temp pe press evdwl ecoul vol
|
||||||
|
thermo_modify norm yes
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
velocity all create 300.0 41279 loop geom
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
|
run $t
|
||||||
|
run 100
|
||||||
|
|
||||||
|
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 = 20 steps, delay = 0 steps, check = no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 11
|
||||||
|
ghost atom cutoff = 11
|
||||||
|
binsize = 5.5, bins = 10 5 6
|
||||||
|
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) = 215 | 215 | 215 Mbytes
|
||||||
|
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||||
|
0 300 -113.27833 437.52149 -111.57687 -1.7014647 27418.867
|
||||||
|
10 299.38517 -113.27631 1439.2564 -111.57492 -1.7013814 27418.867
|
||||||
|
20 300.27107 -113.27884 3764.4017 -111.57762 -1.7012246 27418.867
|
||||||
|
30 302.21064 -113.28428 7007.6558 -111.58335 -1.7009364 27418.867
|
||||||
|
40 303.52265 -113.28799 9844.8196 -111.58747 -1.7005186 27418.867
|
||||||
|
50 301.8706 -113.28324 9663.08 -111.58318 -1.7000523 27418.867
|
||||||
|
60 296.67808 -113.26777 7273.8875 -111.56815 -1.6996136 27418.867
|
||||||
|
70 292.19999 -113.25435 5533.625 -111.55514 -1.6992157 27418.867
|
||||||
|
80 293.58678 -113.25831 5993.4679 -111.55946 -1.6988532 27418.867
|
||||||
|
90 300.62637 -113.27925 7202.8453 -111.58069 -1.6985592 27418.867
|
||||||
|
100 305.38277 -113.29357 10085.747 -111.59518 -1.6983875 27418.867
|
||||||
|
Loop time of 17.6114 on 1 procs for 100 steps with 2432 atoms
|
||||||
|
|
||||||
|
Performance: 0.049 ns/day, 489.205 hours/ns, 5.678 timesteps/s, 13.809 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 | 13.081 | 13.081 | 13.081 | 0.0 | 74.27
|
||||||
|
Neigh | 0.25469 | 0.25469 | 0.25469 | 0.0 | 1.45
|
||||||
|
Comm | 0.0061082 | 0.0061082 | 0.0061082 | 0.0 | 0.03
|
||||||
|
Output | 0.00035315 | 0.00035315 | 0.00035315 | 0.0 | 0.00
|
||||||
|
Modify | 4.2687 | 4.2687 | 4.2687 | 0.0 | 24.24
|
||||||
|
Other | | 0.0007784 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 2432 ave 2432 max 2432 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 10685 ave 10685 max 10685 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 823958 ave 823958 max 823958 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 823958
|
||||||
|
Ave neighs/atom = 338.79852
|
||||||
|
Neighbor list builds = 5
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:17
|
||||||
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
Normal file
149
examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
Normal file
@ -0,0 +1,149 @@
|
|||||||
|
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
|
||||||
|
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
||||||
|
# See README for more info
|
||||||
|
|
||||||
|
variable x index 2
|
||||||
|
variable y index 2
|
||||||
|
variable z index 2
|
||||||
|
variable t index 100
|
||||||
|
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style charge
|
||||||
|
atom_modify sort 100 0.0 # optional
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
read_data data.hns-equil
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (22.326 11.1412 13.778966) with tilt (0 -5.02603 0)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
304 atoms
|
||||||
|
reading velocities ...
|
||||||
|
304 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
replicate $x $y $z bbox
|
||||||
|
replicate 2 $y $z bbox
|
||||||
|
replicate 2 2 $z bbox
|
||||||
|
replicate 2 2 2 bbox
|
||||||
|
Replication is creating a 2x2x2 = 8 times larger system...
|
||||||
|
triclinic box = (0 0 0) to (44.652 22.2824 27.557932) with tilt (0 -10.05206 0)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
bounding box image = (0 -1 -1) to (0 1 1)
|
||||||
|
bounding box extra memory = 0.03 MB
|
||||||
|
average # of replicas added to proc = 5.00 out of 8 (62.50%)
|
||||||
|
2432 atoms
|
||||||
|
replicate CPU = 0.000 seconds
|
||||||
|
|
||||||
|
|
||||||
|
pair_style reaxff NULL
|
||||||
|
pair_coeff * * ffield.reax.hns C H O N
|
||||||
|
|
||||||
|
compute reax all pair reaxff
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 20 delay 0 check no
|
||||||
|
|
||||||
|
timestep 0.1
|
||||||
|
|
||||||
|
thermo_style custom step temp pe press evdwl ecoul vol
|
||||||
|
thermo_modify norm yes
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
velocity all create 300.0 41279 loop geom
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
|
||||||
|
|
||||||
|
run $t
|
||||||
|
run 100
|
||||||
|
|
||||||
|
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 = 20 steps, delay = 0 steps, check = no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 11
|
||||||
|
ghost atom cutoff = 11
|
||||||
|
binsize = 5.5, bins = 10 5 6
|
||||||
|
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) = 103.8 | 103.8 | 103.8 Mbytes
|
||||||
|
Step Temp PotEng Press E_vdwl E_coul Volume
|
||||||
|
0 300 -113.27833 437.52125 -111.57687 -1.7014647 27418.867
|
||||||
|
10 299.38517 -113.27631 1439.2564 -111.57492 -1.7013814 27418.867
|
||||||
|
20 300.27106 -113.27884 3764.3691 -111.57762 -1.7012246 27418.867
|
||||||
|
30 302.21062 -113.28428 7007.6981 -111.58335 -1.7009363 27418.867
|
||||||
|
40 303.52264 -113.28799 9844.8446 -111.58747 -1.7005186 27418.867
|
||||||
|
50 301.87059 -113.28324 9663.0539 -111.58318 -1.7000523 27418.867
|
||||||
|
60 296.67807 -113.26777 7273.8306 -111.56815 -1.6996136 27418.867
|
||||||
|
70 292.19997 -113.25435 5533.612 -111.55514 -1.6992157 27418.867
|
||||||
|
80 293.58675 -113.25831 5993.4344 -111.55946 -1.6988533 27418.867
|
||||||
|
90 300.62636 -113.27925 7202.8636 -111.58069 -1.6985591 27418.867
|
||||||
|
100 305.38278 -113.29357 10085.719 -111.59518 -1.6983876 27418.867
|
||||||
|
Loop time of 6.63333 on 4 procs for 100 steps with 2432 atoms
|
||||||
|
|
||||||
|
Performance: 0.130 ns/day, 184.259 hours/ns, 15.075 timesteps/s, 36.663 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 | 4.1006 | 4.5745 | 5.0624 | 17.4 | 68.96
|
||||||
|
Neigh | 0.11589 | 0.11637 | 0.11669 | 0.1 | 1.75
|
||||||
|
Comm | 0.0077297 | 0.49567 | 0.96958 | 52.7 | 7.47
|
||||||
|
Output | 0.00027396 | 0.00031049 | 0.00038633 | 0.0 | 0.00
|
||||||
|
Modify | 1.4458 | 1.4461 | 1.4465 | 0.0 | 21.80
|
||||||
|
Other | | 0.0004201 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 608 ave 612 max 604 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Nghost: 5737.25 ave 5744 max 5732 min
|
||||||
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||||
|
Neighs: 231539 ave 233090 max 229970 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 926155
|
||||||
|
Ave neighs/atom = 380.82031
|
||||||
|
Neighbor list builds = 5
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:06
|
||||||
@ -1,115 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
|
||||||
# See README for more info
|
|
||||||
|
|
||||||
variable x index 2
|
|
||||||
variable y index 2
|
|
||||||
variable z index 2
|
|
||||||
variable t index 100
|
|
||||||
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style charge
|
|
||||||
atom_modify sort 100 0.0 # optional
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
box tilt large
|
|
||||||
|
|
||||||
read_data data.hns-equil
|
|
||||||
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
304 atoms
|
|
||||||
reading velocities ...
|
|
||||||
304 velocities
|
|
||||||
replicate $x $y $z bbox
|
|
||||||
replicate 2 $y $z bbox
|
|
||||||
replicate 2 2 $z bbox
|
|
||||||
replicate 2 2 2 bbox
|
|
||||||
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
2432 atoms
|
|
||||||
Time spent = 0.000789404 secs
|
|
||||||
|
|
||||||
|
|
||||||
pair_style reax/c NULL
|
|
||||||
pair_coeff * * ffield.reax.hns C H O N
|
|
||||||
|
|
||||||
compute reax all pair reax/c
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 20 delay 0 check no
|
|
||||||
|
|
||||||
timestep 0.1
|
|
||||||
|
|
||||||
thermo_style custom step temp pe press evdwl ecoul vol
|
|
||||||
thermo_modify norm yes
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
velocity all create 300.0 41279 loop geom
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 20 steps, delay 0 steps, check no
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 11
|
|
||||||
ghost atom cutoff = 11
|
|
||||||
binsize = 5.5, bins = 10 5 6
|
|
||||||
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) = 262.4 | 262.4 | 262.4 Mbytes
|
|
||||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
|
||||||
0 300 -113.27833 437.52103 -111.57687 -1.7014647 27418.867
|
|
||||||
10 299.87174 -113.27778 2033.6337 -111.57645 -1.7013325 27418.867
|
|
||||||
20 300.81718 -113.28046 4817.5889 -111.57931 -1.7011463 27418.867
|
|
||||||
30 301.8622 -113.28323 8303.0039 -111.58237 -1.7008608 27418.867
|
|
||||||
40 302.4646 -113.28493 10519.459 -111.58446 -1.700467 27418.867
|
|
||||||
50 300.79064 -113.27989 10402.291 -111.57987 -1.7000218 27418.867
|
|
||||||
60 296.11534 -113.26599 7929.1348 -111.5664 -1.6995929 27418.867
|
|
||||||
70 291.73354 -113.25289 5071.5459 -111.5537 -1.6991916 27418.867
|
|
||||||
80 292.189 -113.25399 5667.0962 -111.55519 -1.6987993 27418.867
|
|
||||||
90 298.40792 -113.27253 7513.3806 -111.57409 -1.6984403 27418.867
|
|
||||||
100 303.58246 -113.28809 10017.879 -111.58991 -1.698177 27418.867
|
|
||||||
Loop time of 59.5461 on 1 procs for 100 steps with 2432 atoms
|
|
||||||
|
|
||||||
Performance: 0.015 ns/day, 1654.060 hours/ns, 1.679 timesteps/s
|
|
||||||
97.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 49.922 | 49.922 | 49.922 | 0.0 | 83.84
|
|
||||||
Neigh | 0.53154 | 0.53154 | 0.53154 | 0.0 | 0.89
|
|
||||||
Comm | 0.011399 | 0.011399 | 0.011399 | 0.0 | 0.02
|
|
||||||
Output | 0.00064397 | 0.00064397 | 0.00064397 | 0.0 | 0.00
|
|
||||||
Modify | 9.0782 | 9.0782 | 9.0782 | 0.0 | 15.25
|
|
||||||
Other | | 0.002116 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 2432 ave 2432 max 2432 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 10687 ave 10687 max 10687 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 823977 ave 823977 max 823977 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 823977
|
|
||||||
Ave neighs/atom = 338.806
|
|
||||||
Neighbor list builds = 5
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:01:00
|
|
||||||
@ -1,115 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
|
|
||||||
# See README for more info
|
|
||||||
|
|
||||||
variable x index 2
|
|
||||||
variable y index 2
|
|
||||||
variable z index 2
|
|
||||||
variable t index 100
|
|
||||||
|
|
||||||
|
|
||||||
units real
|
|
||||||
atom_style charge
|
|
||||||
atom_modify sort 100 0.0 # optional
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
box tilt large
|
|
||||||
|
|
||||||
read_data data.hns-equil
|
|
||||||
triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
304 atoms
|
|
||||||
reading velocities ...
|
|
||||||
304 velocities
|
|
||||||
replicate $x $y $z bbox
|
|
||||||
replicate 2 $y $z bbox
|
|
||||||
replicate 2 2 $z bbox
|
|
||||||
replicate 2 2 2 bbox
|
|
||||||
triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
2432 atoms
|
|
||||||
Time spent = 0.000398397 secs
|
|
||||||
|
|
||||||
|
|
||||||
pair_style reax/c NULL
|
|
||||||
pair_coeff * * ffield.reax.hns C H O N
|
|
||||||
|
|
||||||
compute reax all pair reax/c
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 20 delay 0 check no
|
|
||||||
|
|
||||||
timestep 0.1
|
|
||||||
|
|
||||||
thermo_style custom step temp pe press evdwl ecoul vol
|
|
||||||
thermo_modify norm yes
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
velocity all create 300.0 41279 loop geom
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 20 steps, delay 0 steps, check no
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 11
|
|
||||||
ghost atom cutoff = 11
|
|
||||||
binsize = 5.5, bins = 10 5 6
|
|
||||||
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) = 126.6 | 126.6 | 126.6 Mbytes
|
|
||||||
Step Temp PotEng Press E_vdwl E_coul Volume
|
|
||||||
0 300 -113.27833 437.52112 -111.57687 -1.7014647 27418.867
|
|
||||||
10 299.87174 -113.27778 2033.632 -111.57645 -1.7013325 27418.867
|
|
||||||
20 300.81719 -113.28046 4817.5761 -111.57931 -1.7011463 27418.867
|
|
||||||
30 301.8622 -113.28323 8302.9767 -111.58237 -1.7008609 27418.867
|
|
||||||
40 302.4646 -113.28493 10519.481 -111.58446 -1.700467 27418.867
|
|
||||||
50 300.79064 -113.27989 10402.312 -111.57987 -1.7000217 27418.867
|
|
||||||
60 296.11534 -113.26599 7929.1393 -111.5664 -1.6995929 27418.867
|
|
||||||
70 291.73354 -113.25289 5071.5368 -111.5537 -1.6991916 27418.867
|
|
||||||
80 292.18901 -113.25399 5667.1118 -111.55519 -1.6987993 27418.867
|
|
||||||
90 298.40793 -113.27253 7513.4029 -111.57409 -1.6984403 27418.867
|
|
||||||
100 303.58247 -113.28809 10017.892 -111.58991 -1.698177 27418.867
|
|
||||||
Loop time of 21.3933 on 4 procs for 100 steps with 2432 atoms
|
|
||||||
|
|
||||||
Performance: 0.040 ns/day, 594.257 hours/ns, 4.674 timesteps/s
|
|
||||||
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 14.863 | 16.367 | 18.027 | 28.6 | 76.51
|
|
||||||
Neigh | 0.23943 | 0.2422 | 0.24658 | 0.6 | 1.13
|
|
||||||
Comm | 0.024331 | 1.6845 | 3.189 | 89.2 | 7.87
|
|
||||||
Output | 0.00051165 | 0.00056899 | 0.00068665 | 0.0 | 0.00
|
|
||||||
Modify | 3.0933 | 3.0969 | 3.0999 | 0.1 | 14.48
|
|
||||||
Other | | 0.001784 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 608 ave 608 max 608 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 5738.25 ave 5742 max 5734 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
||||||
Neighs: 231544 ave 231625 max 231466 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 926176
|
|
||||||
Ave neighs/atom = 380.829
|
|
||||||
Neighbor list builds = 5
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:21
|
|
||||||
@ -1,23 +1,23 @@
|
|||||||
# REAX potential for high energy CHON systems
|
# REAX potential for high energy CHON systems
|
||||||
# .....
|
# .....
|
||||||
|
|
||||||
units real
|
units real
|
||||||
|
|
||||||
atom_style charge
|
atom_style charge
|
||||||
read_data data.RDX
|
read_data data.RDX
|
||||||
|
|
||||||
pair_style reax/c lmp_control
|
pair_style reaxff lmp_control
|
||||||
pair_coeff * * ffield.reax.rdx H C O N
|
pair_coeff * * ffield.reax.rdx H C O N
|
||||||
|
|
||||||
neighbor 2 bin
|
neighbor 2 bin
|
||||||
neigh_modify every 10 delay 0 check no
|
neigh_modify every 10 delay 0 check no
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
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
|
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||||
|
|
||||||
timestep 0.25
|
timestep 0.25
|
||||||
|
thermo 100
|
||||||
|
#dump 1 all atom 30 dump.reax.rdx
|
||||||
|
|
||||||
#dump 1 all atom 30 dump.reax.rdx
|
run 3000
|
||||||
|
|
||||||
run 3000
|
|
||||||
|
|||||||
@ -1,17 +1,8 @@
|
|||||||
simulation_name RDX_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
|
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
|
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
|
||||||
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
|
||||||
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
|
||||||
thb_cutoff 0.001 ! cutoff value for three body interactions
|
thb_cutoff 0.001 ! cutoff value for three body interactions
|
||||||
|
|
||||||
write_freq 1 ! write trajectory after so many steps
|
|
||||||
traj_title RDX ! (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
|
|
||||||
|
|||||||
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.1
Normal file
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.1
Normal file
@ -0,0 +1,140 @@
|
|||||||
|
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 high energy CHON systems
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.RDX
|
||||||
|
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 lmp_control
|
||||||
|
pair_coeff * * ffield.reax.rdx H C O N
|
||||||
|
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||||
|
|
||||||
|
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.rdx
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 16.3 | 16.3 | 16.3 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -10197.932 0 -10197.932 38.347492
|
||||||
|
100 47.478574 -10176.425 0 -10161.706 632.99863
|
||||||
|
200 166.95277 -10181.513 0 -10129.757 -27.107717
|
||||||
|
300 142.53594 -10148.039 0 -10103.853 5120.6794
|
||||||
|
400 322.68495 -10178.868 0 -10078.834 2342.89
|
||||||
|
500 193.81476 -10117.984 0 -10057.901 8412.5289
|
||||||
|
600 300.27155 -10134.473 0 -10041.388 -2801.8661
|
||||||
|
700 272.63426 -10110.146 0 -10025.629 10749.023
|
||||||
|
800 339.99867 -10114.124 0 -10008.723 5122.9966
|
||||||
|
900 231.65547 -10068.587 0 -9996.7728 5306.059
|
||||||
|
1000 329.92918 -10088.776 0 -9986.4964 3190.1697
|
||||||
|
1100 376.60905 -10092.398 0 -9975.6476 2921.9605
|
||||||
|
1200 361.98746 -10076.599 0 -9964.3813 3612.0455
|
||||||
|
1300 358.65631 -10069.365 0 -9958.1802 4339.8435
|
||||||
|
1400 470.15262 -10098.553 0 -9952.8035 -146.0811
|
||||||
|
1500 509.62274 -10106.57 0 -9948.5844 2356.8592
|
||||||
|
1600 417.89364 -10075.274 0 -9945.7249 1760.5655
|
||||||
|
1700 453.21317 -10084.329 0 -9943.8306 -570.32375
|
||||||
|
1800 472.92112 -10087.83 0 -9941.2221 1550.3495
|
||||||
|
1900 507.18794 -10096.441 0 -9939.2102 -460.65809
|
||||||
|
2000 443.55347 -10076.832 0 -9939.3281 -145.14295
|
||||||
|
2100 485.44451 -10088.451 0 -9937.9611 -614.40787
|
||||||
|
2200 507.52411 -10095.157 0 -9937.8226 1308.3869
|
||||||
|
2300 496.44961 -10089.637 0 -9935.7354 206.44147
|
||||||
|
2400 457.99343 -10078.114 0 -9936.1344 810.80538
|
||||||
|
2500 507.88115 -10092.692 0 -9935.2463 -464.87873
|
||||||
|
2600 437.84198 -10069.789 0 -9934.0561 1323.4191
|
||||||
|
2700 503.09017 -10088.945 0 -9932.9853 1133.3561
|
||||||
|
2800 481.73908 -10082.193 0 -9932.852 -27.838881
|
||||||
|
2900 487.56555 -10082.752 0 -9931.6045 1772.2131
|
||||||
|
3000 510.30601 -10091.368 0 -9933.1706 1273.0501
|
||||||
|
Loop time of 5.35022 on 1 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 12.112 ns/day, 1.982 hours/ns, 560.725 timesteps/s, 58.876 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 | 4.7927 | 4.7927 | 4.7927 | 0.0 | 89.58
|
||||||
|
Neigh | 0.15169 | 0.15169 | 0.15169 | 0.0 | 2.84
|
||||||
|
Comm | 0.011036 | 0.011036 | 0.011036 | 0.0 | 0.21
|
||||||
|
Output | 0.00080628 | 0.00080628 | 0.00080628 | 0.0 | 0.02
|
||||||
|
Modify | 0.3906 | 0.3906 | 0.3906 | 0.0 | 7.30
|
||||||
|
Other | | 0.003436 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 105 ave 105 max 105 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 645 ave 645 max 645 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3065 ave 3065 max 3065 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3065
|
||||||
|
Ave neighs/atom = 29.190476
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:05
|
||||||
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4
Normal file
140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4
Normal file
@ -0,0 +1,140 @@
|
|||||||
|
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 high energy CHON systems
|
||||||
|
# .....
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.RDX
|
||||||
|
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 = 0.001 seconds
|
||||||
|
|
||||||
|
pair_style reaxff lmp_control
|
||||||
|
pair_coeff * * ffield.reax.rdx H C O N
|
||||||
|
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
||||||
|
|
||||||
|
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.rdx
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
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) = 10.78 | 11.56 | 12.26 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -10197.932 0 -10197.932 38.347492
|
||||||
|
100 47.47852 -10176.425 0 -10161.706 632.97359
|
||||||
|
200 166.95287 -10181.513 0 -10129.757 -27.146803
|
||||||
|
300 142.53582 -10148.039 0 -10103.852 5120.6397
|
||||||
|
400 322.68523 -10178.868 0 -10078.834 2342.7187
|
||||||
|
500 193.81484 -10117.984 0 -10057.901 8412.4559
|
||||||
|
600 300.27165 -10134.473 0 -10041.388 -2801.9143
|
||||||
|
700 272.63408 -10110.146 0 -10025.629 10749.2
|
||||||
|
800 339.99669 -10114.123 0 -10008.723 5123.2489
|
||||||
|
900 231.65632 -10068.587 0 -9996.7729 5306.0392
|
||||||
|
1000 329.93324 -10088.777 0 -9986.4967 3190.4707
|
||||||
|
1100 376.60924 -10092.398 0 -9975.6478 2920.8475
|
||||||
|
1200 361.98231 -10076.598 0 -9964.3816 3612.0573
|
||||||
|
1300 358.6599 -10069.366 0 -9958.1803 4341.9871
|
||||||
|
1400 470.14856 -10098.552 0 -9952.8036 -146.9069
|
||||||
|
1500 509.6454 -10106.577 0 -9948.5847 2355.4022
|
||||||
|
1600 417.9276 -10075.284 0 -9945.7249 1749.565
|
||||||
|
1700 453.25817 -10084.343 0 -9943.8306 -570.48011
|
||||||
|
1800 472.9517 -10087.84 0 -9941.2226 1532.6424
|
||||||
|
1900 507.14171 -10096.428 0 -9939.212 -404.84948
|
||||||
|
2000 443.62843 -10076.86 0 -9939.3329 -132.17302
|
||||||
|
2100 485.441 -10088.414 0 -9937.925 -609.75758
|
||||||
|
2200 507.23914 -10095.067 0 -9937.8209 1288.5372
|
||||||
|
2300 499.64956 -10090.665 0 -9935.7719 149.06622
|
||||||
|
2400 457.97848 -10078.107 0 -9936.1317 2065.2075
|
||||||
|
2500 510.58254 -10093.537 0 -9935.2543 -559.75965
|
||||||
|
2600 440.97503 -10070.865 0 -9934.1605 1164.1078
|
||||||
|
2700 500.4945 -10088.165 0 -9933.0096 1051.9016
|
||||||
|
2800 485.77814 -10083.543 0 -9932.9498 294.64404
|
||||||
|
2900 487.73983 -10082.939 0 -9931.7373 2208.263
|
||||||
|
3000 504.69717 -10089.803 0 -9933.3447 1723.6386
|
||||||
|
Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
|
||||||
|
|
||||||
|
Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 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 | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
|
||||||
|
Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
|
||||||
|
Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
|
||||||
|
Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
|
||||||
|
Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
|
||||||
|
Other | | 0.003062 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 26.25 ave 46 max 8 min
|
||||||
|
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||||
|
Nghost: 399.5 ave 512 max 288 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Neighs: 1011.25 ave 1819 max 420 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 4045
|
||||||
|
Ave neighs/atom = 38.52381
|
||||||
|
Neighbor list builds = 300
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for high energy CHON systems
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.RDX
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.rdx H C O N
|
|
||||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
|
||||||
|
|
||||||
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.rdx
|
|
||||||
|
|
||||||
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 | 19 | 19 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -10197.932 0 -10197.932 38.347492
|
|
||||||
3000 510.63767 -10091.537 0 -9933.2374 1144.545
|
|
||||||
Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s
|
|
||||||
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40
|
|
||||||
Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56
|
|
||||||
Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10
|
|
||||||
Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00
|
|
||||||
Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92
|
|
||||||
Other | | 0.006125 | | | 0.03
|
|
||||||
|
|
||||||
Nlocal: 105 ave 105 max 105 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 645 ave 645 max 645 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 3063 ave 3063 max 3063 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 3063
|
|
||||||
Ave neighs/atom = 29.1714
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:21
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (8 Mar 2018)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# REAX potential for high energy CHON systems
|
|
||||||
# .....
|
|
||||||
|
|
||||||
units real
|
|
||||||
|
|
||||||
atom_style charge
|
|
||||||
read_data data.RDX
|
|
||||||
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 lmp_control
|
|
||||||
pair_coeff * * ffield.reax.rdx H C O N
|
|
||||||
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
|
|
||||||
|
|
||||||
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.rdx
|
|
||||||
|
|
||||||
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) = 12.14 | 13.04 | 13.9 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -10197.932 0 -10197.932 38.347492
|
|
||||||
3000 509.89257 -10091.36 0 -9933.2916 1406.1215
|
|
||||||
Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms
|
|
||||||
|
|
||||||
Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s
|
|
||||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40
|
|
||||||
Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68
|
|
||||||
Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53
|
|
||||||
Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00
|
|
||||||
Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35
|
|
||||||
Other | | 0.004379 | | | 0.04
|
|
||||||
|
|
||||||
Nlocal: 26.25 ave 46 max 8 min
|
|
||||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
|
||||||
Nghost: 399.5 ave 512 max 288 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Neighs: 1011.25 ave 1819 max 420 min
|
|
||||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 4045
|
|
||||||
Ave neighs/atom = 38.5238
|
|
||||||
Neighbor list builds = 300
|
|
||||||
Dangerous builds not checked
|
|
||||||
|
|
||||||
Please see the log.cite file for references relevant to this simulation
|
|
||||||
|
|
||||||
Total wall time: 0:00:11
|
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user