diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 28e02bbee7..f7e9b314bd 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -971,33 +971,53 @@ if(PKG_KOKKOS)
endif()
endif()
if(PKG_KSPACE)
- 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(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()
+ if (LMP_HEFFTE)
+ message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib: heFFTe")
+ if (HEFFTE_BACKEND)
+ message(STATUS "heFFTe backend: ${HEFFTE_BACKEND}")
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()
diff --git a/cmake/Modules/Packages/KSPACE.cmake b/cmake/Modules/Packages/KSPACE.cmake
index de7e7e5b20..9c9c879cd4 100644
--- a/cmake/Modules/Packages/KSPACE.cmake
+++ b/cmake/Modules/Packages/KSPACE.cmake
@@ -46,6 +46,42 @@ else()
target_compile_definitions(lammps PRIVATE -DFFT_KISS)
endif()
+option(FFT_USE_HEFFTE "Use heFFTe as the distributed FFT engine, overrides the FFT option." OFF)
+if(FFT_USE_HEFFTE)
+ # if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
+ set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
+ set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+ set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
+
+ if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
+ set(HEFFTE_COMPONENTS "FFTW")
+ set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
+ elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
+ set(HEFFTE_COMPONENTS "MKL")
+ set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
+ else()
+ message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
+ endif()
+
+ find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
+ if (NOT Heffte_FOUND) # download and build
+ include(FetchContent)
+ FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
+ URL "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
+ URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
+ )
+ FetchContent_Populate(HEFFTE_PROJECT)
+ add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
+ set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+ set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+ add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
+ target_link_libraries(Heffte::Heffte INTERFACE Heffte)
+ endif()
+
+ target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
+ target_link_libraries(lammps PRIVATE Heffte::Heffte)
+endif()
+
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
diff --git a/cmake/Modules/Packages/ML-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake
index ce8f02f5f4..248b8eea76 100644
--- a/cmake/Modules/Packages/ML-PACE.cmake
+++ b/cmake/Modules/Packages/ML-PACE.cmake
@@ -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_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
-# download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
- file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
- 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()
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+# to make it easier to check local build without going through the public github releases
+if(LOCAL_ML-PACE)
+ set(lib-pace "${LOCAL_ML-PACE}")
else()
- message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+ # download library sources to build folder
+ if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+ file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+ endif()
+ if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+ 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(
- COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
- COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+
+ # uncompress downloaded sources
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+ COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ )
+ get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
index 7576cae3eb..e2b096c6e0 100644
--- a/doc/src/Build_settings.rst
+++ b/doc/src/Build_settings.rst
@@ -43,6 +43,12 @@ When the KSPACE package is included in a LAMMPS build, the
require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS, but other libraries can be faster.
LAMMPS can use them if they are available on your system.
+Alternatively, LAMMPS can use the
+`heFFTe `_
+library for the MPI communication algorithms,
+which comes with many optimizations for special cases,
+e.g., leveraging 2D and 3D backend transforms and
+better pipelining for packing and communication.
.. tabs::
@@ -53,6 +59,7 @@ LAMMPS can use them if they are available on your system.
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
+ -D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
.. note::
@@ -76,6 +83,15 @@ LAMMPS can use them if they are available on your system.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
+ -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock backend
+ -D Heffte_ROOT=path # path to an existing heFFTe installation
+
+ .. note::
+
+ heFFTe comes with a builtin stock backend for FFTs; however, the backend
+ is intended for testing purposes and is not performance optimized
+ for large scale production runs.
+
.. tab:: Traditional make
@@ -111,6 +127,24 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link.
+ Traditional make can also link to heFFTe using an existing installation
+
+ .. code-block:: make
+
+ include /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 `_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
@@ -170,6 +204,16 @@ Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing install
+with hints provided by ``-DHeffte_ROOT``, as recommended by the CMake
+standard and note that the name is case sensitive. If CMake cannot find
+a heFFTe installation with the correct backend (e.g., FFTW or MKL),
+it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific variables
+listed in the
+`heFFTe documentation `_
+and those variables will be passed into the heFFTe build.
+
----------
.. _size:
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 3f32fb8ed1..ab4d8d64a2 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -100,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`nbond/atom `
* :doc:`omega/chunk `
* :doc:`orientorder/atom (k) `
+ * :doc:`pace `
* :doc:`pair `
* :doc:`pair/local `
* :doc:`pe `
@@ -115,6 +116,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`property/grid `
* :doc:`property/local `
* :doc:`ptm/atom `
+ * :doc:`rattlers/atom `
* :doc:`rdf `
* :doc:`reduce `
* :doc:`reduce/chunk `
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 7301d1345e..e89e302673 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -122,6 +122,7 @@ OPT.
* :doc:`mvv/tdpd `
* :doc:`neb `
* :doc:`neb/spin `
+ * :doc:`nonaffine/displacement `
* :doc:`nph (ko) `
* :doc:`nph/asphere (o) `
* :doc:`nph/body `
@@ -238,10 +239,10 @@ OPT.
* :doc:`store/force `
* :doc:`store/state `
* :doc:`tdpd/source `
- * :doc:`temp/berendsen `
+ * :doc:`temp/berendsen (k) `
* :doc:`temp/csld `
* :doc:`temp/csvr `
- * :doc:`temp/rescale `
+ * :doc:`temp/rescale (k) `
* :doc:`temp/rescale/eff `
* :doc:`tfmc `
* :doc:`tgnpt/drude `
diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst
index 8a00c63734..98a52fc2d7 100644
--- a/doc/src/Commands_removed.rst
+++ b/doc/src/Commands_removed.rst
@@ -126,6 +126,17 @@ syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
+USER-REAXC package
+------------------
+
+.. deprecated:: TBD
+
+The USER-REAXC package has been renamed to :ref:`REAXFF `.
+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
-----------------
diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst
index b1f5da8abc..85c98bd6de 100644
--- a/doc/src/Howto.rst
+++ b/doc/src/Howto.rst
@@ -101,6 +101,7 @@ Tutorials howto
Howto_cmake
Howto_github
Howto_lammps_gui
+ Howto_moltemplate
Howto_pylammps
Howto_wsl
diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst
index 115b7797c8..968e10edd8 100644
--- a/doc/src/Howto_body.rst
+++ b/doc/src/Howto_body.rst
@@ -335,7 +335,7 @@ faces are listed, so that M = 6 + 3\*N + 1.
The integer line has three values: number of vertices (N), number of
edges (E) and number of faces (F). The floating point line(s) list 6
moments of inertia followed by the coordinates of the N vertices (x1
-to zN) as 3N values, followed by 2N vertex indices corresponding to
+to zN) as 3N values, followed by 2E vertex indices corresponding to
the end points of the E edges, then 4\*F vertex indices defining F
faces. The last value is the diameter value = the rounded diameter of
the sphere that surrounds each vertex. The diameter value can be
diff --git a/doc/src/Howto_moltemplate.rst b/doc/src/Howto_moltemplate.rst
new file mode 100644
index 0000000000..bb068a2e93
--- /dev/null
+++ b/doc/src/Howto_moltemplate.rst
@@ -0,0 +1,371 @@
+Moltemplate Tutorial
+====================
+
+In this tutorial, we are going to use the tool :ref:`Moltemplate
+` to set up a classical molecular dynamic simulation using
+the :ref:`OPLS-AA force field `. 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).
diff --git a/doc/src/JPG/PolyNIPAM.jpg b/doc/src/JPG/PolyNIPAM.jpg
new file mode 100644
index 0000000000..4ad3ce8274
Binary files /dev/null and b/doc/src/JPG/PolyNIPAM.jpg differ
diff --git a/doc/src/JPG/sample01.png b/doc/src/JPG/sample01.png
new file mode 100644
index 0000000000..3a00176edd
Binary files /dev/null and b/doc/src/JPG/sample01.png differ
diff --git a/doc/src/JPG/solv_01.png b/doc/src/JPG/solv_01.png
new file mode 100644
index 0000000000..fc52d44928
Binary files /dev/null and b/doc/src/JPG/solv_01.png differ
diff --git a/doc/src/compute.rst b/doc/src/compute.rst
index b258f986b7..afe57d9048 100644
--- a/doc/src/compute.rst
+++ b/doc/src/compute.rst
@@ -264,6 +264,7 @@ The individual style names on the :doc:`Commands compute ` pag
* :doc:`nbond/atom ` - calculates number of bonds per atom
* :doc:`omega/chunk ` - angular velocity for each chunk
* :doc:`orientorder/atom ` - Steinhardt bond orientational order parameters Ql
+* :doc:`pace ` - atomic cluster expansion descriptors and related quantities
* :doc:`pair ` - values computed by a pair style
* :doc:`pair/local ` - distance/energy/force of each pairwise interaction
* :doc:`pe ` - potential energy
@@ -279,6 +280,7 @@ The individual style names on the :doc:`Commands compute ` pag
* :doc:`property/grid ` - convert per-grid attributes to per-grid vectors/arrays
* :doc:`property/local ` - convert local attributes to local vectors/arrays
* :doc:`ptm/atom ` - determines the local lattice structure based on the Polyhedral Template Matching method
+* :doc:`rattlers/atom ` - identify under-coordinated rattler atoms
* :doc:`rdf ` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reduce ` - combine per-atom quantities into a single global value
* :doc:`reduce/chunk ` - reduce per-atom quantities within each chunk
diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst
index 31aa24aa60..b7ed062ff6 100644
--- a/doc/src/compute_contact_atom.rst
+++ b/doc/src/compute_contact_atom.rst
@@ -36,6 +36,9 @@ sum of the radii of the two particles.
The value of the contact number will be 0.0 for atoms not in the
specified compute group.
+The optional *group2-ID* argument allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'.
+
Output info
"""""""""""
@@ -47,9 +50,6 @@ overview of LAMMPS output options.
The per-atom vector values will be a number :math:`\ge 0.0`, as explained
above.
-The optional *group2-ID* argument allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all.'
-
Restrictions
""""""""""""
@@ -69,6 +69,3 @@ Default
"""""""
*group2-ID* = all
-
-
-none
diff --git a/doc/src/compute_pace.rst b/doc/src/compute_pace.rst
new file mode 100644
index 0000000000..0c4a295f1b
--- /dev/null
+++ b/doc/src/compute_pace.rst
@@ -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 ` command
+* pace = style name of this compute command
+* ace_potential_filename = file name (in the .yace or .ace format from :doc:`pace pair_style `) 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) `. These descriptors are used in the
+:doc:`pace pair_style `. Quantities obtained from `compute pace`
+are related to those used in :doc:`pace pair_style ` 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) `.
+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 `, 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) `. 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 `.yace` potential
+file for `pace pair_style`. When these bracketed terms are multiplied by the
+products of the atomic base from :ref:`(Drautz) `,
+: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 `_. Examples on using outputs from
+this compute to construct general ACE potential forms are demonstrated in
+:ref:`(Goff) `. The various keywords and inputs to `compute pace`
+determine what ACE descriptors and related quantities are returned in a compute
+array.
+
+The coefficient file, `.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) `. These may
+be modeled after the potential files in :doc:`pace pair_style `,
+and have the same format. Details on how to generate the coefficient files
+to train ACE models may be found in `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 `,
+ 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
+ ` command can remove pairwise interactions between
+ atoms in the same bond, angle, or dihedral. This is the default
+ setting for the :doc:`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 ` command to
+ compute the ACE descriptors for snapshots in the dump file.
+ The rerun script can use a :doc:`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 `. 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 ` 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
+` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style pace `
+:doc:`pair_style snap `
+:doc:`compute snap `
+
+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).
diff --git a/doc/src/compute_rattlers_atom.rst b/doc/src/compute_rattlers_atom.rst
new file mode 100644
index 0000000000..a69d091466
--- /dev/null
+++ b/doc/src/compute_rattlers_atom.rst
@@ -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 ` 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 ` 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 ` page for more info.
+
+The *radius* cutoff option requires that atoms store a radius as defined by the
+:doc:`atom_style sphere ` or similar commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom `
+:doc:`compute contact/atom `
+
+Default
+"""""""
+
+none
diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst
index 8673ce9199..18bb4c886f 100644
--- a/doc/src/compute_xrd.rst
+++ b/doc/src/compute_xrd.rst
@@ -62,28 +62,29 @@ equations:
\frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
-:math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering
-factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
-scattering angle of diffraction. The Lorentz-polarization factor can be turned
-off using the optional *LP* keyword.
+:math:`r_j` is the position of each atom, :math:`f_j` are atomic
+scattering factors, *Lp* is the Lorentz-polarization factor, and
+:math:`\theta` is the scattering angle of diffraction. The
+Lorentz-polarization factor can be turned off using the optional *LP*
+keyword.
Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
-simulation domain or (b) manually using selected values as
-shown in the 2D diagram below.
+reciprocal lattice nodes. The mesh spacing is defined either (a) by the
+entire simulation domain or (b) manually using selected values as shown
+in the 2D diagram below.
-.. image:: img/xrd_mesh.jpg
+.. image:: img/xrd_mesh.png
:scale: 75%
:align: center
For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
-axis, where :math:`A` is a matrix containing the vectors corresponding to the
-edges of the simulation cell. If one or two directions has non-periodic
-boundary conditions, then the spacing in these directions is defined from the
-average of the (inversed) box lengths with periodic boundary conditions.
-Meshes defined by the simulation domain must contain at least one periodic
-boundary.
+axis, where :math:`A` is a matrix containing the vectors corresponding
+to the edges of the simulation cell. If one or two directions has
+non-periodic boundary conditions, then the spacing in these directions
+is defined from the average of the (inversed) box lengths with periodic
+boundary conditions. Meshes defined by the simulation domain must
+contain at least one periodic boundary.
If the *manual* flag is included, the mesh of reciprocal lattice nodes
will be defined using the *c* values for the spacing along each
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index 0889fe281f..69a7212487 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -287,6 +287,7 @@ accelerated styles exist.
* :doc:`mvv/tdpd ` - constant temperature DPD using the modified velocity-Verlet algorithm
* :doc:`neb ` - nudged elastic band (NEB) spring forces
* :doc:`neb/spin ` - nudged elastic band (NEB) spring forces for spins
+* :doc:`nonaffine/displacement ` - calculate nonaffine displacement of atoms
* :doc:`nph ` - constant NPH time integration via Nose/Hoover
* :doc:`nph/asphere ` - NPH for aspherical particles
* :doc:`nph/body ` - NPH for body particles
diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst
index 86eec3eadb..9cfbef7a11 100644
--- a/doc/src/fix_adapt.rst
+++ b/doc/src/fix_adapt.rst
@@ -205,6 +205,8 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`pace, pace/extrapolation ` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`quip ` | scale | type global |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`snap ` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`spin/dmi ` | coulombic_cutoff | type global |
@@ -315,21 +317,21 @@ Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`class2 ` | r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`fene ` | k,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`fene/nm ` | k,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`gromos ` | k,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`harmonic ` | k,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`morse ` | r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
| :doc:`nonlinear ` | epsilon,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
----------
@@ -353,11 +355,11 @@ Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
-+------------------------------------+-------+-----------------+
-| :doc:`harmonic ` | k,theta0 | type angles |
-+------------------------------------+-------+-----------------+
-| :doc:`cosine ` | k | type angles |
-+------------------------------------+-------+-----------------+
++------------------------------------+----------+-------------+
+| :doc:`harmonic ` | k,theta0 | type angles |
++------------------------------------+----------+-------------+
+| :doc:`cosine ` | k | type angles |
++------------------------------------+----------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.
@@ -482,7 +484,7 @@ Restrictions
Related commands
""""""""""""""""
-:doc:`compute ti `
+:doc:`compute ti `, :doc:`fix adapt/fep `
Default
"""""""
diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst
index a515375746..60d47994f0 100644
--- a/doc/src/fix_nh_uef.rst
+++ b/doc/src/fix_nh_uef.rst
@@ -23,7 +23,7 @@ Syntax
.. parsed-literal::
keyword = *erate* or *ext* or *strain* or *temp* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk*
- *erate* values = e_x e_y = engineering strain rates (required)
+ *erate* values = e_x e_y = true strain rates (required)
*ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions
sets the external dimensions used to calculate the scalar pressure
*strain* values = e_x e_y = initial strain
@@ -62,7 +62,7 @@ performed using the :doc:`fix deform `, :doc:`fix nvt/sllod
`, and :doc:`compute temp/deform `
commands.
-The applied flow field is set by the *eps* keyword. The values
+The applied flow field is set by the *erate* keyword. The values
*edot_x* and *edot_y* correspond to the strain rates in the xx and yy
directions. It is implicitly assumed that the flow field is
traceless, and therefore the strain rate in the zz direction is eqal
diff --git a/doc/src/fix_nonaffine_displacement.rst b/doc/src/fix_nonaffine_displacement.rst
new file mode 100644
index 0000000000..363b0a747a
--- /dev/null
+++ b/doc/src/fix_nonaffine_displacement.rst
@@ -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 ` 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) `.
+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 ` with remap x,
+:doc:`fix press/berendsen `, or :doc:`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 `.
+
+None of the :doc:`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 ` page for more info.
+
+Related commands
+""""""""""""""""
+
+none
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _d2min-Falk:
+
+**(Falk)** Falk and Langer PRE, 57, 7192 (1998).
diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst
index a50e215681..3174a0929c 100644
--- a/doc/src/fix_rigid.rst
+++ b/doc/src/fix_rigid.rst
@@ -80,7 +80,7 @@ Syntax
groupID1, groupID2, ... = list of N group IDs
* zero or more keyword/value pairs may be appended
-* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
+* keyword = *langevin* or *reinit* or *temp* or *mol* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
.. parsed-literal::
@@ -92,6 +92,8 @@ Syntax
*temp* values = Tstart Tstop Tdamp
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
+ *mol* value = template-ID
+ template-ID = ID of molecule template specified in a separate :doc:`molecule ` command
*iso* or *aniso* values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
diff --git a/doc/src/fix_temp_berendsen.rst b/doc/src/fix_temp_berendsen.rst
index 67e496e6c5..541f3191d5 100644
--- a/doc/src/fix_temp_berendsen.rst
+++ b/doc/src/fix_temp_berendsen.rst
@@ -1,8 +1,11 @@
.. index:: fix temp/berendsen
+.. index:: fix temp/berendsen/kk
fix temp/berendsen command
==========================
+Accelerator Variants: *temp/berendsen/kk*
+
Syntax
""""""
@@ -118,6 +121,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
+.. include:: accel_styles.rst
+
+----------
+
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst
index bfdcaa90f8..2dd2178346 100644
--- a/doc/src/fix_temp_rescale.rst
+++ b/doc/src/fix_temp_rescale.rst
@@ -1,8 +1,11 @@
.. index:: fix temp/rescale
+.. index:: fix temp/rescale/kk
fix temp/rescale command
========================
+Accelerator Variants: *temp/rescale/kk*
+
Syntax
""""""
@@ -125,6 +128,10 @@ remaining thermal degrees of freedom, and the bias is added back in.
----------
+.. include:: accel_styles.rst
+
+----------
+
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
diff --git a/doc/src/img/xrd_mesh.jpg b/doc/src/img/xrd_mesh.jpg
deleted file mode 100644
index 677234caab..0000000000
Binary files a/doc/src/img/xrd_mesh.jpg and /dev/null differ
diff --git a/doc/src/img/xrd_mesh.png b/doc/src/img/xrd_mesh.png
new file mode 100644
index 0000000000..e58c7322a5
Binary files /dev/null and b/doc/src/img/xrd_mesh.png differ
diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst
index 480e175e7b..1de905886c 100644
--- a/doc/src/molecule.rst
+++ b/doc/src/molecule.rst
@@ -154,21 +154,25 @@ These are the recognized header keywords. Header lines can come in
any order. The numeric value(s) are read from the beginning of the
line. The keyword should appear at the end of the line. All these
settings have default values, as explained below. A line need only
-appear if the value(s) are different than the default.
+appear if the value(s) are different than the default, except when
+defining a *body* particle, which requires setting the number of
+*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
-* Nf *fragments* = # of fragments in molecule, default = 0
+* Nf *fragments* = # of fragments Nf in molecule, default = 0
+* Ninteger Ndouble *body* = # of integer and floating-point values in body
+particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
-consists of a set of point particles or finite-size particles (with a
+consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
@@ -188,6 +192,7 @@ These are the allowed section keywords for the body of the file.
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
+* *Body Integers, Body Doubles* = body-property sections
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
atom/bond/angle/etc type can be specified either as a number (numeric
@@ -515,6 +520,67 @@ of SHAKE clusters.
----------
+*Body Integers* section:
+
+* one line
+* line syntax: N E F
+* N = number of sub-particles or number or vertices
+* E,F = number of edges and faces
+
+This section is only needed when the molecule is a body particle. the other
+Body section must also appear in the file.
+
+The total number of values that must appear is determined by the body style, and
+must be equal to the Ninteger value given in the *body* header.
+
+For *nparticle* and *rounded/polygon*, only the number of sub-particles or
+vertices N is required, and Ninteger should have a value of 1.
+
+For *rounded/polyhedron*, the number of edges E and faces F is required, and
+Ninteger should have a value of 3.
+
+See the :doc:`Howto body ` 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 ` page for a further description of
+the file format.
+
+----------
+
Restrictions
""""""""""""
diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst
index 2bf027515c..6bb4afdc80 100644
--- a/doc/src/pair_beck.rst
+++ b/doc/src/pair_beck.rst
@@ -30,11 +30,11 @@ Description
Style *beck* computes interactions based on the potential by
:ref:`(Beck) `, originally designed for simulation of Helium. It
-includes truncation at a cutoff distance Rc.
+includes truncation at a cutoff distance :math:`r_c`.
.. math::
- E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\
+ E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < r_c \\
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff ` command as in the examples
@@ -50,7 +50,7 @@ commands.
* cutoff (distance units)
The last coefficient is optional. If not specified, the global cutoff
-:math:`R_c` is used.
+:math:`r_c` is used.
----------
diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst
index 7198b60159..d95f356ab7 100644
--- a/doc/src/pair_lj_cut_tip4p.rst
+++ b/doc/src/pair_lj_cut_tip4p.rst
@@ -58,6 +58,40 @@ Examples
Description
"""""""""""
+The *lj/cut/tip4p* styles implement the TIP4P water model of
+:ref:`(Jorgensen) ` 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 ` page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2\*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules. Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
+shrink the size of the neighbor list. This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
+
The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
given by
@@ -91,34 +125,6 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
-The *lj/cut/tip4p* styles implement the TIP4P
-water model of :ref:`(Jorgensen) `, 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 ` 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
""""""""""""
diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst
index 7a3ba7a3d5..20b5e6cbda 100644
--- a/doc/src/pair_lj_smooth_linear.rst
+++ b/doc/src/pair_lj_smooth_linear.rst
@@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
interaction (aka Shifted Force Lennard-Jones) that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term based
on the cutoff distance, so that both, the potential and the force, go
-continuously to zero at the cutoff Rc :ref:`(Toxvaerd) `:
+continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) `:
.. math::
\phi\left(r\right) & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
- E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
+ E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff ` command as in the examples
@@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
-This pair style writes its information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need
-to be specified in an input script that reads a restart file.
+This pair style writes its information to :doc:`binary restart files `,
+so pair_style and pair_coeff commands do not need to be specified
+in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa ` command. It does not support the
diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst
index 089f8d3d29..6e9eec1f5c 100644
--- a/doc/src/pair_mie.rst
+++ b/doc/src/pair_mie.rst
@@ -35,7 +35,7 @@ The *mie/cut* style computes the Mie potential, given by
E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
\qquad r < r_c
-Rc is the cutoff and C is a function that depends on the repulsive and
+:math:`r_c` is the cutoff and C is a function that depends on the repulsive and
attractive exponents, given by:
.. math::
diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst
index 807882980d..4b93d182bb 100644
--- a/doc/src/pair_morse.rst
+++ b/doc/src/pair_morse.rst
@@ -53,7 +53,7 @@ Style *morse* computes pairwise interactions with the formula
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
\qquad r < r_c
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff ` command as in the examples
@@ -78,7 +78,7 @@ so that both, potential energy and force, go to zero at the cut-off:
.. math::
\phi\left(r\right) & = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\
- E\left(r\right) & = \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
+ E\left(r\right) & = \phi\left(r\right) - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c} \qquad r < r_c
The syntax of the pair_style and pair_coeff commands are the same for
the *morse* and *morse/smooth/linear* styles.
diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst
index d815f663fe..001214370c 100644
--- a/doc/src/pair_pace.rst
+++ b/doc/src/pair_pace.rst
@@ -40,6 +40,9 @@ Examples
pair_style pace product chunksize 2048
pair_coeff * * Cu-PBE-core-rep.ace Cu
+ pair_style pace
+ pair_coeff * * Cu.yaml Cu
+
pair_style pace/extrapolation
pair_coeff * * Cu.yaml Cu.asi Cu
@@ -64,7 +67,7 @@ specifies an ACE coefficient file followed by N additional arguments
specifying the mapping of ACE elements to LAMMPS atom types, where N is
the number of LAMMPS atom types:
-* ACE coefficient file
+* ACE coefficient file (.yaml or .yace/.ace format)
* N element names = mapping of ACE elements to atom types
Only a single pair_coeff command is used with the *pace* style which
@@ -136,6 +139,22 @@ product B-basis evaluator is always used and only *linear* ASI is supported.
See the :doc:`pair_coeff ` page for alternate ways
to specify the path for the ACE coefficient file.
+Core repulsion
+"""""""""""""""""""
+The ACE potential can be configured to initiate core-repulsion from an inner cutoff,
+seamlessly transitioning from ACE to ZBL. The core repulsion factor can be accessed
+as a per-atom quantity, as demonstrated in the example below:
+
+.. code-block:: LAMMPS
+
+ pair_style pace
+ pair_coeff * * CuNi.yaml Cu Ni
+
+ fix pace_corerep all pair 1 pace corerep 1
+
+In this case, per-atom `f_pace_corerep` quantities represent the fraction of ZBL
+core-repulsion for each atom.
+
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst
index 1702811ed9..e21ae28432 100644
--- a/doc/src/pair_soft.rst
+++ b/doc/src/pair_soft.rst
@@ -44,8 +44,9 @@ It is useful for pushing apart overlapping atoms, since it does not
blow up as r goes to 0. A is a prefactor that can be made to vary in
time from the start to the end of the run (see discussion below),
e.g. to start with a very soft potential and slowly harden the
-interactions over time. Rc is the cutoff. See the :doc:`fix nve/limit ` command for another way to push apart
-overlapping atoms.
+interactions over time. :math:`r_c` is the cutoff.
+See the :doc:`fix nve/limit ` command for another way
+to push apart overlapping atoms.
The following coefficients must be defined for each pair of atom types
via the :doc:`pair_coeff ` command as in the examples above,
diff --git a/doc/src/pair_spica.rst b/doc/src/pair_spica.rst
index 74a069d8a2..859506593f 100644
--- a/doc/src/pair_spica.rst
+++ b/doc/src/pair_spica.rst
@@ -81,7 +81,7 @@ given by
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `.
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/spica/coul/long* computes the adds Coulombic interactions
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 9a99bb7718..272e747358 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1077,6 +1077,7 @@ facesets
factorizable
factorizations
Fahrenberger
+Falk
Faken
Farago
Fasolino
@@ -1176,6 +1177,7 @@ Foiles
fopenmp
forceclear
forestgreen
+formamide
formatarg
formulae
Forschungszentrum
@@ -1826,6 +1828,7 @@ Lanczos
Lande
Landron
Landsgesell
+Langer
langevin
Langevin
Langston
@@ -1976,6 +1979,7 @@ lpsapi
lr
lrt
lsfftw
+lt
ltbbmalloc
Lua
lubricateU
@@ -2510,6 +2514,7 @@ noforce
noguess
Noid
nolib
+nonaffine
nonequilibrium
nongauss
nonGaussian
@@ -2582,6 +2587,7 @@ nthreads
ntimestep
Ntptask
Ntriples
+ntries
ntris
Ntype
ntypes
@@ -3387,6 +3393,7 @@ Sodani
Soderlind
Solaris
Solida
+solv
solvated
solvation
someuser
@@ -3633,6 +3640,7 @@ timestepping
timesteps
TiN
TiO
+Tirado
Tirrell
Titer
Tji
diff --git a/examples/PACKAGES/pace/README.md b/examples/PACKAGES/pace/README.md
new file mode 100644
index 0000000000..66254b5241
--- /dev/null
+++ b/examples/PACKAGES/pace/README.md
@@ -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`
+
diff --git a/examples/PACKAGES/pace/compute/coupling_coefficients.yace b/examples/PACKAGES/pace/compute/coupling_coefficients.yace
new file mode 100644
index 0000000000..2953222216
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/coupling_coefficients.yace
@@ -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]}
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+ - {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]}
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+ - {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]}
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+ - {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]}
diff --git a/examples/PACKAGES/pace/compute/in.compute b/examples/PACKAGES/pace/compute/in.compute
new file mode 100644
index 0000000000..a0ef25f606
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/in.compute
@@ -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
diff --git a/examples/PACKAGES/pace/compute/latte_cell_0.data b/examples/PACKAGES/pace/compute/latte_cell_0.data
new file mode 100644
index 0000000000..b18ec13a4d
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/latte_cell_0.data
@@ -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
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diff --git a/examples/PACKAGES/pace/compute/latte_cell_0.xyz b/examples/PACKAGES/pace/compute/latte_cell_0.xyz
new file mode 100644
index 0000000000..afe0a27f35
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/latte_cell_0.xyz
@@ -0,0 +1,163 @@
+161
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diff --git a/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1 b/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1
new file mode 100644
index 0000000000..e5036cfe5b
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.1
@@ -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
diff --git a/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.4 b/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.4
new file mode 100644
index 0000000000..49ca6129b6
--- /dev/null
+++ b/examples/PACKAGES/pace/compute/log.5Dec23.compute.g++.4
@@ -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
diff --git a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana
index 6312466e58..ca49cd50c6 100644
--- a/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana
+++ b/examples/PACKAGES/phonon/2-1D-diatomic/in.Ana
@@ -2,15 +2,15 @@
dimension 2
boundary p f p
-units lj
-atom_style bond
+units lj
+atom_style bond
atom_modify sort 0 1.
bond_style harmonic
pair_style none
-communicate single cutoff 2.0
+comm_modify cutoff 2.0
# geometry
-read_data data.pos
+read_data data.pos
#
neighbor 1.0 nsq
@@ -43,4 +43,4 @@ thermo_modify temp MyTemp
thermo 100
#
-run 2000000
+run 2000000
diff --git a/examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst b/examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
new file mode 100644
index 0000000000..99d60e52d7
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qbmsst/in.methane_qbmsst
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.1 b/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.1
new file mode 100644
index 0000000000..d46e62cfd5
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.1
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.4 b/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.4
new file mode 100644
index 0000000000..357f31a300
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qbmsst/log.30Nov23.methane_qbmsst.g++.4
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in b/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in
deleted file mode 100644
index 507164a732..0000000000
--- a/examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in
+++ /dev/null
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod b/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
index 65bfc5d7f7..ac1735ca7b 100644
--- a/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
+++ b/examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod
@@ -3,62 +3,62 @@
## This part defines units, methane structure, and atomic information
#General
-units real
-dimension 3
-boundary p p p
-atom_style charge
+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 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}
+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
+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
+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
+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 ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output
-thermo_style custom step temp press etotal vol
-thermo 100
+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
-timestep ${delta_t}
-run 2000 #500 fs
-unfix methane_qtb
-unfix scapegoat_qtb
+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 500 #500 fs
+unfix methane_qtb
+unfix scapegoat_qtb
diff --git a/examples/PACKAGES/qtb/methane_qtb/in.methane_qtb b/examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
new file mode 100644
index 0000000000..bfaa8706c4
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qtb/in.methane_qtb
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1 b/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
new file mode 100644
index 0000000000..b6efdb6360
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.1
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4 b/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
new file mode 100644
index 0000000000..c68935df87
--- /dev/null
+++ b/examples/PACKAGES/qtb/methane_qtb/log.30Nov23.methane_qtb.g++.4
@@ -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
diff --git a/examples/PACKAGES/qtb/methane_qtb/methane_qtb.in b/examples/PACKAGES/qtb/methane_qtb/methane_qtb.in
deleted file mode 100644
index e31f0695b9..0000000000
--- a/examples/PACKAGES/qtb/methane_qtb/methane_qtb.in
+++ /dev/null
@@ -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
diff --git a/examples/amoeba/amoeba_ubiquitin.key b/examples/amoeba/amoeba_ubiquitin.key
index 2870d071d4..3d63525258 100644
--- a/examples/amoeba/amoeba_ubiquitin.key
+++ b/examples/amoeba/amoeba_ubiquitin.key
@@ -12,7 +12,8 @@ ewald
ewald-alpha 0.4
pewald-alpha 0.5
ewald-cutoff 7.0
-#pme-grid 60 45 45
pme-grid 60 48 48
-pme-order 5
polar-eps 0.00001
+#pme-grid 15 12 12
+#polar-eps 0.0002
+pme-order 5
diff --git a/examples/qeq/in.qeq.reaxc b/examples/qeq/in.qeq.reaxff
similarity index 90%
rename from examples/qeq/in.qeq.reaxc
rename to examples/qeq/in.qeq.reaxff
index 5271c74671..a60cca269e 100644
--- a/examples/qeq/in.qeq.reaxc
+++ b/examples/qeq/in.qeq.reaxff
@@ -1,19 +1,19 @@
-# This example demonstrates the use of various fix qeq variants with pair reax/c
+# This example demonstrates the use of various fix qeq variants with pair reaxff
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
-# used with pair_style reax/c, provided that the QEq parameters are the same.
+# used with pair_style reaxff, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
-# pair_style reax/c.
+# pair_style reaxff.
units real
atom_style charge
read_data data.CHO
-pair_style reax/c NULL checkqeq no
+pair_style reaxff NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
neighbor 1 bin
diff --git a/examples/qeq/log.27Nov18.qeq.reaxc.g++.1 b/examples/qeq/log.27Nov18.qeq.reaxc.g++.1
deleted file mode 100644
index c88acc39f2..0000000000
--- a/examples/qeq/log.27Nov18.qeq.reaxc.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/qeq/log.27Nov18.qeq.reaxc.g++.4 b/examples/qeq/log.27Nov18.qeq.reaxc.g++.4
deleted file mode 100644
index c54a99577e..0000000000
--- a/examples/qeq/log.27Nov18.qeq.reaxc.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/qeq/log.30Nov23.reaxff.g++.1 b/examples/qeq/log.30Nov23.reaxff.g++.1
new file mode 100644
index 0000000000..c79d9fa662
--- /dev/null
+++ b/examples/qeq/log.30Nov23.reaxff.g++.1
@@ -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
diff --git a/examples/qeq/log.30Nov23.reaxff.g++.4 b/examples/qeq/log.30Nov23.reaxff.g++.4
new file mode 100644
index 0000000000..6f58a13a7f
--- /dev/null
+++ b/examples/qeq/log.30Nov23.reaxff.g++.4
@@ -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
diff --git a/examples/reaxff/AB/in.AB b/examples/reaxff/AB/in.AB
index 5f19b30b6c..30d96f2622 100644
--- a/examples/reaxff/AB/in.AB
+++ b/examples/reaxff/AB/in.AB
@@ -1,23 +1,23 @@
# REAX potential for Nitroamines system
# .....
-units real
+units real
-atom_style charge
-read_data data.AB
+atom_style charge
+read_data data.AB
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.AB H B N
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.AB H B N
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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 3000
+run 2000
diff --git a/examples/reaxff/AB/lmp_control b/examples/reaxff/AB/lmp_control
index c5d98968a5..b97ad8a67f 100644
--- a/examples/reaxff/AB/lmp_control
+++ b/examples/reaxff/AB/lmp_control
@@ -1,17 +1,8 @@
-simulation_name AB_example ! output files will carry this name + their specific ext
-tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
+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
-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 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
diff --git a/examples/reaxff/AB/log.30Nov23.AB.g++.1 b/examples/reaxff/AB/log.30Nov23.AB.g++.1
new file mode 100644
index 0000000000..e966977f54
--- /dev/null
+++ b/examples/reaxff/AB/log.30Nov23.AB.g++.1
@@ -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
diff --git a/examples/reaxff/AB/log.30Nov23.AB.g++.4 b/examples/reaxff/AB/log.30Nov23.AB.g++.4
new file mode 100644
index 0000000000..5b3ae33fbe
--- /dev/null
+++ b/examples/reaxff/AB/log.30Nov23.AB.g++.4
@@ -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
diff --git a/examples/reaxff/AB/log.8Mar18.AB.g++.1 b/examples/reaxff/AB/log.8Mar18.AB.g++.1
deleted file mode 100644
index 065b1a1e67..0000000000
--- a/examples/reaxff/AB/log.8Mar18.AB.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/AB/log.8Mar18.AB.g++.4 b/examples/reaxff/AB/log.8Mar18.AB.g++.4
deleted file mode 100644
index 1e02ec5725..0000000000
--- a/examples/reaxff/AB/log.8Mar18.AB.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/AuO/in.AuO b/examples/reaxff/AuO/in.AuO
index 90ae812f7d..4e5162d620 100644
--- a/examples/reaxff/AuO/in.AuO
+++ b/examples/reaxff/AuO/in.AuO
@@ -1,23 +1,25 @@
# REAX potential for AuO system
# .....
-units real
+units real
-atom_style charge
-read_data data.AuO
+atom_style charge
+read_data data.AuO
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.AuO O Au
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.AuO O Au
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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
diff --git a/examples/reaxff/AuO/lmp_control b/examples/reaxff/AuO/lmp_control
index d24ae0a055..ecf22940b7 100644
--- a/examples/reaxff/AuO/lmp_control
+++ b/examples/reaxff/AuO/lmp_control
@@ -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
-energy_update_freq 1
+nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
+hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
+bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
+thb_cutoff 0.001 ! cutoff value for three body interactions
-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
diff --git a/examples/reaxff/AuO/log.30Nov23.AuO.g++.1 b/examples/reaxff/AuO/log.30Nov23.AuO.g++.1
new file mode 100644
index 0000000000..8896ef1015
--- /dev/null
+++ b/examples/reaxff/AuO/log.30Nov23.AuO.g++.1
@@ -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
diff --git a/examples/reaxff/AuO/log.30Nov23.AuO.g++.4 b/examples/reaxff/AuO/log.30Nov23.AuO.g++.4
new file mode 100644
index 0000000000..ba3b81ea1b
--- /dev/null
+++ b/examples/reaxff/AuO/log.30Nov23.AuO.g++.4
@@ -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
diff --git a/examples/reaxff/AuO/log.8Mar18.AuO.g++.1 b/examples/reaxff/AuO/log.8Mar18.AuO.g++.1
deleted file mode 100644
index 3c609ac023..0000000000
--- a/examples/reaxff/AuO/log.8Mar18.AuO.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/AuO/log.8Mar18.AuO.g++.4 b/examples/reaxff/AuO/log.8Mar18.AuO.g++.4
deleted file mode 100644
index ed98e1f2f4..0000000000
--- a/examples/reaxff/AuO/log.8Mar18.AuO.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/CHO/in.CHO b/examples/reaxff/CHO/in.CHO
index 668be5eee0..3baa885ae5 100644
--- a/examples/reaxff/CHO/in.CHO
+++ b/examples/reaxff/CHO/in.CHO
@@ -1,23 +1,24 @@
# REAX potential for CHO system
# .....
-units real
+units real
-atom_style charge
-read_data data.CHO
+atom_style charge
+read_data data.CHO
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.cho H C O
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.cho H C O
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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
diff --git a/examples/reaxff/CHO/lmp_control b/examples/reaxff/CHO/lmp_control
index 6db169bf70..b97ad8a67f 100644
--- a/examples/reaxff/CHO/lmp_control
+++ b/examples/reaxff/CHO/lmp_control
@@ -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
-energy_update_freq 1
+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
-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 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
diff --git a/examples/reaxff/CHO/log.30Nov23.CHO.g++.1 b/examples/reaxff/CHO/log.30Nov23.CHO.g++.1
new file mode 100644
index 0000000000..de8da4edad
--- /dev/null
+++ b/examples/reaxff/CHO/log.30Nov23.CHO.g++.1
@@ -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
diff --git a/examples/reaxff/CHO/log.30Nov23.CHO.g++.4 b/examples/reaxff/CHO/log.30Nov23.CHO.g++.4
new file mode 100644
index 0000000000..158b1aa657
--- /dev/null
+++ b/examples/reaxff/CHO/log.30Nov23.CHO.g++.4
@@ -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
diff --git a/examples/reaxff/CHO/log.8Mar18.CHO.g++.1 b/examples/reaxff/CHO/log.8Mar18.CHO.g++.1
deleted file mode 100644
index 305ccbf3a0..0000000000
--- a/examples/reaxff/CHO/log.8Mar18.CHO.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/CHO/log.8Mar18.CHO.g++.4 b/examples/reaxff/CHO/log.8Mar18.CHO.g++.4
deleted file mode 100644
index 2bc19dc789..0000000000
--- a/examples/reaxff/CHO/log.8Mar18.CHO.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/FC/in.FC b/examples/reaxff/FC/in.FC
index 3679a9bc19..eaa2b3c444 100644
--- a/examples/reaxff/FC/in.FC
+++ b/examples/reaxff/FC/in.FC
@@ -3,33 +3,33 @@
dimension 3
boundary p p p
-units real
+units real
-atom_style charge
-read_data data.FC
+atom_style charge
+read_data data.FC
-pair_style reax/c NULL
-pair_coeff * * ffield.reax.FC C F
-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
+pair_style reaxff NULL
+pair_coeff * * ffield.reax.FC C F
+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
+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
+run 10
unfix 1
fix 1 all nvt temp 100.0 100.0 100.0
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
-run 10
+run 10
diff --git a/examples/reaxff/FC/log.30Nov23.FC.g++.1 b/examples/reaxff/FC/log.30Nov23.FC.g++.1
new file mode 100644
index 0000000000..a8f8c0ff83
--- /dev/null
+++ b/examples/reaxff/FC/log.30Nov23.FC.g++.1
@@ -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
diff --git a/examples/reaxff/FC/log.30Nov23.FC.g++.4 b/examples/reaxff/FC/log.30Nov23.FC.g++.4
new file mode 100644
index 0000000000..1a53bb8c03
--- /dev/null
+++ b/examples/reaxff/FC/log.30Nov23.FC.g++.4
@@ -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
diff --git a/examples/reaxff/FC/log.8Mar18.FC.g++.1 b/examples/reaxff/FC/log.8Mar18.FC.g++.1
deleted file mode 100644
index 1e2f723966..0000000000
--- a/examples/reaxff/FC/log.8Mar18.FC.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/FC/log.8Mar18.FC.g++.4 b/examples/reaxff/FC/log.8Mar18.FC.g++.4
deleted file mode 100644
index 76dcadfb0f..0000000000
--- a/examples/reaxff/FC/log.8Mar18.FC.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/FeOH3/in.FeOH3 b/examples/reaxff/FeOH3/in.FeOH3
index 8b56f2a7d2..72afbe5416 100644
--- a/examples/reaxff/FeOH3/in.FeOH3
+++ b/examples/reaxff/FeOH3/in.FeOH3
@@ -1,23 +1,24 @@
# REAX potential for Fe/O/H system
# .....
-units real
+units real
-atom_style charge
-read_data data.FeOH3
+atom_style charge
+read_data data.FeOH3
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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
diff --git a/examples/reaxff/FeOH3/lmp_control b/examples/reaxff/FeOH3/lmp_control
index 779c7da7ec..6b26c6427a 100644
--- a/examples/reaxff/FeOH3/lmp_control
+++ b/examples/reaxff/FeOH3/lmp_control
@@ -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
-energy_update_freq 1
+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
-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 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
+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
diff --git a/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1 b/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
new file mode 100644
index 0000000000..0acb09bdc0
--- /dev/null
+++ b/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.1
@@ -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
diff --git a/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4 b/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
new file mode 100644
index 0000000000..3357947749
--- /dev/null
+++ b/examples/reaxff/FeOH3/log.30Nov23.FeOH3.g++.4
@@ -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
diff --git a/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1 b/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1
deleted file mode 100644
index fd9b310bb2..0000000000
--- a/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4 b/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4
deleted file mode 100644
index 399c5dbe3c..0000000000
--- a/examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/HNS/in.reaxc.hns b/examples/reaxff/HNS/in.reaxff.hns
similarity index 82%
rename from examples/reaxff/HNS/in.reaxc.hns
rename to examples/reaxff/HNS/in.reaxff.hns
index 5b83698917..0f40814bff 100644
--- a/examples/reaxff/HNS/in.reaxc.hns
+++ b/examples/reaxff/HNS/in.reaxff.hns
@@ -12,16 +12,15 @@ atom_style charge
atom_modify sort 100 0.0 # optional
dimension 3
boundary p p p
-box tilt large
read_data data.hns-equil
replicate $x $y $z bbox
-pair_style reax/c NULL
+pair_style reaxff NULL
pair_coeff * * ffield.reax.hns C H O N
-compute reax all pair reax/c
+compute reax all pair reaxff
neighbor 1.0 bin
neigh_modify every 20 delay 0 check no
@@ -35,6 +34,6 @@ 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
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
run $t
diff --git a/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1 b/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
new file mode 100644
index 0000000000..b2c9778994
--- /dev/null
+++ b/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.1
@@ -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
diff --git a/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4 b/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
new file mode 100644
index 0000000000..d7c3b76f7a
--- /dev/null
+++ b/examples/reaxff/HNS/log.30Nov23.reaxff.hns.g++.4
@@ -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
diff --git a/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1 b/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1
deleted file mode 100644
index d418d287b1..0000000000
--- a/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4 b/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4
deleted file mode 100644
index aef07f80eb..0000000000
--- a/examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/RDX/in.RDX b/examples/reaxff/RDX/in.RDX
index 67d6145787..a510390a03 100644
--- a/examples/reaxff/RDX/in.RDX
+++ b/examples/reaxff/RDX/in.RDX
@@ -1,23 +1,23 @@
# REAX potential for high energy CHON systems
# .....
-units real
+units real
-atom_style charge
-read_data data.RDX
+atom_style charge
+read_data data.RDX
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.rdx H C O N
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.rdx H C O N
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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
diff --git a/examples/reaxff/RDX/lmp_control b/examples/reaxff/RDX/lmp_control
index c729255b45..b97ad8a67f 100644
--- a/examples/reaxff/RDX/lmp_control
+++ b/examples/reaxff/RDX/lmp_control
@@ -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
-energy_update_freq 1
+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
-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 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
diff --git a/examples/reaxff/RDX/log.30Nov23.RDX.g++.1 b/examples/reaxff/RDX/log.30Nov23.RDX.g++.1
new file mode 100644
index 0000000000..7d2214a6c8
--- /dev/null
+++ b/examples/reaxff/RDX/log.30Nov23.RDX.g++.1
@@ -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
diff --git a/examples/reaxff/RDX/log.30Nov23.RDX.g++.4 b/examples/reaxff/RDX/log.30Nov23.RDX.g++.4
new file mode 100644
index 0000000000..37481acd1b
--- /dev/null
+++ b/examples/reaxff/RDX/log.30Nov23.RDX.g++.4
@@ -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
diff --git a/examples/reaxff/RDX/log.8Mar18.RDX.g++.1 b/examples/reaxff/RDX/log.8Mar18.RDX.g++.1
deleted file mode 100644
index d0765a97a5..0000000000
--- a/examples/reaxff/RDX/log.8Mar18.RDX.g++.1
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/RDX/log.8Mar18.RDX.g++.4 b/examples/reaxff/RDX/log.8Mar18.RDX.g++.4
deleted file mode 100644
index 7082d30636..0000000000
--- a/examples/reaxff/RDX/log.8Mar18.RDX.g++.4
+++ /dev/null
@@ -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
diff --git a/examples/reaxff/VOH/in.VOH b/examples/reaxff/VOH/in.VOH
index 82fa8d1811..3a1047f2c3 100644
--- a/examples/reaxff/VOH/in.VOH
+++ b/examples/reaxff/VOH/in.VOH
@@ -1,23 +1,23 @@
# REAX potential for VOH system
# .....
-units real
+units real
-atom_style charge
-read_data data.VOH
+atom_style charge
+read_data data.VOH
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.V_O_C_H H C O V
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.V_O_C_H H C O V
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 3 all temp/berendsen 500.0 500.0 100.0
-timestep 0.25
+timestep 0.25
-#dump 1 all atom 30 dump.reax.voh
-
-run 3000
+#dump 1 all atom 30 dump.reax.voh
+thermo 100
+run 2000
diff --git a/examples/reaxff/VOH/lmp_control b/examples/reaxff/VOH/lmp_control
index 735540053f..b97ad8a67f 100644
--- a/examples/reaxff/VOH/lmp_control
+++ b/examples/reaxff/VOH/lmp_control
@@ -1,17 +1,8 @@
-simulation_name VOH_example ! output files will carry this name + their specific ext
-tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
+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
-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 VOH ! (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
diff --git a/examples/reaxff/VOH/log.30Nov23.VOH.g++.1 b/examples/reaxff/VOH/log.30Nov23.VOH.g++.1
new file mode 100644
index 0000000000..d649653444
--- /dev/null
+++ b/examples/reaxff/VOH/log.30Nov23.VOH.g++.1
@@ -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 VOH system
+# .....
+
+units real
+
+atom_style charge
+read_data data.VOH
+Reading data file ...
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 100 atoms
+ read_data CPU = 0.001 seconds
+
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.V_O_C_H H C O V
+Reading potential file ffield.reax.V_O_C_H 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
+
+#dump 1 all atom 30 dump.reax.voh
+thermo 100
+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) = 15.34 | 15.34 | 15.34 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 0 -10246.825 0 -10246.825 42.256089
+ 100 83.813625 -10238.056 0 -10213.322 -246.37234
+ 200 128.47312 -10221.424 0 -10183.511 -896.05588
+ 300 199.45833 -10218.343 0 -10159.482 -66.676466
+ 400 243.93496 -10211.648 0 -10139.663 -1073.274
+ 500 314.81116 -10216.592 0 -10123.692 542.54772
+ 600 361.45977 -10217.717 0 -10111.05 205.47425
+ 700 392.16954 -10215.815 0 -10100.086 -283.06967
+ 800 392.49036 -10206.909 0 -10091.085 953.23712
+ 900 426.51015 -10209.352 0 -10083.489 473.9928
+ 1000 398.23517 -10195.103 0 -10077.584 243.59494
+ 1100 414.05403 -10192.081 0 -10069.893 1063.7609
+ 1200 442.70037 -10196.631 0 -10065.99 -1189.773
+ 1300 470.32545 -10201.252 0 -10062.459 -132.3016
+ 1400 446.97236 -10189.078 0 -10057.176 9.8938187
+ 1500 475.7665 -10195.598 0 -10055.199 -877.81691
+ 1600 440.45154 -10181.071 0 -10051.093 579.85471
+ 1700 517.45211 -10201.067 0 -10048.367 136.58133
+ 1800 461.86671 -10182.818 0 -10046.521 -260.09694
+ 1900 463.99242 -10181.136 0 -10044.211 1567.8398
+ 2000 476.73786 -10184.032 0 -10043.346 -883.50859
+Loop time of 1.94324 on 1 procs for 2000 steps with 100 atoms
+
+Performance: 22.231 ns/day, 1.080 hours/ns, 1029.207 timesteps/s, 102.921 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 | 1.5707 | 1.5707 | 1.5707 | 0.0 | 80.83
+Neigh | 0.1054 | 0.1054 | 0.1054 | 0.0 | 5.42
+Comm | 0.005606 | 0.005606 | 0.005606 | 0.0 | 0.29
+Output | 0.00053398 | 0.00053398 | 0.00053398 | 0.0 | 0.03
+Modify | 0.2594 | 0.2594 | 0.2594 | 0.0 | 13.35
+Other | | 0.001603 | | | 0.08
+
+Nlocal: 100 ave 100 max 100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 638 ave 638 max 638 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3434 ave 3434 max 3434 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3434
+Ave neighs/atom = 34.34
+Neighbor list builds = 200
+Dangerous builds not checked
+Total wall time: 0:00:01
diff --git a/examples/reaxff/VOH/log.30Nov23.VOH.g++.4 b/examples/reaxff/VOH/log.30Nov23.VOH.g++.4
new file mode 100644
index 0000000000..a7363ee766
--- /dev/null
+++ b/examples/reaxff/VOH/log.30Nov23.VOH.g++.4
@@ -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 VOH system
+# .....
+
+units real
+
+atom_style charge
+read_data data.VOH
+Reading data file ...
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 100 atoms
+ read_data CPU = 0.001 seconds
+
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.V_O_C_H H C O V
+Reading potential file ffield.reax.V_O_C_H 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
+
+#dump 1 all atom 30 dump.reax.voh
+thermo 100
+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) = 10.04 | 11.12 | 12.06 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 0 -10246.825 0 -10246.825 42.256092
+ 100 83.813732 -10238.056 0 -10213.322 -246.39794
+ 200 128.4729 -10221.424 0 -10183.511 -896.07308
+ 300 199.45765 -10218.342 0 -10159.482 -66.695871
+ 400 243.93632 -10211.649 0 -10139.663 -1073.2779
+ 500 314.81228 -10216.592 0 -10123.691 542.5312
+ 600 361.46099 -10217.717 0 -10111.05 205.56032
+ 700 392.16903 -10215.815 0 -10100.086 -283.00265
+ 800 392.48962 -10206.909 0 -10091.085 953.23878
+ 900 426.50866 -10209.352 0 -10083.489 474.04312
+ 1000 398.23724 -10195.104 0 -10077.584 243.52194
+ 1100 414.05514 -10192.081 0 -10069.893 1063.726
+ 1200 442.70432 -10196.633 0 -10065.99 -1189.8309
+ 1300 470.32067 -10201.251 0 -10062.459 -132.41831
+ 1400 447.00366 -10189.087 0 -10057.177 10.168781
+ 1500 475.77239 -10195.599 0 -10055.199 -877.85409
+ 1600 440.43788 -10181.066 0 -10051.092 580.25473
+ 1700 517.37824 -10201.044 0 -10048.366 136.09841
+ 1800 461.75464 -10182.78 0 -10046.517 -259.88878
+ 1900 464.0812 -10181.158 0 -10044.207 1566.4734
+ 2000 476.55134 -10183.975 0 -10043.344 -884.37537
+Loop time of 1.16101 on 4 procs for 2000 steps with 100 atoms
+
+Performance: 37.209 ns/day, 0.645 hours/ns, 1722.640 timesteps/s, 172.264 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 | 0.65447 | 0.69002 | 0.77443 | 6.0 | 59.43
+Neigh | 0.050397 | 0.060259 | 0.06883 | 2.7 | 5.19
+Comm | 0.03061 | 0.1145 | 0.15016 | 14.5 | 9.86
+Output | 0.00039488 | 0.00043537 | 0.00055434 | 0.0 | 0.04
+Modify | 0.28585 | 0.29446 | 0.30467 | 1.2 | 25.36
+Other | | 0.00134 | | | 0.12
+
+Nlocal: 25 ave 36 max 10 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Nghost: 385.75 ave 472 max 299 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs: 1077 ave 1693 max 379 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 4308
+Ave neighs/atom = 43.08
+Neighbor list builds = 200
+Dangerous builds not checked
+Total wall time: 0:00:01
diff --git a/examples/reaxff/VOH/log.8Mar18.VOH.g++.1 b/examples/reaxff/VOH/log.8Mar18.VOH.g++.1
deleted file mode 100644
index 924769e570..0000000000
--- a/examples/reaxff/VOH/log.8Mar18.VOH.g++.1
+++ /dev/null
@@ -1,81 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# REAX potential for VOH system
-# .....
-
-units real
-
-atom_style charge
-read_data data.VOH
- orthogonal box = (0 0 0) to (25 25 25)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 100 atoms
-
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.V_O_C_H H C O V
-Reading potential file ffield.reax.V_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.voh
-
-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) = 17.79 | 17.79 | 17.79 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -10246.825 0 -10246.825 42.256089
- 3000 476.73301 -10185.256 0 -10044.572 -694.70737
-Loop time of 11.0577 on 1 procs for 3000 steps with 100 atoms
-
-Performance: 5.860 ns/day, 4.095 hours/ns, 271.304 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 | 9.6785 | 9.6785 | 9.6785 | 0.0 | 87.53
-Neigh | 0.32599 | 0.32599 | 0.32599 | 0.0 | 2.95
-Comm | 0.017231 | 0.017231 | 0.017231 | 0.0 | 0.16
-Output | 2.5511e-05 | 2.5511e-05 | 2.5511e-05 | 0.0 | 0.00
-Modify | 1.0311 | 1.0311 | 1.0311 | 0.0 | 9.32
-Other | | 0.004857 | | | 0.04
-
-Nlocal: 100 ave 100 max 100 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 598 ave 598 max 598 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3390 ave 3390 max 3390 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3390
-Ave neighs/atom = 33.9
-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
diff --git a/examples/reaxff/VOH/log.8Mar18.VOH.g++.4 b/examples/reaxff/VOH/log.8Mar18.VOH.g++.4
deleted file mode 100644
index 0395af6671..0000000000
--- a/examples/reaxff/VOH/log.8Mar18.VOH.g++.4
+++ /dev/null
@@ -1,81 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# REAX potential for VOH system
-# .....
-
-units real
-
-atom_style charge
-read_data data.VOH
- orthogonal box = (0 0 0) to (25 25 25)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 100 atoms
-
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.V_O_C_H H C O V
-Reading potential file ffield.reax.V_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.voh
-
-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) = 11.21 | 12.52 | 13.64 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -10246.825 0 -10246.825 42.256092
- 3000 489.67803 -10188.866 0 -10044.362 -553.7513
-Loop time of 6.49847 on 4 procs for 3000 steps with 100 atoms
-
-Performance: 9.972 ns/day, 2.407 hours/ns, 461.647 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 | 4.7412 | 4.8453 | 4.9104 | 2.9 | 74.56
-Neigh | 0.1468 | 0.17834 | 0.20151 | 4.7 | 2.74
-Comm | 0.071841 | 0.14037 | 0.24502 | 17.2 | 2.16
-Output | 2.1219e-05 | 2.408e-05 | 3.1948e-05 | 0.0 | 0.00
-Modify | 1.3072 | 1.3308 | 1.3627 | 1.7 | 20.48
-Other | | 0.003713 | | | 0.06
-
-Nlocal: 25 ave 38 max 11 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost: 369.75 ave 453 max 283 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs: 1082.25 ave 1788 max 417 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 4329
-Ave neighs/atom = 43.29
-Neighbor list builds = 300
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:06
diff --git a/examples/reaxff/ZnOH2/in.ZnOH2 b/examples/reaxff/ZnOH2/in.ZnOH2
index f39b1a29dd..75a2d05f4b 100644
--- a/examples/reaxff/ZnOH2/in.ZnOH2
+++ b/examples/reaxff/ZnOH2/in.ZnOH2
@@ -1,23 +1,24 @@
# REAX potential for ZnOH2 system
# .....
-units real
+units real
-atom_style charge
-read_data data.ZnOH2
+atom_style charge
+read_data data.ZnOH2
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.ZnOH H O Zn
+pair_style reaxff lmp_control
+pair_coeff * * ffield.reax.ZnOH H O Zn
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
+neighbor 2 bin
+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 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.znoh
+#dump 1 all atom 30 dump.reax.znoh
-run 3000
+run 1000
diff --git a/examples/reaxff/ZnOH2/lmp_control b/examples/reaxff/ZnOH2/lmp_control
index 0fb44fe862..10c27d025d 100644
--- a/examples/reaxff/ZnOH2/lmp_control
+++ b/examples/reaxff/ZnOH2/lmp_control
@@ -1,17 +1,7 @@
-simulation_name ZnOH2_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
-energy_update_freq 1
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
-
-write_freq 1 ! write trajectory after so many steps
-traj_title ZnOH2 ! (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
diff --git a/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.1 b/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.1
new file mode 100644
index 0000000000..850eeb3f3e
--- /dev/null
+++ b/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.1
@@ -0,0 +1,122 @@
+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 ZnOH2 system
+# .....
+
+units real
+
+atom_style charge
+read_data data.ZnOH2
+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.ZnOH H O Zn
+Reading potential file ffield.reax.ZnOH 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.znoh
+
+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
+ 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) = 15.8 | 15.8 | 15.8 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 0 -7900.2668 0 -7900.2668 60.076093
+ 100 89.745108 -7892.7937 0 -7864.9724 -359.37879
+ 200 151.73431 -7883.2823 0 -7836.244 118.04838
+ 300 223.74392 -7881.6513 0 -7812.2898 -97.069674
+ 400 293.70909 -7883.7754 0 -7792.7243 -384.10332
+ 500 301.22843 -7869.313 0 -7775.9309 76.604433
+ 600 317.45476 -7860.4665 0 -7762.0541 40.95095
+ 700 335.70939 -7853.865 0 -7749.7937 -173.3119
+ 800 380.48725 -7857.8679 0 -7739.9152 -139.88773
+ 900 502.93129 -7891.7095 0 -7735.7987 488.40109
+ 1000 510.36735 -7894.0653 0 -7735.8493 -222.85193
+Loop time of 0.583996 on 1 procs for 1000 steps with 105 atoms
+
+Performance: 36.987 ns/day, 0.649 hours/ns, 1712.342 timesteps/s, 179.796 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.41526 | 0.41526 | 0.41526 | 0.0 | 71.11
+Neigh | 0.058908 | 0.058908 | 0.058908 | 0.0 | 10.09
+Comm | 0.0028308 | 0.0028308 | 0.0028308 | 0.0 | 0.48
+Output | 0.00021295 | 0.00021295 | 0.00021295 | 0.0 | 0.04
+Modify | 0.1061 | 0.1061 | 0.1061 | 0.0 | 18.17
+Other | | 0.0006844 | | | 0.12
+
+Nlocal: 105 ave 105 max 105 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 640 ave 640 max 640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3934 ave 3934 max 3934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3934
+Ave neighs/atom = 37.466667
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.4 b/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.4
new file mode 100644
index 0000000000..d98fe1df74
--- /dev/null
+++ b/examples/reaxff/ZnOH2/log.30Nov23.ZnOH2.g++.4
@@ -0,0 +1,122 @@
+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 ZnOH2 system
+# .....
+
+units real
+
+atom_style charge
+read_data data.ZnOH2
+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.ZnOH H O Zn
+Reading potential file ffield.reax.ZnOH 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.znoh
+
+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
+ 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) = 10.1 | 11.34 | 12.51 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 0 -7900.2668 0 -7900.2668 60.076093
+ 100 89.745102 -7892.7938 0 -7864.9724 -359.39279
+ 200 151.73402 -7883.2823 0 -7836.2441 118.03582
+ 300 223.74416 -7881.6514 0 -7812.2897 -97.060088
+ 400 293.70926 -7883.7754 0 -7792.7242 -384.10477
+ 500 301.22851 -7869.3129 0 -7775.9308 76.601414
+ 600 317.45436 -7860.4664 0 -7762.0542 40.946828
+ 700 335.70975 -7853.8651 0 -7749.7936 -173.31084
+ 800 380.48744 -7857.868 0 -7739.9153 -139.87915
+ 900 502.93034 -7891.7094 0 -7735.7989 488.3973
+ 1000 510.36634 -7894.0651 0 -7735.8493 -222.85474
+Loop time of 0.345754 on 4 procs for 1000 steps with 105 atoms
+
+Performance: 62.472 ns/day, 0.384 hours/ns, 2892.228 timesteps/s, 303.684 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 | 0.18043 | 0.18884 | 0.19544 | 1.3 | 54.62
+Neigh | 0.027479 | 0.033519 | 0.039456 | 2.3 | 9.69
+Comm | 0.01673 | 0.023479 | 0.031605 | 3.6 | 6.79
+Output | 0.00019732 | 0.0002106 | 0.00024979 | 0.0 | 0.06
+Modify | 0.093437 | 0.099224 | 0.10519 | 1.3 | 28.70
+Other | | 0.0004842 | | | 0.14
+
+Nlocal: 26.25 ave 41 max 11 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost: 390.25 ave 491 max 286 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 1154 ave 1912 max 445 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 4616
+Ave neighs/atom = 43.961905
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.1 b/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.1
deleted file mode 100644
index 58b1a36719..0000000000
--- a/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.1
+++ /dev/null
@@ -1,81 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# REAX potential for ZnOH2 system
-# .....
-
-units real
-
-atom_style charge
-read_data data.ZnOH2
- 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.ZnOH H O Zn
-Reading potential file ffield.reax.ZnOH 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.znoh
-
-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) = 18.36 | 18.36 | 18.36 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -7900.2668 0 -7900.2668 60.076093
- 3000 535.58577 -7934.7287 0 -7768.6948 -475.46237
-Loop time of 7.29784 on 1 procs for 3000 steps with 105 atoms
-
-Performance: 8.879 ns/day, 2.703 hours/ns, 411.081 timesteps/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 | 5.9988 | 5.9988 | 5.9988 | 0.0 | 82.20
-Neigh | 0.37455 | 0.37455 | 0.37455 | 0.0 | 5.13
-Comm | 0.019186 | 0.019186 | 0.019186 | 0.0 | 0.26
-Output | 2.4557e-05 | 2.4557e-05 | 2.4557e-05 | 0.0 | 0.00
-Modify | 0.89915 | 0.89915 | 0.89915 | 0.0 | 12.32
-Other | | 0.006108 | | | 0.08
-
-Nlocal: 105 ave 105 max 105 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 649 ave 649 max 649 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3971 ave 3971 max 3971 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3971
-Ave neighs/atom = 37.819
-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
diff --git a/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.4 b/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.4
deleted file mode 100644
index 77c5cbe1b7..0000000000
--- a/examples/reaxff/ZnOH2/log.8Mar18.ZnOH2.g++.4
+++ /dev/null
@@ -1,81 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# REAX potential for ZnOH2 system
-# .....
-
-units real
-
-atom_style charge
-read_data data.ZnOH2
- 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.ZnOH H O Zn
-Reading potential file ffield.reax.ZnOH 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.znoh
-
-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) = 11.28 | 12.77 | 14.21 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -7900.2668 0 -7900.2668 60.076093
- 3000 538.25796 -7935.6159 0 -7768.7536 -525.47078
-Loop time of 4.48824 on 4 procs for 3000 steps with 105 atoms
-
-Performance: 14.438 ns/day, 1.662 hours/ns, 668.414 timesteps/s
-97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 3.1031 | 3.1698 | 3.2378 | 3.3 | 70.62
-Neigh | 0.16642 | 0.20502 | 0.25003 | 6.6 | 4.57
-Comm | 0.074932 | 0.14224 | 0.21025 | 15.6 | 3.17
-Output | 0.00011349 | 0.00011736 | 0.00012231 | 0.0 | 0.00
-Modify | 0.92089 | 0.96736 | 1.0083 | 3.2 | 21.55
-Other | | 0.003731 | | | 0.08
-
-Nlocal: 26.25 ave 45 max 15 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Nghost: 399 ave 509 max 295 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-Neighs: 1151.5 ave 2066 max 701 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 4606
-Ave neighs/atom = 43.8667
-Neighbor list builds = 300
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04
diff --git a/examples/reaxff/ci-reaxFF/in.ci-reax.CH b/examples/reaxff/ci-reaxFF/in.ci-reax.CH
index b3a2406a56..bee76b3eea 100644
--- a/examples/reaxff/ci-reaxFF/in.ci-reax.CH
+++ b/examples/reaxff/ci-reaxFF/in.ci-reax.CH
@@ -4,8 +4,8 @@ units real
read_data CH4.dat
-pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
-pair_coeff * * reax/c ffield.ci-reax.CH C H
+pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
+pair_coeff * * reaxff ffield.ci-reax.CH C H
pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
diff --git a/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.1 b/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.1
new file mode 100644
index 0000000000..08f2f4b47b
--- /dev/null
+++ b/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.1
@@ -0,0 +1,105 @@
+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
+#ci-reax potential for CH systems with tabulated ZBL correction
+atom_style charge
+units real
+
+read_data CH4.dat
+Reading data file ...
+ orthogonal box = (0 0 0) to (20 20 20)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 315 atoms
+ reading velocities ...
+ 315 velocities
+ read_data CPU = 0.003 seconds
+
+pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
+pair_coeff * * reaxff ffield.ci-reax.CH C H
+Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
+pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
+WARNING: 2 of 10000 force values in table CC_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
+WARNING: 2 of 11000 force values in table CH_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
+WARNING: 2 of 6000 force values in table HH_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep 0.25
+fix 1 all nve
+fix 2 all temp/berendsen 500.0 500.0 100.0
+
+#dump 1 all atom 30 dump.ci-reax.lammpstrj
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (src/REAXFF/pair_reaxff.cpp:365)
+Neighbor list info ...
+ update: every = 1 steps, delay = 0 steps, check = yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 9.5
+ ghost atom cutoff = 9.5
+ binsize = 4.75, 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) pair table, perpetual
+ attributes: half, newton on, cut 3.1
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 35.64 | 35.64 | 35.64 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 508.42043 -28736.654 0 -28260.785 1678.3276
+ 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
+Loop time of 13.2263 on 1 procs for 3000 steps with 315 atoms
+
+Performance: 4.899 ns/day, 4.899 hours/ns, 226.821 timesteps/s, 71.449 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 13.046 | 13.046 | 13.046 | 0.0 | 98.64
+Neigh | 0.12783 | 0.12783 | 0.12783 | 0.0 | 0.97
+Comm | 0.025611 | 0.025611 | 0.025611 | 0.0 | 0.19
+Output | 2.2361e-05 | 2.2361e-05 | 2.2361e-05 | 0.0 | 0.00
+Modify | 0.017722 | 0.017722 | 0.017722 | 0.0 | 0.13
+Other | | 0.008824 | | | 0.07
+
+Nlocal: 315 ave 315 max 315 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2056 ave 2056 max 2056 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 32754 ave 32754 max 32754 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 32754
+Ave neighs/atom = 103.98095
+Neighbor list builds = 37
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.4 b/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.4
new file mode 100644
index 0000000000..cc6c386f03
--- /dev/null
+++ b/examples/reaxff/ci-reaxFF/log.30Nov23.ci-reax.CH.g++.4
@@ -0,0 +1,105 @@
+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
+#ci-reax potential for CH systems with tabulated ZBL correction
+atom_style charge
+units real
+
+read_data CH4.dat
+Reading data file ...
+ orthogonal box = (0 0 0) to (20 20 20)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 315 atoms
+ reading velocities ...
+ 315 velocities
+ read_data CPU = 0.002 seconds
+
+pair_style hybrid/overlay reaxff control checkqeq no table linear 11000
+pair_coeff * * reaxff ffield.ci-reax.CH C H
+Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
+pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
+WARNING: 2 of 10000 force values in table CC_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
+WARNING: 2 of 11000 force values in table CH_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
+WARNING: 2 of 6000 force values in table HH_cireaxFF are inconsistent with -dE/dr.
+WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep 0.25
+fix 1 all nve
+fix 2 all temp/berendsen 500.0 500.0 100.0
+
+#dump 1 all atom 30 dump.ci-reax.lammpstrj
+
+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}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (src/REAXFF/pair_reaxff.cpp:365)
+Neighbor list info ...
+ update: every = 1 steps, delay = 0 steps, check = yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 9.5
+ ghost atom cutoff = 9.5
+ binsize = 4.75, 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) pair table, perpetual
+ attributes: half, newton on, cut 3.1
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 20.4 | 21.35 | 22.73 Mbytes
+ Step Temp E_pair E_mol TotEng Press
+ 0 508.42043 -28736.654 0 -28260.785 1678.3276
+ 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
+Loop time of 8.18251 on 4 procs for 3000 steps with 315 atoms
+
+Performance: 7.919 ns/day, 3.031 hours/ns, 366.636 timesteps/s, 115.490 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 | 6.7983 | 7.3808 | 7.9976 | 16.3 | 90.20
+Neigh | 0.062309 | 0.065996 | 0.07006 | 1.4 | 0.81
+Comm | 0.083586 | 0.70629 | 1.2934 | 53.1 | 8.63
+Output | 1.8365e-05 | 2.0853e-05 | 2.7615e-05 | 0.0 | 0.00
+Modify | 0.016829 | 0.019422 | 0.02157 | 1.4 | 0.24
+Other | | 0.01001 | | | 0.12
+
+Nlocal: 78.75 ave 96 max 65 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 1233 ave 1348 max 1116 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 9467.25 ave 12150 max 7160 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 37869
+Ave neighs/atom = 120.21905
+Neighbor list builds = 37
+Dangerous builds = 0
+Total wall time: 0:00:08
diff --git a/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1 b/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
deleted file mode 100644
index e966fd26b6..0000000000
--- a/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
+++ /dev/null
@@ -1,86 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-#ci-reax potential for CH systems with tabulated ZBL correction
-atom_style charge
-units real
-
-read_data CH4.dat
- orthogonal box = (0 0 0) to (20 20 20)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 315 atoms
- reading velocities ...
- 315 velocities
-
-pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
-pair_coeff * * reax/c ffield.ci-reax.CH C H
-Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
-pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
-WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
-WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
-WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-
-timestep 0.25
-fix 1 all nve
-fix 2 all temp/berendsen 500.0 500.0 100.0
-
-#dump 1 all atom 30 dump.ci-reax.lammpstrj
-
-run 3000
-WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
-Neighbor list info ...
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 9.5
- ghost atom cutoff = 9.5
- binsize = 4.75, 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) pair table, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 43.46 | 43.46 | 43.46 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 508.42043 -28736.654 0 -28260.785 1678.3276
- 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
-Loop time of 45.3959 on 1 procs for 3000 steps with 315 atoms
-
-Performance: 1.427 ns/day, 16.813 hours/ns, 66.085 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 | 44.955 | 44.955 | 44.955 | 0.0 | 99.03
-Neigh | 0.29903 | 0.29903 | 0.29903 | 0.0 | 0.66
-Comm | 0.056547 | 0.056547 | 0.056547 | 0.0 | 0.12
-Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.00
-Modify | 0.058722 | 0.058722 | 0.058722 | 0.0 | 0.13
-Other | | 0.02632 | | | 0.06
-
-Nlocal: 315 ave 315 max 315 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2056 ave 2056 max 2056 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 32754 ave 32754 max 32754 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 32754
-Ave neighs/atom = 103.981
-Neighbor list builds = 37
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:45
diff --git a/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 b/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4
deleted file mode 100644
index ccc87b3536..0000000000
--- a/examples/reaxff/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4
+++ /dev/null
@@ -1,86 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-#ci-reax potential for CH systems with tabulated ZBL correction
-atom_style charge
-units real
-
-read_data CH4.dat
- orthogonal box = (0 0 0) to (20 20 20)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 315 atoms
- reading velocities ...
- 315 velocities
-
-pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
-pair_coeff * * reax/c ffield.ci-reax.CH C H
-Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
-pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
-WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
-WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
-WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:481)
-
-timestep 0.25
-fix 1 all nve
-fix 2 all temp/berendsen 500.0 500.0 100.0
-
-#dump 1 all atom 30 dump.ci-reax.lammpstrj
-
-run 3000
-WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
-Neighbor list info ...
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 9.5
- ghost atom cutoff = 9.5
- binsize = 4.75, 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) pair table, perpetual
- attributes: half, newton on
- pair build: half/bin/atomonly/newton
- stencil: half/bin/3d/newton
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 24.48 | 25.61 | 27.27 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 508.42043 -28736.654 0 -28260.785 1678.3276
- 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
-Loop time of 24.7034 on 4 procs for 3000 steps with 315 atoms
-
-Performance: 2.623 ns/day, 9.149 hours/ns, 121.441 timesteps/s
-95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 18.945 | 21.367 | 24.046 | 39.3 | 86.49
-Neigh | 0.1456 | 0.15254 | 0.16101 | 1.6 | 0.62
-Comm | 0.39168 | 3.0859 | 5.5185 | 103.9 | 12.49
-Output | 3.5763e-05 | 4.065e-05 | 5.2452e-05 | 0.0 | 0.00
-Modify | 0.05831 | 0.068811 | 0.077666 | 2.9 | 0.28
-Other | | 0.0292 | | | 0.12
-
-Nlocal: 78.75 ave 96 max 65 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Nghost: 1233 ave 1348 max 1116 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Neighs: 9467.25 ave 12150 max 7160 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 37869
-Ave neighs/atom = 120.219
-Neighbor list builds = 37
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:24
diff --git a/lib/pace/Install.py b/lib/pace/Install.py
index 8d31852e44..fcd9497937 100644
--- a/lib/pace/Install.py
+++ b/lib/pace/Install.py
@@ -18,11 +18,11 @@ from install_helpers import fullpath, geturl, checkmd5sum, getfallback
# settings
thisdir = fullpath('.')
-version ='v.2023.10.04'
+version ='v.2023.11.25.fix'
# known checksums for different PACE versions. used to validate the download.
checksums = { \
- 'v.2023.10.04': '70ff79f4e59af175e55d24f3243ad1ff'
+ 'v.2023.11.25.fix': 'b45de9a633f42ed65422567e3ce56f9f'
}
parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script")
diff --git a/src/.gitignore b/src/.gitignore
index 5c6891c35e..3b7902303d 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -100,6 +100,8 @@
/lepton_utils.cpp
/lepton_utils.h
+/compute_pace.cpp
+/compute_pace.h
/pair_pace.cpp
/pair_pace.h
/pair_pace_extrapolation.cpp
@@ -629,6 +631,8 @@
/compute_pressure_grem.h
/compute_ptm_atom.cpp
/compute_ptm_atom.h
+/compute_rattlers_atom.cpp
+/compute_rattlers_atom.h
/compute_rigid_local.cpp
/compute_rigid_local.h
/compute_slcsa_atom.cpp
@@ -914,6 +918,8 @@
/fix_nvt_sllod_eff.h
/fix_nve_tri.cpp
/fix_nve_tri.h
+/fix_nonaffine_displacement.cpp
+/fix_nonaffine_displacement.h
/fix_oneway.cpp
/fix_oneway.h
/fix_orient_bcc.cpp
diff --git a/src/AMOEBA/amoeba_multipole.cpp b/src/AMOEBA/amoeba_multipole.cpp
index a1503a91f3..d0ae03401a 100644
--- a/src/AMOEBA/amoeba_multipole.cpp
+++ b/src/AMOEBA/amoeba_multipole.cpp
@@ -18,6 +18,7 @@
#include "atom.h"
#include "comm.h"
#include "domain.h"
+#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "neigh_list.h"
@@ -1000,3 +1001,61 @@ void PairAmoeba::damppole(double r, int rorder, double alphai, double alphak,
}
}
}
+
+/* ----------------------------------------------------------------------
+ estimate the accuracy of m_kspace solver based on the monopoles
+ based on Ewald
+------------------------------------------------------------------------- */
+
+double PairAmoeba::final_accuracy_mpole()
+{
+ const int nlocal = atom->nlocal;
+ double qsqsum_local(0.0), qsqsum;
+ for (int i = 0; i < nlocal; i++) {
+ qsqsum_local += rpole[i][0]*rpole[i][0];
+ }
+ MPI_Allreduce(&qsqsum_local,&qsqsum,1,MPI_DOUBLE,MPI_SUM,world);
+ double q2 = qsqsum * force->qqrd2e;
+
+ const double * const prd = domain->prd;
+ const double xprd = prd[0];
+ const double yprd = prd[1];
+ const double zprd = prd[2];
+ const double slab_volfactor = 1.0;
+ const double zprd_slab = zprd*slab_volfactor;
+ bigint natoms = atom->natoms;
+
+ int nx_fft = m_kspace->nx;
+ int ny_fft = m_kspace->ny;
+ int nz_fft = m_kspace->nz;
+ double cutoff = mpolecut;
+
+ double lprx = rms(nx_fft,xprd,natoms,aeewald,q2);
+ double lpry = rms(ny_fft,yprd,natoms,aeewald,q2);
+ double lprz = rms(nz_fft,zprd_slab,natoms,aeewald,q2);
+ double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
+ double q2_over_sqrt = q2 / sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
+ double spr = 2.0 *q2_over_sqrt * exp(-aeewald*aeewald*cutoff*cutoff);
+ double tpr = 0;
+ double estimated_accuracy = sqrt(lpr*lpr + spr*spr + tpr*tpr);
+
+ two_charge_force = force->qqr2e *
+ (force->qelectron * force->qelectron) /
+ (force->angstrom * force->angstrom);
+
+ return estimated_accuracy;
+}
+
+/* ----------------------------------------------------------------------
+ compute RMS accuracy for a dimension
+------------------------------------------------------------------------- */
+
+double PairAmoeba::rms(int km, double prd, bigint natoms, double g_ewald, double q2)
+{
+ if (natoms == 0) natoms = 1; // avoid division by zero
+ double value = 2.0*q2*g_ewald/prd *
+ sqrt(1.0/(MY_PI*km*natoms)) *
+ exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd));
+
+ return value;
+}
diff --git a/src/AMOEBA/pair_amoeba.cpp b/src/AMOEBA/pair_amoeba.cpp
index 72efa76523..cad9e2b628 100644
--- a/src/AMOEBA/pair_amoeba.cpp
+++ b/src/AMOEBA/pair_amoeba.cpp
@@ -347,8 +347,6 @@ void PairAmoeba::compute(int eflag, int vflag)
}
}
- first_flag_compute = 0;
-
// -------------------------------------------------------------------
// end of one-time initializations
// -------------------------------------------------------------------
@@ -428,6 +426,12 @@ void PairAmoeba::compute(int eflag, int vflag)
else cfstyle = SETUP_HIPPO;
comm->forward_comm(this);
+ // output FF settings to screen and logfile
+ // delay until here because RMS force accuracy is computed based on rpole
+
+ if (first_flag_compute && (comm->me == 0)) print_settings();
+ first_flag_compute = 0;
+
if (amoeba) pbc_xred();
time1 = platform::walltime();
@@ -978,10 +982,6 @@ void PairAmoeba::init_style()
for (int i = 0; i < nlocal; i++) pval[i] = 0.0;
}
- // output FF settings to screen and logfile
-
- if (first_flag && (comm->me == 0)) print_settings();
-
// all done with one-time initializations
first_flag = 0;
@@ -1098,9 +1098,13 @@ void PairAmoeba::print_settings()
if (use_ewald) {
choose(MPOLE_LONG);
- mesg += fmt::format(" multipole: cut {} aewald {} bsorder {} FFT {} {} {} "
+ double estimated_accuracy = final_accuracy_mpole();
+ mesg += fmt::format(" multipole: cut {} aewald {} bsorder {} FFT {} {} {}; "
+ "estimated absolute RMS force accuracy = {:.8g}; "
+ "estimated relative RMS force accuracy = {:.8g}; "
"mscale {} {} {} {}\n",
sqrt(off2),aewald,bseorder,nefft1,nefft2,nefft3,
+ estimated_accuracy,estimated_accuracy/two_charge_force,
special_mpole[1],special_mpole[2],special_mpole[3],special_mpole[4]);
} else {
choose(MPOLE);
diff --git a/src/AMOEBA/pair_amoeba.h b/src/AMOEBA/pair_amoeba.h
index 1f3a4b799a..648fc86126 100644
--- a/src/AMOEBA/pair_amoeba.h
+++ b/src/AMOEBA/pair_amoeba.h
@@ -419,6 +419,10 @@ class PairAmoeba : public Pair {
double ewaldcof(double);
int factorable(int);
+ double final_accuracy_mpole();
+ double rms(int km, double prd, bigint natoms, double g_ewald, double q2);
+ double two_charge_force;
+
// debug methods
FILE *fp_uind;
diff --git a/src/EXTRA-COMPUTE/compute_rattlers_atom.cpp b/src/EXTRA-COMPUTE/compute_rattlers_atom.cpp
new file mode 100644
index 0000000000..602923b58a
--- /dev/null
+++ b/src/EXTRA-COMPUTE/compute_rattlers_atom.cpp
@@ -0,0 +1,312 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
+#include "compute_rattlers_atom.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include
+#include
+
+using namespace LAMMPS_NS;
+
+enum { TYPE, RADIUS };
+
+/* ---------------------------------------------------------------------- */
+
+ComputeRattlersAtom::ComputeRattlersAtom(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg), ncontacts(nullptr), rattler(nullptr)
+{
+ if (narg != 6) error->all(FLERR, "Illegal compute rattlers/atom command");
+
+ if (strcmp(arg[3], "type") == 0)
+ cutstyle = TYPE;
+ else if (strcmp(arg[3], "radius") == 0)
+ cutstyle = RADIUS;
+ else
+ error->all(FLERR, "Illegal compute rattlers/atom command");
+
+ if (cutstyle == RADIUS && !atom->radius_flag)
+ error->all(FLERR, "Compute rattlers/atom radius style requires atom attribute radius");
+
+ ncontacts_rattler = utils::inumeric(FLERR, arg[4], false, lmp);
+ max_tries = utils::inumeric(FLERR, arg[5], false, lmp);
+
+ nmax = 0;
+ invoked_peratom = -1;
+
+ scalar_flag = 1;
+ extscalar = 1;
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+ comm_forward = 1;
+ comm_reverse = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeRattlersAtom::~ComputeRattlersAtom()
+{
+ memory->destroy(ncontacts);
+ memory->destroy(rattler);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeRattlersAtom::init()
+{
+ if (force->pair == nullptr) error->all(FLERR, "No pair style is defined for compute rattlers");
+
+ // Cannot calculate distance from radii for JKR/DMT
+ if (force->pair->beyond_contact)
+ error->all(FLERR, "Compute rattlers does not currently support pair styles that extend beyond contact");
+
+ // need an occasional half neighbor list
+ // set size to same value as request made by force->pair
+ // this should enable it to always be a copy list (e.g. for granular pstyle)
+
+ auto pairrequest = neighbor->find_request(force->pair);
+ if (pairrequest && pairrequest->get_size())
+ neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL);
+ else
+ neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeRattlersAtom::init_list(int /*id*/, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeRattlersAtom::compute_peratom()
+{
+ if (invoked_peratom == update->ntimestep) return;
+ invoked_peratom = update->ntimestep;
+
+ int i, j, ii, jj, inum, jnum, itype, jtype, tmp_flag;
+ tagint itag, jtag;
+ double xtmp, ytmp, ztmp, delx, dely, delz;
+ double rsq, radsum;
+
+ if (nmax < atom->nmax) {
+ nmax = atom->nmax;
+ memory->destroy(ncontacts);
+ memory->destroy(rattler);
+ memory->create(ncontacts, nmax, "rattlers:ncontacts");
+ memory->create(rattler, nmax, "rattlers:rattler");
+ vector_atom = rattler;
+ }
+
+ for (i = 0; i < nmax; i++) rattler[i] = 0;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+
+ double **x = atom->x;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ // invoke half neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ Pair *pair = force->pair;
+ double **cutsq = force->pair->cutsq;
+
+ int change_flag = 1;
+ int ntry = 0;
+ while (ntry < max_tries) {
+ change_flag = 0;
+
+ for (i = 0; i < nmax; i++) ncontacts[i] = 0;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
+ if (rattler[i] == 1) continue;
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itag = tag[i];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbit)) continue;
+ if (rattler[j] == 1) continue;
+
+ // itag = jtag is possible for long cutoffs that include images of self
+
+ if (newton_pair == 0 && j >= nlocal) {
+ jtag = tag[j];
+ if (itag > jtag) {
+ if ((itag + jtag) % 2 == 0) continue;
+ } else if (itag < jtag) {
+ if ((itag + jtag) % 2 == 1) continue;
+ } else {
+ if (x[j][2] < ztmp) continue;
+ if (x[j][2] == ztmp) {
+ if (x[j][1] < ytmp) continue;
+ if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
+ }
+ }
+ }
+
+ jtype = type[j];
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+
+ if (cutstyle == TYPE) {
+ if (rsq >= cutsq[itype][jtype]) continue;
+ } else {
+ radsum = radius[i] + radius[j];
+ if (rsq >= radsum * radsum) continue;
+ }
+ ncontacts[i] += 1;
+ if (newton_pair || j < nlocal)
+ ncontacts[j] += 1;
+ }
+ }
+
+ // add contributions from ghosts
+ if (force->newton_pair) comm->reverse_comm(this);
+
+ // Set flags for rattlers
+ for (i = 0; i < atom->nlocal; i++) {
+ if (ncontacts[i] < ncontacts_rattler && rattler[i] == 0) {
+ rattler[i] = 1;
+ change_flag = 1;
+ }
+ }
+
+ comm->forward_comm(this);
+
+ MPI_Allreduce(&change_flag, &tmp_flag, 1, MPI_INT, MPI_MAX, world);
+ change_flag = tmp_flag;
+ if (change_flag == 0) break;
+
+ ntry += 1;
+ }
+
+ if (change_flag == 1)
+ error->warning(FLERR, "Rattler calculation failed to converge within max tries");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeRattlersAtom::compute_scalar()
+{
+ if (invoked_peratom != update->ntimestep)
+ compute_peratom();
+
+ invoked_scalar = update->ntimestep;
+
+ double total_rattlers = 0;
+ for (int i = 0; i < atom->nlocal; i++) {
+ if (rattler[i] == 1) {
+ total_rattlers += 1;
+ }
+ }
+
+ //Total across processors
+ MPI_Allreduce(&total_rattlers, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
+ return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeRattlersAtom::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = ubuf(ncontacts[i]).d;
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeRattlersAtom::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ ncontacts[j] += (int) ubuf(buf[m++]).i;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeRattlersAtom::pack_forward_comm(int n, int *list, double *buf,
+ int /*pbc_flag*/, int * /*pbc*/)
+{
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rattler[j];
+ }
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeRattlersAtom::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ rattler[i] = buf[m++];
+ }
+}
diff --git a/src/EXTRA-COMPUTE/compute_rattlers_atom.h b/src/EXTRA-COMPUTE/compute_rattlers_atom.h
new file mode 100644
index 0000000000..257bae8374
--- /dev/null
+++ b/src/EXTRA-COMPUTE/compute_rattlers_atom.h
@@ -0,0 +1,52 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+// clang-format off
+ComputeStyle(rattlers/atom,ComputeRattlersAtom);
+// clang-format on
+#else
+
+#ifndef LMP_COMPUTE_RATTLERS_ATOM_H
+#define LMP_COMPUTE_RATTLERS_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeRattlersAtom : public Compute {
+ public:
+ ComputeRattlersAtom(class LAMMPS *, int, char **);
+ ~ComputeRattlersAtom() override;
+ void init() override;
+ void init_list(int, class NeighList *) override;
+ void compute_peratom() override;
+ double compute_scalar() override;
+ int pack_forward_comm(int, int *, double *, int, int *) override;
+ void unpack_forward_comm(int, int, double *) override;
+ int pack_reverse_comm(int, int, double *) override;
+ void unpack_reverse_comm(int, int *, double *) override;
+
+ private:
+ int pstyle, cutstyle;
+ int ncontacts_rattler, max_tries, nmax, invoked_peratom;
+ int *ncontacts;
+ double *rattler;
+ class NeighList *list;
+
+};
+
+} // namespace LAMMPS_NS
+
+#endif
+#endif
diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp
new file mode 100644
index 0000000000..ef5481601f
--- /dev/null
+++ b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp
@@ -0,0 +1,736 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
+#include "fix_nonaffine_displacement.h"
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "fix_store_atom.h"
+#include "force.h"
+#include "group.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
+
+#include
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathExtra;
+
+enum { TYPE, RADIUS, CUSTOM };
+enum { INTEGRATED, D2MIN };
+enum { FIXED, OFFSET, UPDATE };
+
+static const char cite_nonaffine_d2min[] =
+ "@article{PhysRevE.57.7192,\n"
+ " title = {Dynamics of viscoplastic deformation in amorphous solids},\n"
+ " author = {Falk, M. L. and Langer, J. S.},\n"
+ " journal = {Phys. Rev. E},\n"
+ " volume = {57},\n"
+ " issue = {6},\n"
+ " pages = {7192--7205},\n"
+ " numpages = {0},\n"
+ " year = {1998},\n"
+ " month = {Jun},\n"
+ " publisher = {American Physical Society},\n"
+ " doi = {10.1103/PhysRevE.57.7192},\n"
+ "url = {https://link.aps.org/doi/10.1103/PhysRevE.57.7192}\n"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg), id_fix(nullptr), X(nullptr), Y(nullptr), F(nullptr), norm(nullptr)
+{
+ if (narg < 4) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+
+ nevery = utils::inumeric(FLERR, arg[3], false, lmp);
+ if (nevery <= 0) error->all(FLERR,"Illegal nevery value {} in fix nonaffine/displacement", nevery);
+
+ int iarg = 4;
+ if (strcmp(arg[iarg], "integrated") == 0) {
+ nad_style = INTEGRATED;
+ nevery = 1;
+ iarg += 1;
+ } else if (strcmp(arg[iarg], "d2min") == 0) {
+ if (iarg + 1 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+ nad_style = D2MIN;
+ if (strcmp(arg[iarg + 1], "type") == 0) {
+ cut_style = TYPE;
+ } else if (strcmp(arg[iarg + 1], "radius") == 0) {
+ cut_style = RADIUS;
+ } else if (strcmp(arg[iarg + 1], "custom") == 0) {
+ if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+ cut_style = CUSTOM;
+ cutoff_custom = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
+ cutsq_custom = cutoff_custom * cutoff_custom;
+ if (cutoff_custom <= 0)
+ error->all(FLERR, "Illegal custom cutoff length {}", arg[iarg + 2]);
+ iarg += 1;
+ } else error->all(FLERR,"Illegal cutoff style {} in fix nonaffine/displacement", arg[iarg + 1]);
+ iarg += 2;
+ } else error->all(FLERR,"Illegal nonaffine displacement style {} in fix nonaffine/displacement", arg[iarg]);
+
+ if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+ if (strcmp(arg[iarg], "fixed") == 0) {
+ reference_style = FIXED;
+ reference_timestep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+ if (update_timestep < 0)
+ error->all(FLERR, "Illegal reference timestep {} in fix nonaffine/displacement", arg[iarg + 1]);
+ } else if (strcmp(arg[iarg], "update") == 0) {
+ reference_style = UPDATE;
+ update_timestep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+ if (update_timestep < 0)
+ error->all(FLERR, "Illegal update timestep {} in fix nonaffine/displacement", arg[iarg + 1]);
+ } else if (strcmp(arg[iarg], "offset") == 0) {
+ reference_style = OFFSET;
+ offset_timestep = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+ if ((offset_timestep <= 0) || (offset_timestep > nevery))
+ error->all(FLERR, "Illegal offset timestep {} in fix nonaffine/displacement", arg[iarg + 1]);
+ } else error->all(FLERR,"Illegal reference style {} in fix nonaffine/displacement", arg[iarg]);
+
+ if (nad_style == D2MIN)
+ if (cut_style == RADIUS && (!atom->radius_flag))
+ error->all(FLERR, "Fix nonaffine/displacement radius style requires atom attribute radius");
+
+ if (nad_style == INTEGRATED && reference_style == OFFSET)
+ error->all(FLERR, "Fix nonaffine/displacement cannot use the integrated style with an offset reference state");
+
+ peratom_flag = 1;
+ peratom_freq = nevery;
+ nmax = -1;
+ reference_saved = 0;
+ restart_global = 1;
+
+ size_peratom_cols = 3;
+ comm_reverse = 0;
+ comm_forward = 0;
+ if (nad_style == D2MIN) {
+ comm_reverse = 18;
+ comm_forward = 9;
+ }
+
+ if (nad_style == D2MIN && lmp->citeme) lmp->citeme->add(cite_nonaffine_d2min);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixNonaffineDisplacement::~FixNonaffineDisplacement()
+{
+ if (id_fix && modify->nfix) modify->delete_fix(id_fix);
+ delete[] id_fix;
+
+ if (nad_style == D2MIN) {
+ memory->destroy(X);
+ memory->destroy(Y);
+ memory->destroy(F);
+ memory->destroy(norm);
+ memory->destroy(array_atom);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNonaffineDisplacement::setmask()
+{
+ int mask = 0;
+ mask |= POST_FORCE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::post_constructor()
+{
+ // Create persistent peratom storage for either an integrated velocity or reference position
+ // Ghost atoms need reference coordinates for D2min
+ std::string ghost_status = "0";
+ if (nad_style == D2MIN) ghost_status = "1";
+
+ id_fix = utils::strdup(id + std::string("_FIX_PA"));
+ fix = dynamic_cast(modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 {} 1", id_fix, group->names[igroup], ghost_status)));
+
+ if (nad_style == INTEGRATED)
+ array_atom = fix->astore;
+
+ if (nad_style == D2MIN)
+ grow_arrays(atom->nmax);
+
+ for (int i = 0; i < atom->nlocal; i++)
+ for (int j = 0; j < 3; j++) array_atom[i][j] = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::init()
+{
+ dtv = update->dt;
+
+ if ((!reference_saved) && (reference_style == FIXED) && (update->ntimestep > reference_timestep))
+ error->all(FLERR, "Initial timestep exceeds that of the reference state in fix nonaffine/displacement");
+
+ if (nad_style == D2MIN) {
+ if ((!force->pair) && (cut_style == TYPE))
+ error->all(FLERR,"Fix nonaffine/displacement D2Min option requires a pair style be defined "
+ "or cutoff specified");
+
+ // need an occasional half neighbor list
+
+ if (cut_style == RADIUS) {
+ auto req = neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL);
+ } else {
+ auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
+ if (cut_style == CUSTOM) {
+ double skin = neighbor->skin;
+ mycutneigh = cutoff_custom + skin;
+
+ double cutghost; // as computed by Neighbor and Comm
+ if (force->pair)
+ cutghost = MAX(force->pair->cutforce + skin, comm->cutghostuser);
+ else
+ cutghost = comm->cutghostuser;
+
+ if (mycutneigh > cutghost)
+ error->all(FLERR,"Fix nonaffine/displacement D2Min option cutoff exceeds ghost atom range - use comm_modify cutoff command");
+
+ req->set_cutoff(mycutneigh);
+ }
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::init_list(int /*id*/, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::setup(int vflag)
+{
+ post_force(0); // Save state if needed before starting the 1st timestep
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::post_force(int /*vflag*/)
+{
+ if (reference_saved && (!update->setupflag)) {
+ if (nad_style == INTEGRATED) {
+ integrate_velocity();
+ } else {
+ if ((update->ntimestep % nevery) == 0) calculate_D2Min();
+ }
+ }
+
+ if (reference_style == FIXED)
+ if (update->ntimestep == reference_timestep)
+ save_reference_state();
+
+ if (reference_style == UPDATE)
+ if ((update->ntimestep % update_timestep) == 0)
+ save_reference_state();
+
+ if (reference_style == OFFSET)
+ if (((update->ntimestep + offset_timestep) % nevery) == 0)
+ save_reference_state();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::write_restart(FILE *fp)
+{
+ if (comm->me == 0) {
+ int size = sizeof(int);
+ fwrite(&size, sizeof(int), 1, fp);
+ fwrite(&reference_saved, sizeof(int), 1, fp);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::restart(char *buf)
+{
+ reference_saved = (int) ubuf(buf[0]).i;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::integrate_velocity()
+{
+ int i,n;
+ dtv = update->dt;
+
+ double **v = atom->v;
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int m = 0; m < 3; m++) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ array_atom[i][m] += dtv * v[i][m];
+ }
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::save_reference_state()
+{
+ int i, n;
+ double **x = atom->x;
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
+
+ if (nad_style == D2MIN) {
+ for (int m = 0; m < 3; m++) {
+ for (int i = 0; i < nall; i++) {
+ if (mask[i] & groupbit) array_atom[i][m] = x[i][m];
+ }
+ }
+ } else {
+ for (int m = 0; m < 3; m++) {
+ for (int i = 0; i < nall; i++) {
+ if (mask[i] & groupbit) array_atom[i][m] = 0.0;
+ }
+ }
+ }
+
+ if (nad_style == D2MIN) {
+ xprd0 = domain->xprd;
+ yprd0 = domain->yprd;
+ zprd0 = domain->zprd;
+ xprd0_half = domain->xprd_half;
+ yprd0_half = domain->yprd_half;
+ zprd0_half = domain->zprd_half;
+ xy0 = domain->xy;
+ xz0 = domain->xz;
+ yz0 = domain->yz;
+ }
+
+ reference_saved = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::calculate_D2Min()
+{
+ // invoke half neighbor list (will copy or build if necessary)
+ neighbor->build_one(list);
+
+ if (atom->nmax > nmax)
+ grow_arrays(atom->nmax);
+
+ int i, j, k, l, ii, jj, inum, jnum, itype, jtype;
+ double evol, j2, edev;
+ double r[3], r0[3], rsq, rsq0, radsum, temp[3];
+ double X_tmp[3][3], Y_tmp[3][3], F_tmp[3][3], E[3][3];
+ double Y_inv[3][3] = {0.0}; // Zero for 2d since not all entries used
+ int *ilist, *jlist, *numneigh, **firstneigh;
+
+ double **x = atom->x;
+ double **x0 = array_atom;
+ double *radius = atom->radius;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+ int dim = domain->dimension;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ Pair *pair = force->pair;
+ double **cutsq;
+ if (pair) cutsq = force->pair->cutsq;
+
+ for (i = 0; i < nmax; i++) {
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l++) {
+ X[i][k][l] = 0.0;
+ Y[i][k][l] = 0.0;
+ }
+ }
+ norm[i] = 0;
+ array_atom[i][0] = 0;
+ }
+
+ // First loop through neighbors
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
+
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbit)) continue;
+
+ jtype = type[j];
+ r[0] = x[i][0] - x[j][0];
+ r[1] = x[i][1] - x[j][1];
+ r[2] = x[i][2] - x[j][2];
+ rsq = lensq3(r);
+
+ // Only include contributions from atoms that are CURRENTLY neighbors
+ if (cut_style == TYPE) {
+ if (rsq > cutsq[itype][jtype]) continue;
+ } else if (cut_style == CUSTOM) {
+ if (rsq > cutsq_custom) continue;
+ } else {
+ radsum = radius[i] + radius[j];
+ if (rsq > (radsum * radsum)) continue;
+ }
+
+ r0[0] = x0[i][0] - x0[j][0];
+ r0[1] = x0[i][1] - x0[j][1];
+ r0[2] = x0[i][2] - x0[j][2];
+ minimum_image0(r0);
+
+ // Using notation from Falk & Langer 1998
+ outer3(r, r0, X_tmp);
+ outer3(r0, r0, Y_tmp);
+
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l++) {
+ X[i][k][l] += X_tmp[k][l];
+ Y[i][k][l] += Y_tmp[k][l];
+ }
+ }
+
+ if (newton_pair || j < nlocal) {
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l++) {
+ X[j][k][l] += X_tmp[k][l];
+ Y[j][k][l] += Y_tmp[k][l];
+ }
+ }
+ }
+ }
+ }
+
+ comm_flag = 0;
+ if (newton_pair) comm->reverse_comm(this, 18);
+
+ // Calculate contributions to strain tensor
+ double denom;
+ for (i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+ for (j = 0; j < 3; j++) {
+ for (k = 0; k < 3; k++) {
+ Y_tmp[j][k] = Y[i][j][k];
+ X_tmp[j][k] = X[i][j][k];
+ }
+ }
+
+ if (dim == 3) {
+ invert3(Y_tmp, Y_inv);
+ } else {
+ denom = Y_tmp[0][0] * Y_tmp[1][1] - Y_tmp[0][1] * Y_tmp[1][0];
+ if (denom != 0.0) denom = 1.0 / denom;
+ Y_inv[0][0] = Y_tmp[1][1] * denom;
+ Y_inv[0][1] = -Y_tmp[0][1] * denom;
+ Y_inv[1][0] = -Y_tmp[1][0] * denom;
+ Y_inv[1][1] = Y_tmp[0][0] * denom;
+ }
+
+ times3(X_tmp, Y_inv, F_tmp);
+
+ for (j = 0; j < 3; j++) {
+ for (k = 0; k < 3; k++) {
+ F[i][j][k] = F_tmp[j][k];
+ }
+ }
+ }
+
+ comm->forward_comm(this);
+
+ // Second loop through neighbors
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
+
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbit)) continue;
+
+ jtype = type[j];
+ r[0] = x[i][0] - x[j][0];
+ r[1] = x[i][1] - x[j][1];
+ r[2] = x[i][2] - x[j][2];
+ rsq = lensq3(r);
+
+ // Only include contributions from atoms that are CURRENTLY neighbors
+ if (cut_style == TYPE) {
+ if (rsq >= cutsq[itype][jtype]) continue;
+ } else if (cut_style == CUSTOM) {
+ if (rsq >= cutsq_custom) continue;
+ } else {
+ radsum = radius[i] + radius[j];
+ if (rsq >= radsum * radsum) continue;
+ }
+
+ r0[0] = x0[i][0] - x0[j][0];
+ r0[1] = x0[i][1] - x0[j][1];
+ r0[2] = x0[i][2] - x0[j][2];
+ minimum_image0(r0);
+
+ // E * r0
+ for (k = 0; k < 3; k++) {
+ temp[k] = 0.0;
+ for (l = 0; l < 3; l++)
+ temp[k] += F[i][k][l] * r0[l];
+ }
+
+ sub3(r, temp, temp);
+ array_atom[i][0] += lensq3(temp);
+ norm[i] += 1;
+
+ if (newton_pair || j < nlocal) {
+ for (k = 0; k < 3; k++) {
+ temp[k] = 0.0;
+ for (l = 0; l < 3; l++)
+ temp[k] += F[j][k][l] * r0[l];
+ }
+
+ sub3(r, temp, temp);
+ array_atom[j][0] += lensq3(temp);
+ norm[j] += 1;
+ }
+ }
+ }
+
+ comm_flag = 1;
+ if (newton_pair) comm->reverse_comm(this, 2);
+
+ for (i = 0; i < nlocal; i++) {
+ if (!(mask[i] & groupbit)) continue;
+
+ if (norm[i] != 0)
+ array_atom[i][0] /= norm[i];
+ else
+ array_atom[i][0] = 0.0;
+ array_atom[i][0] = sqrt(array_atom[i][0]);
+
+ for (j = 0; j < 3; j++)
+ for (k = 0; k < 3; k++)
+ F_tmp[j][k] = F[i][j][k];
+
+ transpose_times3(F_tmp, F_tmp, E);
+ for (j = 0; j < dim; j++) E[j][j] -= 1.0;
+
+ evol = (E[0][0] + E[1][1] + E[2][2]) / dim;
+
+ // Calculate deviatoric strain
+ for (j = 0; j < dim; j++) E[j][j] -= evol;
+ j2 = 0.0;
+ for (j = 0; j < 3; j++)
+ for (k = 0; k < 3; k++)
+ j2 += E[j][k] * E[j][k];
+
+ edev = sqrt(0.5 * j2);
+
+ array_atom[i][1] = evol;
+ array_atom[i][2] = edev;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNonaffineDisplacement::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i, m, last, k, l;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (comm_flag == 0) {
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l++) {
+ buf[m++] = X[i][k][l];
+ buf[m++] = Y[i][k][l];
+ }
+ }
+ } else {
+ buf[m++] = array_atom[i][0];
+ buf[m++] = ubuf(norm[i]).d;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i, j, m, k, l;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ if (comm_flag == 0) {
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l++) {
+ X[j][k][l] += buf[m++];
+ Y[j][k][l] += buf[m++];
+ }
+ }
+ } else {
+ array_atom[j][0] += buf[m++];
+ norm[j] += (int) ubuf(buf[m++]).i;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNonaffineDisplacement::pack_forward_comm(int n, int *list, double *buf,
+ int /*pbc_flag*/, int * /*pbc*/)
+{
+ int i, j, m, k, l;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l ++) {
+ buf[m++] = F[j][k][l];
+ }
+ }
+ }
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i, m, last, k, l;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ for (k = 0; k < 3; k++) {
+ for (l = 0; l < 3; l ++) {
+ F[i][k][l] = buf[m++];
+ }
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::minimum_image0(double *delta)
+{
+ if (domain->triclinic == 0) {
+ if (domain->xperiodic) {
+ while (fabs(delta[0]) > xprd0_half) {
+ if (delta[0] < 0.0) delta[0] += xprd0;
+ else delta[0] -= xprd0;
+ }
+ }
+ if (domain->yperiodic) {
+ while (fabs(delta[1]) > yprd0_half) {
+ if (delta[1] < 0.0) delta[1] += yprd0;
+ else delta[1] -= yprd0;
+ }
+ }
+ if (domain->zperiodic) {
+ while (fabs(delta[2]) > zprd0_half) {
+ if (delta[2] < 0.0) delta[2] += zprd0;
+ else delta[2] -= zprd0;
+ }
+ }
+
+ } else {
+ if (domain->zperiodic) {
+ while (fabs(delta[2]) > zprd0_half) {
+ if (delta[2] < 0.0) {
+ delta[2] += zprd0;
+ delta[1] += yz0;
+ delta[0] += xz0;
+ } else {
+ delta[2] -= zprd0;
+ delta[1] -= yz0;
+ delta[0] -= xz0;
+ }
+ }
+ }
+ if (domain->yperiodic) {
+ while (fabs(delta[1]) > yprd0_half) {
+ if (delta[1] < 0.0) {
+ delta[1] += yprd0;
+ delta[0] += xy0;
+ } else {
+ delta[1] -= yprd0;
+ delta[0] -= xy0;
+ }
+ }
+ }
+ if (domain->xperiodic) {
+ while (fabs(delta[0]) > xprd0_half) {
+ if (delta[0] < 0.0) delta[0] += xprd0;
+ else delta[0] -= xprd0;
+ }
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNonaffineDisplacement::grow_arrays(int nmax_new)
+{
+ nmax = nmax_new;
+ memory->destroy(X);
+ memory->destroy(Y);
+ memory->destroy(F);
+ memory->destroy(norm);
+ memory->create(X, nmax, 3, 3, "fix_nonaffine_displacement:X");
+ memory->create(Y, nmax, 3, 3, "fix_nonaffine_displacement:Y");
+ memory->create(F, nmax, 3, 3, "fix_nonaffine_displacement:F");
+ memory->create(norm, nmax, "fix_nonaffine_displacement:norm");
+}
diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.h b/src/EXTRA-FIX/fix_nonaffine_displacement.h
new file mode 100644
index 0000000000..0a195dc08e
--- /dev/null
+++ b/src/EXTRA-FIX/fix_nonaffine_displacement.h
@@ -0,0 +1,71 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(nonaffine/displacement,FixNonaffineDisplacement)
+// clang-format on
+#else
+
+#ifndef LMP_FIX_NONAFFINE_DISPLACEMENT_H
+#define LMP_FIX_NONAFFINE_DISPLACEMENT_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixNonaffineDisplacement : public Fix {
+ public:
+ FixNonaffineDisplacement(class LAMMPS *, int, char **);
+ ~FixNonaffineDisplacement() override;
+ int setmask() override;
+ void post_constructor() override;
+ void init() override;
+ void init_list(int, class NeighList *) override;
+ void setup(int);
+ void post_force(int) override;
+ void write_restart(FILE *fp) override;
+ void restart(char *buf) override;
+ int pack_forward_comm(int, int *, double *, int, int *) override;
+ void unpack_forward_comm(int, int, double *) override;
+ int pack_reverse_comm(int, int, double *) override;
+ void unpack_reverse_comm(int, int *, double *) override;
+
+ private:
+ double dtv;
+ char *id_fix;
+ class FixStoreAtom *fix;
+ int nmax, comm_flag;
+ int nad_style, cut_style;
+ int reference_style, offset_timestep, reference_timestep, update_timestep;
+ int reference_saved;
+ double cutoff_custom, cutsq_custom, mycutneigh;
+ double xprd0, yprd0, zprd0, xprd0_half, yprd0_half, zprd0_half, xy0, xz0, yz0;
+
+ double ***X, ***Y, ***F;
+ int *norm;
+
+ class NeighList *list; // half neighbor list
+
+
+ void integrate_velocity();
+ void calculate_D2Min();
+ void save_reference_state();
+ void minimum_image0(double *);
+ void grow_arrays(int);
+};
+
+} // namespace LAMMPS_NS
+
+#endif
+#endif
diff --git a/src/GRANULAR/compute_fabric.cpp b/src/GRANULAR/compute_fabric.cpp
index fb95a8b446..adaf242c92 100644
--- a/src/GRANULAR/compute_fabric.cpp
+++ b/src/GRANULAR/compute_fabric.cpp
@@ -11,6 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
#include "compute_fabric.h"
#include "atom.h"
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index 489efc55a0..4be74334c9 100755
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -177,6 +177,10 @@ action fix_shardlow_kokkos.cpp fix_shardlow.cpp
action fix_shardlow_kokkos.h fix_shardlow.h
action fix_spring_self_kokkos.cpp
action fix_spring_self_kokkos.h
+action fix_temp_berendsen_kokkos.cpp
+action fix_temp_berendsen_kokkos.h
+action fix_temp_rescale_kokkos.cpp
+action fix_temp_rescale_kokkos.h
action fix_viscous_kokkos.cpp
action fix_viscous_kokkos.h
action fix_wall_gran_kokkos.cpp fix_wall_gran.cpp
diff --git a/src/KOKKOS/fix_reaxff_bonds_kokkos.h b/src/KOKKOS/fix_reaxff_bonds_kokkos.h
index 29c8d457fd..89eb539ca8 100644
--- a/src/KOKKOS/fix_reaxff_bonds_kokkos.h
+++ b/src/KOKKOS/fix_reaxff_bonds_kokkos.h
@@ -16,9 +16,6 @@
FixStyle(reaxff/bonds/kk,FixReaxFFBondsKokkos);
FixStyle(reaxff/bonds/kk/device,FixReaxFFBondsKokkos);
FixStyle(reaxff/bonds/kk/host,FixReaxFFBondsKokkos);
-FixStyle(reax/c/bonds/kk,FixReaxFFBondsKokkos);
-FixStyle(reax/c/bonds/kk/device,FixReaxFFBondsKokkos);
-FixStyle(reax/c/bonds/kk/host,FixReaxFFBondsKokkos);
// clang-format on
#else
diff --git a/src/KOKKOS/fix_reaxff_species_kokkos.h b/src/KOKKOS/fix_reaxff_species_kokkos.h
index 1848825a19..0500c6febf 100644
--- a/src/KOKKOS/fix_reaxff_species_kokkos.h
+++ b/src/KOKKOS/fix_reaxff_species_kokkos.h
@@ -16,9 +16,6 @@
FixStyle(reaxff/species/kk,FixReaxFFSpeciesKokkos);
FixStyle(reaxff/species/kk/device,FixReaxFFSpeciesKokkos);
FixStyle(reaxff/species/kk/host,FixReaxFFSpeciesKokkos);
-FixStyle(reax/c/species/kk,FixReaxFFSpeciesKokkos);
-FixStyle(reax/c/species/kk/device,FixReaxFFSpeciesKokkos);
-FixStyle(reax/c/species/kk/host,FixReaxFFSpeciesKokkos);
// clang-format on
#else
diff --git a/src/KOKKOS/fix_temp_berendsen_kokkos.cpp b/src/KOKKOS/fix_temp_berendsen_kokkos.cpp
new file mode 100644
index 0000000000..b986b3189a
--- /dev/null
+++ b/src/KOKKOS/fix_temp_berendsen_kokkos.cpp
@@ -0,0 +1,135 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_temp_berendsen_kokkos.h"
+
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "compute.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
+#include "input.h"
+#include "modify.h"
+#include "update.h"
+#include "variable.h"
+#include "atom_masks.h"
+
+#include
+#include
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum{NOBIAS,BIAS};
+enum{CONSTANT,EQUAL};
+
+/* ---------------------------------------------------------------------- */
+
+template
+FixTempBerendsenKokkos::FixTempBerendsenKokkos(LAMMPS *lmp, int narg, char **arg) :
+ FixTempBerendsen(lmp, narg, arg)
+{
+ kokkosable = 1;
+ atomKK = (AtomKokkos *)atom;
+ execution_space = ExecutionSpaceFromDevice::space;
+
+ datamask_read = EMPTY_MASK;
+ datamask_modify = EMPTY_MASK;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template
+void FixTempBerendsenKokkos::end_of_step()
+{
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ double t_current = temperature->compute_scalar();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+
+ double tdof = temperature->dof;
+
+ // there is nothing to do, if there are no degrees of freedom
+
+ if (tdof < 1) return;
+
+ if (t_current == 0.0)
+ error->all(FLERR, "Computed current temperature for fix temp/berendsen must not be 0.0");
+
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ // set current t_target
+ // if variable temp, evaluate variable, wrap with clear/add
+
+ if (tstyle == CONSTANT)
+ t_target = t_start + delta * (t_stop-t_start);
+ else {
+ modify->clearstep_compute();
+ t_target = input->variable->compute_equal(tvar);
+ if (t_target < 0.0)
+ error->one(FLERR, "Fix temp/berendsen variable {} returned negative temperature",
+ input->variable->names[tvar]);
+ modify->addstep_compute(update->ntimestep + nevery);
+ }
+
+ // rescale velocities by lamda
+ // for BIAS:
+ // temperature is current, so do not need to re-compute
+ // OK to not test returned v = 0, since lamda is multiplied by v
+
+ double lamda = sqrt(1.0 + update->dt/t_period*(t_target/t_current - 1.0));
+ double efactor = 0.5 * force->boltz * tdof;
+ energy += t_current * (1.0-lamda*lamda) * efactor;
+
+ auto v = atomKK->k_v.view();
+ auto mask = atomKK->k_mask.view();
+ int nlocal = atom->nlocal;
+ auto groupbit = this->groupbit;
+
+ if (which == NOBIAS) {
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ temperature->remove_bias_all();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+ }
+
+ atomKK->sync(execution_space,V_MASK|MASK_MASK);
+
+ Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal), LAMMPS_LAMBDA(int i) {
+ if (mask[i] & groupbit) {
+ v(i,0) *= lamda;
+ v(i,1) *= lamda;
+ v(i,2) *= lamda;
+ }
+ });
+
+ atomKK->modified(execution_space,V_MASK);
+
+ if (which == NOBIAS) {
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ temperature->restore_bias_all();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+ }
+}
+/* ---------------------------------------------------------------------- */
+
+namespace LAMMPS_NS {
+template class FixTempBerendsenKokkos;
+#ifdef LMP_KOKKOS_GPU
+template class FixTempBerendsenKokkos;
+#endif
+}
diff --git a/src/KOKKOS/fix_temp_berendsen_kokkos.h b/src/KOKKOS/fix_temp_berendsen_kokkos.h
new file mode 100644
index 0000000000..6a0aa5ce98
--- /dev/null
+++ b/src/KOKKOS/fix_temp_berendsen_kokkos.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(temp/berendsen/kk,FixTempBerendsenKokkos);
+FixStyle(temp/berendsen/kk/device,FixTempBerendsenKokkos);
+FixStyle(temp/berendsen/kk/host,FixTempBerendsenKokkos);
+// clang-format on
+#else
+
+// clang-format off
+#ifndef LMP_FIX_TEMP_BERENDSEN_KOKKOS_H
+#define LMP_FIX_TEMP_BERENDSEN_KOKKOS_H
+
+#include "fix_temp_berendsen.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+template
+class FixTempBerendsenKokkos : public FixTempBerendsen {
+ public:
+ typedef DeviceType device_type;
+
+ FixTempBerendsenKokkos(class LAMMPS *, int, char **);
+ ~FixTempBerendsenKokkos() override {}
+ void end_of_step() override;
+};
+
+} // namespace LAMMPS_NS
+
+#endif
+#endif
diff --git a/src/KOKKOS/fix_temp_rescale_kokkos.cpp b/src/KOKKOS/fix_temp_rescale_kokkos.cpp
new file mode 100644
index 0000000000..3a1c6ddd26
--- /dev/null
+++ b/src/KOKKOS/fix_temp_rescale_kokkos.cpp
@@ -0,0 +1,140 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_temp_rescale_kokkos.h"
+
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "compute.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
+#include "input.h"
+#include "modify.h"
+#include "update.h"
+#include "variable.h"
+#include "atom_masks.h"
+
+#include
+#include
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum{NOBIAS,BIAS};
+enum{CONSTANT,EQUAL};
+
+/* ---------------------------------------------------------------------- */
+
+template
+FixTempRescaleKokkos::FixTempRescaleKokkos(LAMMPS *lmp, int narg, char **arg) :
+ FixTempRescale(lmp, narg, arg)
+{
+ kokkosable = 1;
+ atomKK = (AtomKokkos *)atom;
+ execution_space = ExecutionSpaceFromDevice::space;
+
+ datamask_read = EMPTY_MASK;
+ datamask_modify = EMPTY_MASK;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template
+void FixTempRescaleKokkos::end_of_step()
+{
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ double t_current = temperature->compute_scalar();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+
+ // there is nothing to do, if there are no degrees of freedom
+
+ if (temperature->dof < 1) return;
+
+ // protect against division by zero
+
+ if (t_current == 0.0)
+ error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0");
+
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ // set current t_target
+ // if variable temp, evaluate variable, wrap with clear/add
+
+ if (tstyle == CONSTANT)
+ t_target = t_start + delta * (t_stop-t_start);
+ else {
+ modify->clearstep_compute();
+ t_target = input->variable->compute_equal(tvar);
+ if (t_target < 0.0)
+ error->one(FLERR, "Fix temp/rescale variable returned negative temperature");
+ modify->addstep_compute(update->ntimestep + nevery);
+ }
+
+ // rescale velocity of appropriate atoms if outside window
+ // for BIAS:
+ // temperature is current, so do not need to re-compute
+ // OK to not test returned v = 0, since factor is multiplied by v
+
+ if (fabs(t_current-t_target) > t_window) {
+ t_target = t_current - fraction*(t_current-t_target);
+ double factor = sqrt(t_target/t_current);
+ double efactor = 0.5 * force->boltz * temperature->dof;
+
+ energy += (t_current-t_target) * efactor;
+
+ auto v = atomKK->k_v.view();
+ auto mask = atomKK->k_mask.view();
+ int nlocal = atom->nlocal;
+ auto groupbit = this->groupbit;
+
+ if (which == NOBIAS) {
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ temperature->remove_bias_all();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+ }
+
+ atomKK->sync(execution_space,V_MASK|MASK_MASK);
+
+ Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal), LAMMPS_LAMBDA(int i) {
+ if (mask[i] & groupbit) {
+ v(i,0) *= factor;
+ v(i,1) *= factor;
+ v(i,2) *= factor;
+ }
+ });
+
+ atomKK->modified(execution_space,V_MASK);
+
+ if (which == NOBIAS) {
+ atomKK->sync(temperature->execution_space,temperature->datamask_read);
+ temperature->restore_bias_all();
+ atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+ atomKK->sync(execution_space,temperature->datamask_modify);
+
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+namespace LAMMPS_NS {
+template class FixTempRescaleKokkos;
+#ifdef LMP_KOKKOS_GPU
+template class FixTempRescaleKokkos;
+#endif
+}
diff --git a/src/KOKKOS/fix_temp_rescale_kokkos.h b/src/KOKKOS/fix_temp_rescale_kokkos.h
new file mode 100644
index 0000000000..7dd3111325
--- /dev/null
+++ b/src/KOKKOS/fix_temp_rescale_kokkos.h
@@ -0,0 +1,44 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS development team: developers@lammps.org
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(temp/rescale/kk,FixTempRescaleKokkos);
+FixStyle(temp/rescale/kk/device,FixTempRescaleKokkos);
+FixStyle(temp/rescale/kk/host,FixTempRescaleKokkos);
+// clang-format on
+#else
+
+// clang-format off
+#ifndef LMP_FIX_TEMP_RESCALE_KOKKOS_H
+#define LMP_FIX_TEMP_RESCALE_KOKKOS_H
+
+#include "fix_temp_rescale.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+template
+class FixTempRescaleKokkos : public FixTempRescale {
+ public:
+ typedef DeviceType device_type;
+
+ FixTempRescaleKokkos(class LAMMPS *, int, char **);
+ ~FixTempRescaleKokkos() override {}
+ void end_of_step() override;
+};
+
+} // namespace LAMMPS_NS
+
+#endif
+#endif
diff --git a/src/KOKKOS/pair_pace_extrapolation_kokkos.cpp b/src/KOKKOS/pair_pace_extrapolation_kokkos.cpp
index 61722bf62d..0980ad776d 100644
--- a/src/KOKKOS/pair_pace_extrapolation_kokkos.cpp
+++ b/src/KOKKOS/pair_pace_extrapolation_kokkos.cpp
@@ -123,6 +123,10 @@ void PairPACEExtrapolationKokkos::grow(int natom, int maxneigh)
// hard-core repulsion
MemKK::realloc_kokkos(rho_core, "pace:rho_core", natom);
MemKK::realloc_kokkos(dF_drho_core, "pace:dF_drho_core", natom);
+ MemKK::realloc_kokkos(dF_dfcut, "pace:dF_dfcut", natom);
+ MemKK::realloc_kokkos(d_d_min, "pace:r_min_pair", natom);
+ MemKK::realloc_kokkos(d_jj_min, "pace:j_min_pair", natom);
+ MemKK::realloc_kokkos(d_corerep, "pace:corerep", natom); // per-atom corerep
MemKK::realloc_kokkos(dB_flatten, "pace:dB_flatten", natom, idx_ms_combs_max, basis_set->rankmax);
@@ -219,6 +223,24 @@ void PairPACEExtrapolationKokkos::copy_pertype()
Kokkos::deep_copy(d_wpre, h_wpre);
Kokkos::deep_copy(d_mexp, h_mexp);
+
+
+ // ZBL core-rep
+ MemKK::realloc_kokkos(d_cut_in, "pace:d_cut_in", nelements, nelements);
+ MemKK::realloc_kokkos(d_dcut_in, "pace:d_dcut_in", nelements, nelements);
+ auto h_cut_in = Kokkos::create_mirror_view(d_cut_in);
+ auto h_dcut_in = Kokkos::create_mirror_view(d_dcut_in);
+
+ for (int mu_i = 0; mu_i < nelements; ++mu_i) {
+ for (int mu_j = 0; mu_j < nelements; ++mu_j) {
+ h_cut_in(mu_i,mu_j) = basis_set->map_bond_specifications.at({mu_i,mu_j}).rcut_in;
+ h_dcut_in(mu_i,mu_j) = basis_set->map_bond_specifications.at({mu_i,mu_j}).dcut_in;
+ }
+ }
+ Kokkos::deep_copy(d_cut_in, h_cut_in);
+ Kokkos::deep_copy(d_dcut_in, h_dcut_in);
+
+ is_zbl = basis_set->radial_functions->inner_cutoff_type == "zbl";
}
/* ---------------------------------------------------------------------- */
@@ -573,13 +595,20 @@ void PairPACEExtrapolationKokkos::compute(int eflag_in, int vflag_in
d_vatom = k_vatom.view();
}
- if (gamma_flag && atom->nlocal > nmax) {
+ if (flag_compute_extrapolation_grade && atom->nlocal > nmax) {
memory->destroy(extrapolation_grade_gamma);
nmax = atom->nlocal;
memory->create(extrapolation_grade_gamma, nmax, "pace/atom:gamma");
//zeroify array
memset(extrapolation_grade_gamma, 0, nmax * sizeof(*extrapolation_grade_gamma));
}
+ if (flag_corerep_factor && atom->nlocal > nmax_corerep) {
+ memory->destroy(corerep_factor);
+ nmax_corerep = atom->nlocal;
+ memory->create(corerep_factor, nmax_corerep, "pace/atom:corerep");
+ //zeroify array
+ memset(corerep_factor, 0, nmax_corerep * sizeof(*corerep_factor));
+ }
copymode = 1;
if (!force->newton_pair)
@@ -631,8 +660,13 @@ void PairPACEExtrapolationKokkos::compute(int eflag_in, int vflag_in
Kokkos::deep_copy(A_rank1, 0.0);
Kokkos::deep_copy(rhos, 0.0);
+ Kokkos::deep_copy(rho_core, 0.0);
+ Kokkos::deep_copy(d_d_min, PairPACEExtrapolation::aceimpl->basis_set->cutoffmax);
+ Kokkos::deep_copy(d_jj_min, -1);
+
Kokkos::deep_copy(projections, 0.0);
Kokkos::deep_copy(d_gamma, 0.0);
+ Kokkos::deep_copy(d_corerep, 0.0);
EV_FLOAT ev_tmp;
@@ -696,7 +730,7 @@ void PairPACEExtrapolationKokkos::compute(int eflag_in, int vflag_in
}
//ComputeGamma
- if (gamma_flag) {
+ if (flag_compute_extrapolation_grade) {
typename Kokkos::RangePolicy policy_gamma(0,chunk_size);
Kokkos::parallel_for("ComputeGamma",policy_gamma,*this);
}
@@ -738,12 +772,17 @@ void PairPACEExtrapolationKokkos::compute(int eflag_in, int vflag_in
}
ev += ev_tmp;
- //if gamma_flag - copy current d_gamma to extrapolation_grade_gamma
- if (gamma_flag){
+ //if flag_compute_extrapolation_grade - copy current d_gamma to extrapolation_grade_gamma
+ if (flag_compute_extrapolation_grade){
h_gamma = Kokkos::create_mirror_view(d_gamma);
Kokkos::deep_copy(h_gamma, d_gamma);
memcpy(extrapolation_grade_gamma+chunk_offset, (void *) h_gamma.data(), sizeof(double)*chunk_size);
}
+ if (flag_corerep_factor) {
+ h_corerep = Kokkos::create_mirror_view(d_corerep);
+ Kokkos::deep_copy(h_corerep,d_corerep);
+ memcpy(corerep_factor+chunk_offset, (void *) h_corerep.data(), sizeof(double)*chunk_size);
+ }
chunk_offset += chunk_size;
} // end while
@@ -799,6 +838,7 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeNeig
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
+ const int mu_i = d_map(type(i));
// get a pointer to scratch memory
// This is used to cache whether or not an atom is within the cutoff
@@ -858,6 +898,36 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeNeig
}
offset++;
});
+
+ if (is_zbl) {
+ //adapted from https://www.osti.gov/servlets/purl/1429450
+ if (ncount > 0) {
+ using minloc_value_type=Kokkos::MinLoc::value_type;
+ minloc_value_type djjmin;
+ djjmin.val=1e20;
+ djjmin.loc=-1;
+ Kokkos::MinLoc reducer_scalar(djjmin);
+ // loop over ncount (actual neighbours withing cutoff) rather than jnum (total number of neigh in cutoff+skin)
+ Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team, ncount),
+ [&](const int offset, minloc_value_type &min_d_dist) {
+ int j = d_nearest(ii,offset);
+ j &= NEIGHMASK;
+ const int jtype = type(j);
+ auto r = d_rnorms(ii,offset);
+ const int mu_j = d_map(type(j));
+ const F_FLOAT d = r - (d_cut_in(mu_i, mu_j) - d_dcut_in(mu_i, mu_j));
+ if (d < min_d_dist.val) {
+ min_d_dist.val = d;
+ min_d_dist.loc = offset;
+ }
+ }, reducer_scalar);
+ d_d_min(ii) = djjmin.val;
+ d_jj_min(ii) = djjmin.loc;// d_jj_min should be NOT in 0..jnum range, but in 0..d_ncount(<=jnum)
+ } else {
+ d_d_min(ii) = 1e20;
+ d_jj_min(ii) = -1;
+ }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -998,7 +1068,7 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeRho,
//gamma_i
- if (gamma_flag)
+ if (flag_compute_extrapolation_grade)
Kokkos::atomic_add(&projections(ii, func_ind), d_gen_cgs(mu_i, idx_ms_comb) * A_cur);
} else { // rank > 1
@@ -1037,7 +1107,7 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeRho,
Kokkos::atomic_add(&rhos(ii, p), B.real_part_product(d_coeffs(mu_i, func_ind, p) * d_gen_cgs(mu_i, idx_ms_comb)));
}
//gamma_i
- if (gamma_flag)
+ if (flag_compute_extrapolation_grade)
Kokkos::atomic_add(&projections(ii, func_ind), B.real_part_product(d_gen_cgs(mu_i, idx_ms_comb)));
}
}
@@ -1056,23 +1126,45 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeFS,
const int ndensity = d_ndensity(mu_i);
double evdwl, fcut, dfcut;
+ double evdwl_cut;
evdwl = fcut = dfcut = 0.0;
inner_cutoff(rho_core(ii), rho_cut, drho_cut, fcut, dfcut);
FS_values_and_derivatives(ii, evdwl, mu_i);
- dF_drho_core(ii) = evdwl * dfcut + 1;
+ if (is_zbl) {
+ if (d_jj_min(ii) != -1) {
+ const int mu_jmin = d_mu(ii,d_jj_min(ii));
+ F_FLOAT dcutin = d_dcut_in(mu_i, mu_jmin);
+ F_FLOAT transition_coordinate = dcutin - d_d_min(ii); // == cutin - r_min
+ cutoff_func_poly(transition_coordinate, dcutin, dcutin, fcut, dfcut);
+ dfcut = -dfcut; // invert, because rho_core = cutin - r_min
+ } else {
+ // no neighbours
+ fcut = 1;
+ dfcut = 0;
+ }
+ evdwl_cut = evdwl * fcut + rho_core(ii) * (1 - fcut); // evdwl * fcut + rho_core_uncut - rho_core_uncut* fcut
+ dF_drho_core(ii) = 1 - fcut;
+ dF_dfcut(ii) = evdwl * dfcut - rho_core(ii) * dfcut;
+ } else {
+ inner_cutoff(rho_core(ii), rho_cut, drho_cut, fcut, dfcut);
+ dF_drho_core(ii) = evdwl * dfcut + 1;
+ evdwl_cut = evdwl * fcut + rho_core(ii);
+ }
for (int p = 0; p < ndensity; ++p)
dF_drho(ii, p) *= fcut;
// tally energy contribution
if (eflag) {
- double evdwl_cut = evdwl * fcut + rho_core(ii);
// E0 shift
evdwl_cut += d_E0vals(mu_i);
e_atom(ii) = evdwl_cut;
}
+
+ if (flag_corerep_factor)
+ d_corerep(ii) = 1-fcut;
}
/* ---------------------------------------------------------------------- */
@@ -1240,6 +1332,15 @@ void PairPACEExtrapolationKokkos::operator() (TagPairPACEComputeDeri
f_ij(ii, jj, 0) = scale * f_ji[0] + fpair * r_hat[0];
f_ij(ii, jj, 1) = scale * f_ji[1] + fpair * r_hat[1];
f_ij(ii, jj, 2) = scale * f_ji[2] + fpair * r_hat[2];
+
+ if (is_zbl) {
+ if (jj==d_jj_min(ii)) {
+ // DCRU = 1.0
+ f_ij(ii, jj, 0) += dF_dfcut(ii) * r_hat[0];
+ f_ij(ii, jj, 1) += dF_dfcut(ii) * r_hat[1];
+ f_ij(ii, jj, 2) += dF_dfcut(ii) * r_hat[2];
+ }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -1777,6 +1878,8 @@ double PairPACEExtrapolationKokkos::memory_usage()
bytes += MemKK::memory_usage(weights_rank1);
bytes += MemKK::memory_usage(rho_core);
bytes += MemKK::memory_usage(dF_drho_core);
+ bytes += MemKK::memory_usage(dF_dfcut);
+ bytes += MemKK::memory_usage(d_corerep);
bytes += MemKK::memory_usage(dB_flatten);
bytes += MemKK::memory_usage(fr);
bytes += MemKK::memory_usage(dfr);
@@ -1794,6 +1897,8 @@ double PairPACEExtrapolationKokkos::memory_usage()
bytes += MemKK::memory_usage(d_mu);
bytes += MemKK::memory_usage(d_rhats);
bytes += MemKK::memory_usage(d_rnorms);
+ bytes += MemKK::memory_usage(d_d_min);
+ bytes += MemKK::memory_usage(d_jj_min);
bytes += MemKK::memory_usage(d_nearest);
bytes += MemKK::memory_usage(f_ij);
bytes += MemKK::memory_usage(d_rho_core_cutoff);
@@ -1842,9 +1947,10 @@ double PairPACEExtrapolationKokkos::memory_usage()
template
void *PairPACEExtrapolationKokkos::extract(const char *str, int &dim)
{
- //check if str=="gamma_flag" then compute extrapolation grades on this iteration
dim = 0;
- if (strcmp(str, "gamma_flag") == 0) return (void *) &gamma_flag;
+ //check if str=="flag_compute_extrapolation_grade" then compute extrapolation grades on this iteration
+ if (strcmp(str, "gamma_flag") == 0) return (void *) &flag_compute_extrapolation_grade;
+ if (strcmp(str, "corerep_flag") == 0) return (void *) &flag_corerep_factor;
dim = 2;
if (strcmp(str, "scale") == 0) return (void *) scale;
@@ -1867,6 +1973,10 @@ void *PairPACEExtrapolationKokkos::extract_peratom(const char *str,
ncol = 0;
return (void *) extrapolation_grade_gamma;
}
+ if (strcmp(str, "corerep") == 0) {
+ ncol = 0;
+ return (void *) corerep_factor;
+ }
return nullptr;
}
diff --git a/src/KOKKOS/pair_pace_extrapolation_kokkos.h b/src/KOKKOS/pair_pace_extrapolation_kokkos.h
index 55bcf4fead..aa6c49c36d 100644
--- a/src/KOKKOS/pair_pace_extrapolation_kokkos.h
+++ b/src/KOKKOS/pair_pace_extrapolation_kokkos.h
@@ -106,7 +106,6 @@ class PairPACEExtrapolationKokkos : public PairPACEExtrapolation {
protected:
int inum, maxneigh, chunk_size, chunk_offset, idx_ms_combs_max, total_num_functions_max;
int host_flag;
- int gamma_flag;
int eflag, vflag;
@@ -130,6 +129,7 @@ class PairPACEExtrapolationKokkos : public PairPACEExtrapolation {
tdual_fparams k_cutsq, k_scale;
typedef Kokkos::View t_fparams;
t_fparams d_cutsq, d_scale;
+ t_fparams d_cut_in, d_dcut_in; // inner cutoff
typename AT::t_int_1d d_map;
@@ -234,12 +234,16 @@ class PairPACEExtrapolationKokkos : public PairPACEExtrapolation {
t_ace_2d rhos;
t_ace_2d dF_drho;
+ t_ace_3c dB_flatten;
+
// hard-core repulsion
t_ace_1d rho_core;
- t_ace_3c dB_flatten;
t_ace_2d cr;
t_ace_2d dcr;
t_ace_1d dF_drho_core;
+ t_ace_1d dF_dfcut;
+ t_ace_1d d_corerep;
+ th_ace_1d h_corerep;
// radial functions
t_ace_4d fr;
@@ -282,6 +286,11 @@ class PairPACEExtrapolationKokkos : public PairPACEExtrapolation {
t_ace_3d3 d_rhats;
t_ace_2i d_nearest;
+ // for ZBL core-rep implementation
+ t_ace_1d d_d_min; // [i] -> min-d for atom ii, d=d = r - (cut_in(mu_i, mu_j) - dcut_in(mu_i, mu_j))
+ t_ace_1i d_jj_min; // [i] -> jj-index of nearest neigh (by r-(cut_in-dcut_in) criterion)
+ bool is_zbl;
+
// per-type
t_ace_1i d_ndensity;
t_ace_1i d_npoti;
diff --git a/src/KOKKOS/pair_pace_kokkos.cpp b/src/KOKKOS/pair_pace_kokkos.cpp
index 153a6d0333..805d7f68bb 100644
--- a/src/KOKKOS/pair_pace_kokkos.cpp
+++ b/src/KOKKOS/pair_pace_kokkos.cpp
@@ -121,6 +121,11 @@ void PairPACEKokkos::grow(int natom, int maxneigh)
// hard-core repulsion
MemKK::realloc_kokkos(rho_core, "pace:rho_core", natom);
MemKK::realloc_kokkos(dF_drho_core, "pace:dF_drho_core", natom);
+ MemKK::realloc_kokkos(dF_dfcut, "pace:dF_dfcut", natom);
+ MemKK::realloc_kokkos(d_d_min, "pace:r_min_pair", natom);
+ MemKK::realloc_kokkos(d_jj_min, "pace:j_min_pair", natom);
+ MemKK::realloc_kokkos(d_corerep, "pace:corerep", natom); // per-atom corerep
+
MemKK::realloc_kokkos(dB_flatten, "pace:dB_flatten", natom, idx_rho_max, basis_set->rankmax);
}
@@ -212,6 +217,23 @@ void PairPACEKokkos::copy_pertype()
Kokkos::deep_copy(d_wpre, h_wpre);
Kokkos::deep_copy(d_mexp, h_mexp);
+
+ // ZBL core-rep
+ MemKK::realloc_kokkos(d_cut_in, "pace:d_cut_in", nelements, nelements);
+ MemKK::realloc_kokkos(d_dcut_in, "pace:d_dcut_in", nelements, nelements);
+ auto h_cut_in = Kokkos::create_mirror_view(d_cut_in);
+ auto h_dcut_in = Kokkos::create_mirror_view(d_dcut_in);
+
+ for (int mu_i = 0; mu_i < nelements; ++mu_i) {
+ for (int mu_j = 0; mu_j < nelements; ++mu_j) {
+ h_cut_in(mu_i,mu_j) = basis_set->map_bond_specifications.at({mu_i,mu_j}).rcut_in;
+ h_dcut_in(mu_i,mu_j) = basis_set->map_bond_specifications.at({mu_i,mu_j}).dcut_in;
+ }
+ }
+ Kokkos::deep_copy(d_cut_in, h_cut_in);
+ Kokkos::deep_copy(d_dcut_in, h_dcut_in);
+
+ is_zbl = basis_set->radial_functions->inner_cutoff_type == "zbl";
}
/* ---------------------------------------------------------------------- */
@@ -535,6 +557,13 @@ void PairPACEKokkos::compute(int eflag_in, int vflag_in)
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom");
d_vatom = k_vatom.view();
}
+ if (flag_corerep_factor && atom->nlocal > nmax_corerep) {
+ memory->destroy(corerep_factor);
+ nmax_corerep = atom->nlocal;
+ memory->create(corerep_factor, nmax_corerep, "pace/atom:corerep");
+ //zeroify array
+ memset(corerep_factor, 0, nmax_corerep * sizeof(*corerep_factor));
+ }
copymode = 1;
if (!force->newton_pair)
@@ -588,6 +617,9 @@ void PairPACEKokkos::compute(int eflag_in, int vflag_in)
Kokkos::deep_copy(A_rank1, 0.0);
Kokkos::deep_copy(rhos, 0.0);
Kokkos::deep_copy(rho_core, 0.0);
+ Kokkos::deep_copy(d_d_min, PairPACE::aceimpl->basis_set->cutoffmax);
+ Kokkos::deep_copy(d_jj_min, -1);
+ Kokkos::deep_copy(d_corerep, 0.0);
EV_FLOAT ev_tmp;
@@ -686,6 +718,13 @@ void PairPACEKokkos::compute(int eflag_in, int vflag_in)
}
}
ev += ev_tmp;
+
+ if (flag_corerep_factor) {
+ h_corerep = Kokkos::create_mirror_view(d_corerep);
+ Kokkos::deep_copy(h_corerep,d_corerep);
+ memcpy(corerep_factor+chunk_offset, (void *) h_corerep.data(), sizeof(double)*chunk_size);
+ }
+
chunk_offset += chunk_size;
} // end while
@@ -741,6 +780,7 @@ void PairPACEKokkos::operator() (TagPairPACEComputeNeigh,const typen
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
+ const int mu_i = d_map(type(i));
// get a pointer to scratch memory
// This is used to cache whether or not an atom is within the cutoff
@@ -800,6 +840,36 @@ void PairPACEKokkos::operator() (TagPairPACEComputeNeigh,const typen
}
offset++;
});
+
+ if (is_zbl) {
+ //adapted from https://www.osti.gov/servlets/purl/1429450
+ if(ncount>0) {
+ using minloc_value_type=Kokkos::MinLoc::value_type;
+ minloc_value_type djjmin;
+ djjmin.val=1e20;
+ djjmin.loc=-1;
+ Kokkos::MinLoc reducer_scalar(djjmin);
+ // loop over ncount (actual neighbours withing cutoff) rather than jnum (total number of neigh in cutoff+skin)
+ Kokkos::parallel_reduce(Kokkos::TeamThreadRange(team, ncount),
+ [&](const int offset, minloc_value_type &min_d_dist) {
+ int j = d_nearest(ii,offset);
+ j &= NEIGHMASK;
+ const int jtype = type(j);
+ auto r = d_rnorms(ii,offset);
+ const int mu_j = d_map(type(j));
+ const F_FLOAT d = r - (d_cut_in(mu_i, mu_j) - d_dcut_in(mu_i, mu_j));
+ if (d < min_d_dist.val) {
+ min_d_dist.val = d;
+ min_d_dist.loc = offset;
+ }
+ }, reducer_scalar);
+ d_d_min(ii) = djjmin.val;
+ d_jj_min(ii) = djjmin.loc;// d_jj_min should be NOT in 0..jnum range, but in 0..d_ncount(<=jnum)
+ } else {
+ d_d_min(ii) = 1e20;
+ d_jj_min(ii) = -1;
+ }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -990,23 +1060,42 @@ void PairPACEKokkos::operator() (TagPairPACEComputeFS, const int& ii
const int ndensity = d_ndensity(mu_i);
double evdwl, fcut, dfcut;
+ double evdwl_cut;
evdwl = fcut = dfcut = 0.0;
- inner_cutoff(rho_core(ii), rho_cut, drho_cut, fcut, dfcut);
FS_values_and_derivatives(ii, evdwl, mu_i);
-
- dF_drho_core(ii) = evdwl * dfcut + 1;
+ if (is_zbl) {
+ if (d_jj_min(ii) != -1) {
+ const int mu_jmin = d_mu(ii,d_jj_min(ii));
+ F_FLOAT dcutin = d_dcut_in(mu_i, mu_jmin);
+ F_FLOAT transition_coordinate = dcutin - d_d_min(ii); // == cutin - r_min
+ cutoff_func_poly(transition_coordinate, dcutin, dcutin, fcut, dfcut);
+ dfcut = -dfcut; // invert, because rho_core = cutin - r_min
+ } else {
+ // no neighbours
+ fcut = 1;
+ dfcut = 0;
+ }
+ evdwl_cut = evdwl * fcut + rho_core(ii) * (1 - fcut); // evdwl * fcut + rho_core_uncut - rho_core_uncut* fcut
+ dF_drho_core(ii) = 1 - fcut;
+ dF_dfcut(ii) = evdwl * dfcut - rho_core(ii) * dfcut;
+ } else {
+ inner_cutoff(rho_core(ii), rho_cut, drho_cut, fcut, dfcut);
+ dF_drho_core(ii) = evdwl * dfcut + 1;
+ evdwl_cut = evdwl * fcut + rho_core(ii);
+ }
for (int p = 0; p < ndensity; ++p)
- dF_drho(ii, p) *= fcut;
-
+ dF_drho(ii, p) *= fcut;
// tally energy contribution
if (eflag) {
- double evdwl_cut = evdwl * fcut + rho_core(ii);
- // E0 shift
- evdwl_cut += d_E0vals(mu_i);
- e_atom(ii) = evdwl_cut;
+ // E0 shift
+ evdwl_cut += d_E0vals(mu_i);
+ e_atom(ii) = evdwl_cut;
}
+
+ if (flag_corerep_factor)
+ d_corerep(ii) = 1-fcut;
}
/* ---------------------------------------------------------------------- */
@@ -1146,6 +1235,15 @@ void PairPACEKokkos::operator() (TagPairPACEComputeDerivative, const
f_ij(ii, jj, 0) = scale * f_ji[0] + fpair * r_hat[0];
f_ij(ii, jj, 1) = scale * f_ji[1] + fpair * r_hat[1];
f_ij(ii, jj, 2) = scale * f_ji[2] + fpair * r_hat[2];
+
+ if (is_zbl) {
+ if (jj==d_jj_min(ii)) {
+ // DCRU = 1.0
+ f_ij(ii, jj, 0) += dF_dfcut(ii) * r_hat[0];
+ f_ij(ii, jj, 1) += dF_dfcut(ii) * r_hat[1];
+ f_ij(ii, jj, 2) += dF_dfcut(ii) * r_hat[2];
+ }
+ }
}
/* ---------------------------------------------------------------------- */
@@ -1683,6 +1781,8 @@ double PairPACEKokkos::memory_usage()
bytes += MemKK::memory_usage(weights_rank1);
bytes += MemKK::memory_usage(rho_core);
bytes += MemKK::memory_usage(dF_drho_core);
+ bytes += MemKK::memory_usage(dF_dfcut);
+ bytes += MemKK::memory_usage(d_corerep);
bytes += MemKK::memory_usage(dB_flatten);
bytes += MemKK::memory_usage(fr);
bytes += MemKK::memory_usage(dfr);
@@ -1700,6 +1800,8 @@ double PairPACEKokkos::memory_usage()
bytes += MemKK::memory_usage(d_mu);
bytes += MemKK::memory_usage(d_rhats);
bytes += MemKK::memory_usage(d_rnorms);
+ bytes += MemKK::memory_usage(d_d_min);
+ bytes += MemKK::memory_usage(d_jj_min);
bytes += MemKK::memory_usage(d_nearest);
bytes += MemKK::memory_usage(f_ij);
bytes += MemKK::memory_usage(d_rho_core_cutoff);
diff --git a/src/KOKKOS/pair_pace_kokkos.h b/src/KOKKOS/pair_pace_kokkos.h
index 39cfd100f8..36486f8628 100644
--- a/src/KOKKOS/pair_pace_kokkos.h
+++ b/src/KOKKOS/pair_pace_kokkos.h
@@ -121,6 +121,7 @@ class PairPACEKokkos : public PairPACE {
tdual_fparams k_cutsq, k_scale;
typedef Kokkos::View t_fparams;
t_fparams d_cutsq, d_scale;
+ t_fparams d_cut_in, d_dcut_in; // inner cutoff
typename AT::t_int_1d d_map;
@@ -209,6 +210,8 @@ class PairPACEKokkos : public PairPACE {
typedef Kokkos::View t_ace_4c;
typedef Kokkos::View t_ace_4c3;
+ typedef typename Kokkos::View::HostMirror th_ace_1d;
+
t_ace_3d A_rank1;
t_ace_4c A;
@@ -222,12 +225,16 @@ class PairPACEKokkos : public PairPACE {
t_ace_2d rhos;
t_ace_2d dF_drho;
+ t_ace_3c dB_flatten;
+
// hard-core repulsion
t_ace_1d rho_core;
- t_ace_3c dB_flatten;
t_ace_2d cr;
t_ace_2d dcr;
t_ace_1d dF_drho_core;
+ t_ace_1d dF_dfcut;
+ t_ace_1d d_corerep;
+ th_ace_1d h_corerep;
// radial functions
t_ace_4d fr;
@@ -265,6 +272,11 @@ class PairPACEKokkos : public PairPACE {
t_ace_3d3 d_rhats;
t_ace_2i d_nearest;
+ // for ZBL core-rep implementation
+ t_ace_1d d_d_min; // [i] -> min-d for atom ii, d=d = r - (cut_in(mu_i, mu_j) - dcut_in(mu_i, mu_j))
+ t_ace_1i d_jj_min; // [i] -> jj-index of nearest neigh (by r-(cut_in-dcut_in) criterion)
+ bool is_zbl;
+
// per-type
t_ace_1i d_ndensity;
t_ace_1i d_npoti;
diff --git a/src/KOKKOS/pair_reaxff_kokkos.h b/src/KOKKOS/pair_reaxff_kokkos.h
index 1ad0955a1e..421d704d03 100644
--- a/src/KOKKOS/pair_reaxff_kokkos.h
+++ b/src/KOKKOS/pair_reaxff_kokkos.h
@@ -16,9 +16,6 @@
PairStyle(reaxff/kk,PairReaxFFKokkos);
PairStyle(reaxff/kk/device,PairReaxFFKokkos);
PairStyle(reaxff/kk/host,PairReaxFFKokkos);
-PairStyle(reax/c/kk,PairReaxFFKokkos);
-PairStyle(reax/c/kk/device,PairReaxFFKokkos);
-PairStyle(reax/c/kk/host,PairReaxFFKokkos);
// clang-format on
#else
diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp
index 478cf6fc9d..7b00543eea 100644
--- a/src/KSPACE/fft3d_wrap.cpp
+++ b/src/KSPACE/fft3d_wrap.cpp
@@ -27,30 +27,66 @@ FFT3d::FFT3d(LAMMPS *lmp, MPI_Comm comm, int nfast, int nmid, int nslow,
int out_klo, int out_khi,
int scaled, int permute, int *nbuf, int usecollective) : Pointers(lmp)
{
+ #ifndef FFT_HEFFTE
plan = fft_3d_create_plan(comm,nfast,nmid,nslow,
in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,
out_ilo,out_ihi,out_jlo,out_jhi,out_klo,out_khi,
scaled,permute,nbuf,usecollective);
if (plan == nullptr) error->one(FLERR,"Could not create 3d FFT plan");
+ #else
+ heffte::plan_options options = heffte::default_options();
+ options.algorithm = (usecollective == 0) ?
+ heffte::reshape_algorithm::p2p_plined
+ : heffte::reshape_algorithm::alltoallv;
+ options.use_reorder = (permute != 0);
+ hscale = (scaled == 0) ? heffte::scale::none : heffte::scale::full;
+
+ heffte_plan = std::unique_ptr>(
+ new heffte::fft3d(
+ heffte::box3d<>({in_ilo,in_jlo,in_klo}, {in_ihi, in_jhi, in_khi}),
+ heffte::box3d<>({out_ilo,out_jlo,out_klo}, {out_ihi, out_jhi, out_khi}),
+ comm, options)
+ );
+ *nbuf = heffte_plan->size_workspace();
+ heffte_workspace.resize(heffte_plan->size_workspace());
+ #endif
}
/* ---------------------------------------------------------------------- */
FFT3d::~FFT3d()
{
+ #ifndef FFT_HEFFTE
fft_3d_destroy_plan(plan);
+ #endif
}
/* ---------------------------------------------------------------------- */
void FFT3d::compute(FFT_SCALAR *in, FFT_SCALAR *out, int flag)
{
+ #ifndef FFT_HEFFTE
fft_3d((FFT_DATA *) in,(FFT_DATA *) out,flag,plan);
+ #else
+ if (flag == 1)
+ heffte_plan->forward(reinterpret_cast*>(in),
+ reinterpret_cast*>(out),
+ reinterpret_cast*>(heffte_workspace.data())
+ );
+ else
+ heffte_plan->backward(reinterpret_cast*>(in),
+ reinterpret_cast*>(out),
+ reinterpret_cast*>(heffte_workspace.data()),
+ hscale
+ );
+ #endif
}
/* ---------------------------------------------------------------------- */
void FFT3d::timing1d(FFT_SCALAR *in, int nsize, int flag)
{
+ #ifndef FFT_HEFFTE
fft_1d_only((FFT_DATA *) in,nsize,flag,plan);
+ #endif
}
diff --git a/src/KSPACE/fft3d_wrap.h b/src/KSPACE/fft3d_wrap.h
index f72cfd4622..04b828b7de 100644
--- a/src/KSPACE/fft3d_wrap.h
+++ b/src/KSPACE/fft3d_wrap.h
@@ -17,6 +17,19 @@
#include "fft3d.h" // IWYU pragma: export
#include "pointers.h"
+#ifdef FFT_HEFFTE
+#include "heffte.h"
+// select the backend
+#if defined(FFT_HEFFTE_FFTW)
+using heffte_backend = heffte::backend::fftw;
+#elif defined(FFT_HEFFTE_MKL)
+using heffte_backend = heffte::backend::mkl;
+#else
+using heffte_backend = heffte::backend::stock;
+#endif
+
+#endif // FFT_HEFFTE
+
namespace LAMMPS_NS {
class FFT3d : protected Pointers {
@@ -30,7 +43,14 @@ class FFT3d : protected Pointers {
void timing1d(FFT_SCALAR *, int, int);
private:
+ #ifdef FFT_HEFFTE
+ // the heFFTe plan supersedes the internal fft_plan_3d
+ std::unique_ptr> heffte_plan;
+ std::vector> heffte_workspace;
+ heffte::scale hscale;
+ #else
struct fft_plan_3d *plan;
+ #endif
};
} // namespace LAMMPS_NS
diff --git a/src/MDI/fix_mdi_engine.cpp b/src/MDI/fix_mdi_engine.cpp
index 0c70678add..0494d08b2d 100644
--- a/src/MDI/fix_mdi_engine.cpp
+++ b/src/MDI/fix_mdi_engine.cpp
@@ -28,7 +28,8 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixMDIEngine::FixMDIEngine(LAMMPS *_lmp, int narg, char **arg) : Fix(_lmp, narg, arg)
+FixMDIEngine::FixMDIEngine(LAMMPS *_lmp, int narg, char **arg) :
+ Fix(_lmp, narg, arg), mdi_engine(nullptr)
{
if (narg != 3) error->all(FLERR, "Illegal fix mdi/engine command");
}
diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp
index fd145e08e6..3ff6b22764 100644
--- a/src/MDI/fix_mdi_qm.cpp
+++ b/src/MDI/fix_mdi_qm.cpp
@@ -35,7 +35,10 @@ static int compare_IDs(const int, const int, void *);
/* ---------------------------------------------------------------------- */
-FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg), id_mcfix(nullptr), mc_active_ptr(nullptr), exclusion_group_ptr(nullptr),
+ elements(nullptr), qmIDs(nullptr), qm2owned(nullptr), eqm(nullptr), eqm_mine(nullptr),
+ tqm(nullptr), tqm_mine(nullptr), xqm(nullptr), xqm_mine(nullptr), fqm(nullptr)
{
// check requirements for LAMMPS to work with MDI as an engine
// atom IDs do not need to be consecutive
@@ -58,9 +61,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
addflag = 1;
every = 1;
connectflag = 1;
- elements = nullptr;
mcflag = 0;
- id_mcfix = nullptr;
int iarg = 3;
while (iarg < narg) {
@@ -178,18 +179,6 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
nqm = nqm_last = max_nqm = 0;
nexclude = 0;
- qmIDs = nullptr;
- qm2owned = nullptr;
-
- eqm = nullptr;
- tqm = nullptr;
- xqm = nullptr;
- fqm = nullptr;
-
- eqm_mine = nullptr;
- tqm_mine = nullptr;
- xqm_mine = nullptr;
-
// per-atom data
nmax = atom->nmax;
@@ -999,9 +988,8 @@ void FixMDIQM::send_box()
ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL data");
- } else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
- domain->zperiodic == 1) {
- error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
+ } else if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
+ error->all(FLERR, "MDI requires fully periodic or fully non-periodic system");
}
}
diff --git a/src/MDI/fix_mdi_qmmm.cpp b/src/MDI/fix_mdi_qmmm.cpp
index cf92a063d4..8e63a34472 100644
--- a/src/MDI/fix_mdi_qmmm.cpp
+++ b/src/MDI/fix_mdi_qmmm.cpp
@@ -39,7 +39,11 @@ static int compare_IDs(const int, const int, void *);
/* ---------------------------------------------------------------------- */
-FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg), elements(nullptr), pair_coul(nullptr), qmIDs(nullptr), qm2owned(nullptr),
+ eqm(nullptr), eqm_mine(nullptr), tqm(nullptr), tqm_mine(nullptr), xqm(nullptr),
+ xqm_mine(nullptr), qqm(nullptr), qqm_mine(nullptr), qpotential(nullptr),
+ qpotential_mine(nullptr), fqm(nullptr), ecoul(nullptr)
{
// check requirements for LAMMPS to work with MDI for a QMMM engine
// atom IDs do not need to be consecutive
@@ -69,7 +73,6 @@ FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
virialflag = 0;
connectflag = 1;
- elements = nullptr;
int iarg = 4;
while (iarg < narg) {
@@ -1782,9 +1785,8 @@ void FixMDIQMMM::send_box()
ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL data");
- } else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
- domain->zperiodic == 1) {
- error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
+ } else if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
+ error->all(FLERR, "MDI requires fully periodic or fully non-periodic system");
}
}
diff --git a/src/MDI/library_mdi.cpp b/src/MDI/library_mdi.cpp
index 2216704e5a..13e318d95f 100644
--- a/src/MDI/library_mdi.cpp
+++ b/src/MDI/library_mdi.cpp
@@ -67,7 +67,7 @@ int MDI_Plugin_init_lammps(void *plugin_state)
// find the -in argument
int iarg = 0;
- char *filename;
+ char *filename = nullptr;
bool found_filename = false;
while (iarg < mdi_argc && !found_filename) {
diff --git a/src/MDI/mdi_engine.cpp b/src/MDI/mdi_engine.cpp
index 58f750f62a..f7025549cd 100644
--- a/src/MDI/mdi_engine.cpp
+++ b/src/MDI/mdi_engine.cpp
@@ -103,9 +103,8 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
for (int i = 1; i <= ntypes; i++) {
int anum;
for (anum = 0; anum < MAXELEMENT; anum++)
- if (strcmp(arg[iarg + i],symbols[anum]) == 0) break;
- if (anum == MAXELEMENT)
- error->all(FLERR,"Invalid chemical element in mdi engine command");
+ if (strcmp(arg[iarg + i], symbols[anum]) == 0) break;
+ if (anum == MAXELEMENT) error->all(FLERR, "Invalid chemical element in mdi engine command");
elements[i] = anum + 1;
}
iarg += ntypes + 1;
diff --git a/src/MDI/mdi_plugin.cpp b/src/MDI/mdi_plugin.cpp
index f02ec3bf57..d7805d0cba 100644
--- a/src/MDI/mdi_plugin.cpp
+++ b/src/MDI/mdi_plugin.cpp
@@ -22,6 +22,7 @@
#include "input.h"
#include "modify.h"
+#include
#include
#include
@@ -66,11 +67,12 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
// do variable substitution in multiple word extra_arg
int ncopy = strlen(extra_arg) + 1;
- char *copy = utils::strdup(extra_arg);
- char *work = new char[ncopy];
+ char *copy = (char *) malloc(ncopy);
+ strncpy(copy, extra_arg, ncopy);
+ char *work = (char *) malloc(ncopy);
int nwork = ncopy;
- input->substitute(copy,work,ncopy,nwork,0);
- delete[] work;
+ input->substitute(copy, work, ncopy, nwork, 0);
+ free(work);
extra_arg = copy;
iarg += 2;
@@ -81,11 +83,12 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
// do variable substitution in multiple word lammps_command
int ncopy = strlen(lammps_command) + 1;
- char *copy = utils::strdup(lammps_command);
- char *work = new char[ncopy];
+ char *copy = (char *) malloc(ncopy);
+ strncpy(copy, extra_arg, ncopy);
+ char *work = (char *) malloc(ncopy);
int nwork = ncopy;
- input->substitute(copy,work,ncopy,nwork,0);
- delete[] work;
+ input->substitute(copy, work, ncopy, nwork, 0);
+ free(work);
lammps_command = copy;
iarg += 2;
diff --git a/src/ML-PACE/compute_pace.cpp b/src/ML-PACE/compute_pace.cpp
new file mode 100644
index 0000000000..cf3be8f47f
--- /dev/null
+++ b/src/ML-PACE/compute_pace.cpp
@@ -0,0 +1,496 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ https://www.lammps.org/, Sandia National Laboratories
+ LAMMPS Development team: developers@lammps.org
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "compute_pace.h"
+#include "ace-evaluator/ace_evaluator.h"
+#include "ace-evaluator/ace_c_basis.h"
+#include "ace-evaluator/ace_abstract_basis.h"
+#include "ace-evaluator/ace_types.h"
+#include
+#include