Merge branch 'develop' into snann_slcsa

cmake/CMakeLists.txt

@@ -971,6 +971,20 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
+  if (LMP_HEFFTE)
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  heFFTe")
+    if (HEFFTE_BACKEND)
+      message(STATUS "heFFTe backend:  ${HEFFTE_BACKEND}")
+    else()
+      message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
+    endif()
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+  else()
     message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")
     if(FFT_SINGLE)
@@ -983,6 +997,11 @@ if(PKG_KSPACE)
     else()
       message(STATUS "Using non-threaded FFTs")
     endif()
+    if (FFT_HEFFTE)
+      message(STATUS "Using distributed algorithms from heFTTe")
+    else()
+      message(STATUS "Using builtin distributed algorithms")
+    endif()
     if(PKG_KOKKOS)
       if(Kokkos_ENABLE_CUDA)
         if(FFT STREQUAL "KISS")
@@ -1000,6 +1019,7 @@ if(PKG_KSPACE)
         message(STATUS "Kokkos FFT: ${FFT}")
       endif()
     endif()
+  endif()
 endif()
 if(BUILD_DOC)
   message(STATUS "<<< Building HTML Manual >>>")

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})

cmake/Modules/Packages/ML-PACE.cmake

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

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 <https://icl-utk-edu.github.io/heffte/>`_
+library for the MPI communication algorithms,
+which comes with many optimizations for special cases,
+e.g., leveraging 2D and 3D backend transforms and
+better pipelining for packing and communication.
 
 .. tabs::
 
@@ -53,6 +59,7 @@ LAMMPS can use them if they are available on your system.
          -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
+         -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
 
       .. note::
 
@@ -76,6 +83,15 @@ LAMMPS can use them if they are available on your system.
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
+         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock backend
+         -D Heffte_ROOT=path         # path to an existing heFFTe installation
+
+      .. note::
+
+         heFFTe comes with a builtin stock backend for FFTs; however, the backend
+         is intended for testing purposes and is not performance optimized
+         for large scale production runs.
+
 
    .. tab:: Traditional make
 
@@ -111,6 +127,24 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
+      Traditional make can also link to heFFTe using an existing installation
+
+      .. code-block:: make
+
+         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
+         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
+         FFT_PATH =
+         FFT_LIB = $(heffte_link) $(heffte_libs)
+
+      The heFFTe install path will contain `HeffteMakefile.in`.
+      which will define the `heffte_` include variables needed to link to heFFTe from
+      an external project using traditional make.
+      The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
+      selects the desired heFFTe backend, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
+      omitting the variable will default to the `stock` backend.
+      The heFFTe `stock` backend is intended to be used for testing and debugging,
+      but is not performance optimized for large scale production runs.
+
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -170,6 +204,16 @@ Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing install
+with hints provided by ``-DHeffte_ROOT``, as recommended by the CMake
+standard and note that the name is case sensitive. If CMake cannot find
+a heFFTe installation with the correct backend (e.g., FFTW or MKL),
+it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific variables
+listed in the
+`heFFTe documentation <https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+and those variables will be passed into the heFFTe build.
+
 ----------
 
 .. _size:

doc/src/Commands_compute.rst

@@ -100,6 +100,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
+   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -115,6 +116,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`

doc/src/Commands_fix.rst

@@ -122,6 +122,7 @@ OPT.
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
@@ -238,10 +239,10 @@ OPT.
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`
-   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`
    * :doc:`temp/csvr <fix_temp_csvr>`
-   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale (k) <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
    * :doc:`tgnpt/drude <fix_tgnh_drude>`

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 <PKG-REAXFF>`.
+In the process also the pair style and related fixes were renamed to use
+the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
+backward compatibility by providing aliases for the styles.  These have
+been removed, so using "reaxff" is now *required*.
+
 USER-CUDA package
 -----------------
 

doc/src/Howto.rst

@@ -101,6 +101,7 @@ Tutorials howto
    Howto_cmake
    Howto_github
    Howto_lammps_gui
+   Howto_moltemplate
    Howto_pylammps
    Howto_wsl
 

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

doc/src/Howto_moltemplate.rst

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

doc/src/compute.rst

@@ -264,6 +264,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`nbond/atom <compute_nbond_atom>` - calculates number of bonds per atom
 * :doc:`omega/chunk <compute_omega_chunk>` - angular velocity for each chunk
 * :doc:`orientorder/atom <compute_orientorder_atom>` - Steinhardt bond orientational order parameters Ql
+* :doc:`pace <compute_pace>` - atomic cluster expansion descriptors and related quantities
 * :doc:`pair <compute_pair>` - values computed by a pair style
 * :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
 * :doc:`pe <compute_pe>` - potential energy
@@ -279,6 +280,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
 * :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
 * :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
+* :doc:`rattlers/atom <compute_rattlers_atom>` - identify under-coordinated rattler atoms
 * :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk

doc/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

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

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 <compute>` command
+* rattlers/atom = style name of this compute command
+* cutoff = *type* or *radius*
+
+  .. parsed-literal::
+
+       *type* = cutoffs determined based on atom types
+       *radius* = cutoffs determined based on atom diameters (atom style sphere)
+
+* zmin = minimum coordination for a non-rattler atom
+* ntries = maximum number of iterations to remove rattlers
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all rattlers/atom type 4 10
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Define a compute that identifies rattlers in a system. Rattlers are often
+identified in granular or glassy packings as undercoordinated atoms that
+do not have the required number of contacts to constrain their translational
+degrees of freedom. Such atoms are not considered rigid and can often freely
+rattle around in the system. This compute identifies rattlers which can be
+helpful for excluding them from analysis or providing extra damping forces
+to accelerate relaxation processes.
+
+Rattlers are identified using an interactive approach. The coordination
+number of all atoms is first calculated.  The *type* and *radius* settings
+are used to select whether interaction cutoffs are determined by atom
+types or by the sum of atomic radii (atom style sphere), respectively.
+Rattlers are then identified as atoms with a coordination number less
+than *zmin* and are removed from consideration. Atomic coordination
+numbers are then recalculated, excluding previously identified rattlers,
+to identify a new set of rattlers. This process is iterated up to a maximum
+of *ntries* or until no new rattlers are identified and the remaining
+atoms form a stable network of contacts.
+
+In dense homogeneous systems where the average atom coordination number
+is expected to be larger than *zmin*, this process usually only takes a few
+iterations and a value of *ntries* around ten may be sufficient. In systems
+with significant heterogeneity or average coordination numbers less than
+*zmin*, an appropriate value of *ntries* depends heavily on the specific
+system. For instance, a linear chain of N rattler atoms with a *zmin* of 2
+would take N/2 iterations to identify that all the atoms are rattlers.
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom vector and a global scalar. The vector
+designates which atoms are rattlers, indicated by a value 1. Non-rattlers
+have a value of 0. The global scalar returns the total number of rattlers
+in the system. See the :doc:`Howto output <Howto_output>` page for an
+overview of LAMMPS output options.
+
+Restrictions
+""""""""""""
+
+This compute is part of the EXTRA-COMPUTE package.  It is only enabled if
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
+
+The *radius* cutoff option requires that atoms store a radius as defined by the
+:doc:`atom_style sphere <atom_style>` or similar commands.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute coord/atom <compute_coord_atom>`
+:doc:`compute contact/atom <compute_contact_atom>`
+
+Default
+"""""""
+
+none

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
+:math:`r_j` is the position of each atom, :math:`f_j` are atomic
-factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
+scattering factors, *Lp* is the Lorentz-polarization factor, and
-scattering angle of diffraction.  The Lorentz-polarization factor can be turned
+:math:`\theta` is the scattering angle of diffraction.  The
-off using the optional *LP* keyword.
+Lorentz-polarization factor can be turned off using the optional *LP*
+keyword.
 
 Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
+reciprocal lattice nodes. The mesh spacing is defined either (a) by the
-simulation domain or (b) manually using selected values as
+entire simulation domain or (b) manually using selected values as shown
-shown in the 2D diagram below.
+in the 2D diagram below.
 
-.. image:: img/xrd_mesh.jpg
+.. image:: img/xrd_mesh.png
    :scale: 75%
    :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
+axis, where :math:`A` is a matrix containing the vectors corresponding
-edges of the simulation cell. If one or two directions has non-periodic
+to the edges of the simulation cell. If one or two directions has
-boundary conditions, then the spacing in these directions is defined from the
+non-periodic boundary conditions, then the spacing in these directions
-average of the (inversed) box lengths with periodic boundary conditions.
+is defined from the average of the (inversed) box lengths with periodic
-Meshes defined by the simulation domain must contain at least one periodic
+boundary conditions.  Meshes defined by the simulation domain must
-boundary.
+contain at least one periodic boundary.
 
 If the *manual* flag is included, the mesh of reciprocal lattice nodes
 will be defined using the *c* values for the spacing along each

doc/src/fix.rst

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

doc/src/fix_adapt.rst

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

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 <fix_deform>`, :doc:`fix nvt/sllod
 <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
 commands.
 
-The applied flow field is set by the *eps* keyword. The values
+The applied flow field is set by the *erate* keyword. The values
 *edot_x* and *edot_y* correspond to the strain rates in the xx and yy
 directions.  It is implicitly assumed that the flow field is
 traceless, and therefore the strain rate in the zz direction is eqal

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

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 <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)

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
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

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
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

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 <Howto_body>` page for a further description of
+the file format.
+
+----------
+
+*Body Doubles* section:
+
+* first line
+* line syntax: Ixx Iyy Izz Ixy Ixz Iyz
+* Ixx Iyy Izz Ixy Ixz Iyz = 6 components of inertia tensor of body particle
+* one line per sub-particle or vertex
+* line syntax: x y z
+* x, y, z = coordinates of sub-particle or vertex
+* one line per edge
+* line syntax: N1 N2
+* N1, N2 = vertex indices
+* one line per face
+* line syntax: N1 N2 N3 N4
+* N1, N2, N3, N4 = vertex indices
+* last line
+* line syntax: diam
+* diam = rounded diameter that surrounds each vertex
+
+This section is only needed when the molecule is a body particle. the other
+Body section must also appear in the file.
+
+The total number of values that must appear is determined by the body style, and
+must be equal to the Ndouble value given in the *body* header. The 6 moments of
+inertia and the 3N coordinates of the sub-particles or vertices are required
+for all body styles.
+
+For *rounded/polygon*, the E = 6 + 3*N + 1 edges are automatically determined
+from the vertices.
+
+For *rounded/polyhedron*, the 2E vertex indices for the end points of the edges
+and 4F vertex indices defining the faces are required.
+
+See the :doc:`Howto body <Howto_body>` page for a further description of
+the file format.
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/pair_beck.rst

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

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

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) <Toxvaerd>`:
+continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) <Toxvaerd>`:
 
 .. math::
 
    \phi\left(r\right) & =  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
                        \left(\frac{\sigma}{r}\right)^6 \right] \\
-   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c}       \qquad r < R_c
+   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c}       \qquad r < r_c
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
 pressure, since the energy of the pair interaction is smoothed to 0.0
 at the cutoff.
 
-This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
+This pair style writes its information to :doc:`binary restart files <restart>`,
-to be specified in an input script that reads a restart file.
+so pair_style and pair_coeff commands do not need to be specified
+in an input script that reads a restart file.
 
 This pair style can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  It does not support the

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::

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 <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.

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 <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
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

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 <fix_nve_limit>` command for another way to push apart
+interactions over time.  :math:`r_c` is the cutoff.
-overlapping atoms.
+See the :doc:`fix nve/limit <fix_nve_limit>` command for another way
+to push apart overlapping atoms.
 
 The following coefficients must be defined for each pair of atom types
 via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,

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) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
 Summary information on these force fields can be found at https://www.spica-ff.org
 
 Style *lj/spica/coul/long* computes the adds Coulombic interactions

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

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`
+

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]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [1, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 1], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 2], ns: [2, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [0, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [1, 1], ns: [1, 1], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [2, 2], ns: [2, 2], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 3, mus: [2, 2], ns: [1, 2], ls: [1, 1], ms_combs: [-1, 1, 0, 0, 1, -1], ctildes: [0.5773502691896257, -0.5773502691896257, 0.5773502691896257]}
+    - {mu0: 0, rank: 2, ndensity: 1, num_ms_combs: 5, mus: [1, 2], ns: [1, 1], ls: [2, 2], ms_combs: [-2, 2, -1, 1, 0, 0, 1, -1, 2, -2], ctildes: [0.4472135954999579, -0.4472135954999579, 0.447213595499958, -0.4472135954999579, 0.4472135954999579]}
+    - {mu0: 0, rank: 3, ndensity: 1, num_ms_combs: 9, mus: [1, 1, 2], ns: [1, 1, 1], ls: [1, 2, 1], ms_combs: [-1, 0, 1, -1, 1, 0, -1, 2, -1, 0, -1, 1, 0, 0, 0, 0, 1, -1, 1, -2, 1, 1, -1, 0, 1, 0, -1], ctildes: [0.10540925533894599, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.21081851067789198, -0.18257418583505536, 0.25819888974716115, -0.18257418583505536, 0.10540925533894599]}
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+    - {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]}
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+    - {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]}
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+    - {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]}
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+    - {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]}
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+    - {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]}

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

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
+    44   1      7.4470362200000002      8.3169646700000008      3.7148003300000001
+    45   1      6.9073805300000002               7.9385021      2.1723768699999999
+    46   1      5.5542868500000004      5.1176065800000003      3.7655251999999999
+    47   1      6.8124309500000004      6.7778811599999997      3.3973232499999999
+    48   2     0.29575823000000001             11.04303794      3.1016142499999999
+    49   1     0.86490721999999998             11.83879228      3.6389974500000002
+    50   3              6.85201686      8.0846369300000003      8.8762878799999996
+    51   1      7.3351430100000004      7.4263498700000001      9.3821674799999997
+    52   1      6.7919613300000004      7.7595477199999996      7.9716174799999999
+    53   1      3.8990487699999998      6.4283490399999996      8.8832409600000002
+    54   1              5.95997296      9.9329723199999993      9.4746654699999997
+    55   3      11.403658979999999      10.371960359999999      9.2766092199999992
+    56   1      10.983666360000001      9.5157199800000001      9.1478757300000009
+    57   3      1.5223279700000001      5.3327331100000004     0.57537605999999997
+    58   1      2.3815113999999999      5.7251991200000001     0.77945295999999997
+    59   1     0.92079957000000001      6.0931282299999996     0.62203253000000003
+    60   3             11.23490924      2.9153355200000002      6.7585064099999999
+    61   1      10.792340190000001      2.9755225099999998      5.9000018399999998
+    62   1      10.751242059999999      2.1896156000000002      7.1807401500000001
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+   146   1      9.9404883900000005              1.11619136              1.18684594
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+   151   1              0.61502181      3.5607405999999999             11.40300991
+   152   1              1.55655312      2.5457368800000002      10.866733030000001
+   153   3      5.8627936099999998      7.1217054800000001              5.89173203
+   154   1      6.3432410700000004      7.9400136699999999      6.0855840299999997
+   155   1      5.5077296699999998      6.8468306800000001      6.7436875799999996
+   156   3      10.887828150000001      9.9637482500000001     0.51092815999999996
+   157   1             11.78841776      10.322043069999999     0.44704989000000001
+   158   1             11.02688182      9.2051906700000004      1.0976661299999999
+   159   3              3.93073389      4.1645674499999998      5.7137877000000001
+   160   1      4.6884062999999996      3.5788913299999998      5.5644605800000004
+   161   1      4.2956948500000003      4.7644888099999996      6.3801669700000003

examples/PACKAGES/pace/compute/latte_cell_0.xyz

@@ -0,0 +1,163 @@
+161
+Lattice="12.0 0.0 0.0 0.0 12.0 0.0 0.0 0.0 12.0" Properties=species:S:1:pos:R:3 pbc="T T T"
+O        1.26880968       2.00799384       2.74468299
+H        1.53430682       2.06387665       3.71056269
+H        1.78482796       2.67550034       2.22688472
+H        1.56251195       1.10891269       2.39781152
+H       11.61728216       5.71881094       2.47320460
+N        6.55018656       4.74395668       3.65260255
+H        6.45648953       4.15716730       2.69752680
+N        2.08355610       1.59406078       8.54980476
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+H        4.29569485       4.76448881       6.38016697

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

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

examples/PACKAGES/phonon/2-1D-diatomic/in.Ana

@@ -7,7 +7,7 @@ atom_style	bond
 atom_modify sort 0 1.
 bond_style  harmonic
 pair_style  none
-communicate single cutoff 2.0
+comm_modify cutoff 2.0
 
 # geometry
 read_data       data.pos

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

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

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

examples/PACKAGES/qtb/methane_qbmsst/methane_qbmsst.in

@@ -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

examples/PACKAGES/qtb/methane_qbmsst/methane_qtb.mod

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

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

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

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

examples/PACKAGES/qtb/methane_qtb/methane_qtb.in

@@ -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

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

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

examples/qeq/log.27Nov18.qeq.reaxc.g++.1

@@ -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

examples/qeq/log.27Nov18.qeq.reaxc.g++.4

@@ -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

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

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

examples/reaxff/AB/in.AB

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

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 
 
 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 

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

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

examples/reaxff/AB/log.8Mar18.AB.g++.1

@@ -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

examples/reaxff/AB/log.8Mar18.AB.g++.4

@@ -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

examples/reaxff/AuO/in.AuO

@@ -6,7 +6,7 @@ units		real
 atom_style      charge
 read_data       data.AuO
 
-pair_style	reax/c lmp_control
+pair_style      reaxff lmp_control
 pair_coeff      * * ffield.reax.AuO O Au
 
 neighbor        2 bin
@@ -18,6 +18,8 @@ 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

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
-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		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 

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

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

examples/reaxff/AuO/log.8Mar18.AuO.g++.1

@@ -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

examples/reaxff/AuO/log.8Mar18.AuO.g++.4

@@ -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

examples/reaxff/CHO/in.CHO

@@ -6,7 +6,7 @@ units		real
 atom_style      charge
 read_data       data.CHO
 
-pair_style	reax/c lmp_control
+pair_style      reaxff lmp_control
 pair_coeff      * * ffield.reax.cho H C O
 
 neighbor        2 bin
@@ -18,6 +18,7 @@ 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

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 
 
 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 

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

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

examples/reaxff/CHO/log.8Mar18.CHO.g++.1

@@ -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

examples/reaxff/CHO/log.8Mar18.CHO.g++.4

@@ -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

examples/reaxff/FC/in.FC

@@ -8,11 +8,11 @@ units		real
 atom_style      charge
 read_data       data.FC
 
-pair_style	reax/c NULL
+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 reax/c
+fix             2 all qeq/reax 1 0.0 10.0 1e-6 reaxff
 
 # should equilibrate much longer in practice
 

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

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

examples/reaxff/FC/log.8Mar18.FC.g++.1

@@ -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

examples/reaxff/FC/log.8Mar18.FC.g++.4

@@ -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

examples/reaxff/FeOH3/in.FeOH3

@@ -6,7 +6,7 @@ units		real
 atom_style      charge
 read_data       data.FeOH3
 
-pair_style	reax/c lmp_control
+pair_style      reaxff lmp_control
 pair_coeff      * * ffield.reax.Fe_O_C_H H O Fe
 
 neighbor        2 bin
@@ -17,6 +17,7 @@ fix             2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
 fix             3 all temp/berendsen 500.0 500.0 100.0
 
 timestep        0.25
+thermo 100
 
 #dump           1 all atom 30 dump.reax.feoh
 

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 
 
 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 

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

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

examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1

@@ -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

examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.4

@@ -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

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

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

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

examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1

@@ -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

examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4

@@ -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

examples/reaxff/RDX/in.RDX

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

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 
 
 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 

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

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

examples/reaxff/RDX/log.8Mar18.RDX.g++.1

@@ -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

examples/reaxff/RDX/log.8Mar18.RDX.g++.4

@@ -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