Merge pull request #2200 from akohlmey/next_lammps_version

Update version strings for next patch release

.github/CODEOWNERS

@@ -119,6 +119,8 @@ src/utils.*               @akohlmey @rbberger
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
+tools/code_standard/* @rbberger
+tools/valgrind/*      @akohlmey
 
 # tests
 unittest/*            @akohlmey @rbberger

cmake/CMakeLists.txt

@@ -57,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 # compiler tests
 # these need ot be done early (before further tests).
 #####################################################################
-include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
@@ -83,15 +82,6 @@ set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-# GNU compiler specific features for testing
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-  endif()
-endif()
-
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -122,8 +112,8 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
-  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
+  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
   USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
   USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
@@ -210,6 +200,7 @@ endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
+pkg_depends(MLIAP SNAP)
 pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)
@@ -248,6 +239,48 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# Compiler specific features for testing
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+endif()
+
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
@@ -335,15 +368,8 @@ endforeach()
 
 set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
 separate_arguments(CMAKE_TUNE_FLAGS)
-include(CheckCXXCompilerFlag)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
-  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
-  if(COMPILER_SUPPORTS${_FLAGX})
-    target_compile_options(lammps PRIVATE ${_FLAG})
-  else()
-    message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
-  endif()
+  target_compile_options(lammps PRIVATE ${_FLAG})
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #

cmake/Modules/Packages/GPU.cmake

@@ -268,10 +268,17 @@ elseif(GPU_API STREQUAL "HIP")
     if(HIP_PLATFORM STREQUAL "hcc")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
-        add_custom_command(OUTPUT ${CUBIN_FILE}
-          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
-          DEPENDS ${CU_CPP_FILE}
-          COMMENT "Generating ${CU_NAME}.cubin")
+        if(HIP_COMPILER STREQUAL "clang")
+          add_custom_command(OUTPUT ${CUBIN_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            DEPENDS ${CU_CPP_FILE}
+            COMMENT "Generating ${CU_NAME}.cubin")
+        else()
+          add_custom_command(OUTPUT ${CUBIN_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            DEPENDS ${CU_CPP_FILE}
+            COMMENT "Generating ${CU_NAME}.cubin")
+        endif()
     elseif(HIP_PLATFORM STREQUAL "nvcc")
         add_custom_command(OUTPUT ${CUBIN_FILE}
           VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}

cmake/Modules/Packages/USER-INTEL.cmake

@@ -77,7 +77,7 @@ else()
     foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
       check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
       if(COMPILER_SUPPORTS${_FLAG})
-	  target_compile_options(lammps PRIVATE ${_FLAG})
+          target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()
   endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -14,40 +14,23 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
-  # create variables to pass our compiler flags along to the subsystem compile
-  # need to apply -fallow-argument-mismatch, if the fortran compiler supports it
-  include(CheckFortranCompilerFlag)
-  check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
-  if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
-    set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
-  endif()
-  if(CMAKE_Fortran_FLAGS)
-    set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
-  else()
-    set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
-  endif()
-  if(CMAKE_CXX_FLAGS)
-      set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-    else()
-      set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
-  endif()
-  if(CMAKE_C_FLAGS)
-      set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
-    else()
-      set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
-  endif()
+
+  # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
+  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+          EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
     URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
     URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                              --with-internal-fftw --with-internal-pfft
                                              --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
-                                             FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
-                                             CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
-                                             CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
+                                             FC=${CMAKE_MPI_Fortran_COMPILER}
+                                             CXX=${CMAKE_MPI_CXX_COMPILER}
+                                             CC=${CMAKE_MPI_C_COMPILER}
                                              F77=
     BUILD_BYPRODUCTS
       <INSTALL_DIR>/lib/libfcs.a

cmake/Modules/Testing.cmake

@@ -3,6 +3,21 @@
 ###############################################################################
 option(ENABLE_TESTING "Enable testing" OFF)
 if(ENABLE_TESTING)
+  find_program(VALGRIND_BINARY NAMES valgrind)
+  # generate custom suppression file
+  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
+    file(READ ${SUPP} SUPPRESSIONS)
+    file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
+  endforeach()
+  set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
+
+  set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
+  set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
+
+  include(CTest)
+
   enable_testing()
   get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
   get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)

cmake/presets/mingw-cross.cmake

@@ -1,6 +1,6 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MOLECULE OPT PERI
-                 POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
+                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
                  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
                  USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD

cmake/presets/most.cmake

@@ -2,8 +2,8 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
-        DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
         POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
         USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
         USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD

doc/github-development-workflow.md

@@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers
 should doing the merging itself.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
 If this assignment needs to be changed, it shall be done right after a
-stable release.  If the currently assigned developer cannot merge outstanding pull 
-requests in a timely manner, or in other extenuating circumstances, 
+stable release.  If the currently assigned developer cannot merge outstanding pull
+requests in a timely manner, or in other extenuating circumstances,
 other core LAMMPS developers with merge rights can merge pull requests,
-when necessary. 
+when necessary.
 
 ## Pull Requests
 

doc/include-file-conventions.md

@@ -65,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
 These header files should have as few include statements as possible.
 This is particularly important for classes that implement a "style" and
 thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
-all be included in the auto-generated `"some_style.h"` files which 
+all be included in the auto-generated `"some_style.h"` files which
 results in a high potential for direct or indirect symbol name clashes.
 
 In the ideal case, the header would only include one file defining the

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "15 June 2020" "2020-06-15"
+.TH LAMMPS "30 June 2020" "2020-06-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_development.rst

@@ -8,8 +8,8 @@ useful during development, testing or debugging.
 
 .. _compilation:
 
-Verify compilation flags
-------------------------
+Monitor compilation flags
+-------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
@@ -19,7 +19,8 @@ compilation you can use the following option.
 
    -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
 
-Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+Another way of doing this without reconfiguration is calling make with
+variable VERBOSE set to 1:
 
 .. code-block:: bash
 
@@ -33,25 +34,27 @@ Address, Undefined Behavior, and Thread Sanitizer Support
 ---------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
-which use different sanitizer libraries to detect problems in code
+which use different sanitizer libraries to detect problems in the code
 during run-time. They can detect issues like:
 
  - `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
  - `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
  - `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
 
-Please note that this kind of instrumentation usually comes with a small
-performance hit (much less than using tools like `Valgrind
-<https://valgrind.org>`_).  The to enable these features additional
-compiler flags need to be added to the compilation and linking stages.
-This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
-variable during configuration. Examples:
+Please note that this kind of instrumentation usually comes with a
+performance hit (but much less than using tools like `Valgrind
+<https://valgrind.org>`_ with a more low level approach).  The to enable
+these features additional compiler flags need to be added to the
+compilation and linking stages.  This is done through setting the
+``ENABLE_SANITIZER`` variable during configuration. Examples:
 
 .. code-block:: bash
 
-   -D CMAKE_TUNE_FLAGS=-fsanitize=address    # enable address sanitizer / memory leak checker
-   -D CMAKE_TUNE_FLAGS=-fsanitize=undefined  # enable undefined behavior sanitizer
-   -D CMAKE_TUNE_FLAGS=-fsanitize=thread     # enable thread sanitizer
+   -D ENABLE_SANITIZER=none       # no sanitizer active (default)
+   -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
+   -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
+   -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
+   -D ENABLE_SANITIZER=thread     # enable thread sanitizer
 
 ----------
 
@@ -86,19 +89,21 @@ The output of this command will be looking something like this::
    [...]$ ctest
    Test project /home/akohlmey/compile/lammps/build-testing
          Start  1: MolPairStyle:hybrid-overlay
-    1/26 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
+   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
          Start  2: MolPairStyle:hybrid
-    2/26 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
+   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
          Start  3: MolPairStyle:lj_class2
     [...]
-         Start 25: AngleStyle:harmonic
-   25/26 Test #25: AngleStyle:harmonic .................   Passed    0.01 sec
-         Start 26: AngleStyle:zero
-   26/26 Test #26: AngleStyle:zero .....................   Passed    0.01 sec
+         Start 107: PotentialFileReader
+ 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
+         Start 108: EIMPotentialFileReader
+ 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
+         Start 109: TestSimpleCommands
+ 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
 
    100% tests passed, 0 tests failed out of 26
 
-   Total Test time (real) =   0.27 sec
+   Total Test time (real) =  25.57 sec
 
 
 The ``ctest`` command has many options, the most important ones are:
@@ -117,6 +122,8 @@ The ``ctest`` command has many options, the most important ones are:
      - exclude subset of tests matching the regular expression <regex>
    * - -N
      - dry-run: display list of tests without running them
+   * - -T memcheck
+     - run tests with valgrind memory checker (if available)
 
 In its full implementation, the unit test framework will consist of multiple
 kinds of tests implemented in different programming languages (C++, C, Python,
@@ -193,8 +200,8 @@ In this particular case, 5 out of 6 sets of tests were conducted, the
 tests for the ``lj/cut/opt`` pair style was skipped, since the tests
 executable did not include it.  To learn what individual tests are performed,
 you (currently) need to read the source code.  You can use code coverage
-recording (see next section) to confirm how well the tests cover the individual
-source files.
+recording (see next section) to confirm how well the tests cover the code
+paths in the individual source files.
 
 The force style test programs have a common set of options:
 
@@ -211,6 +218,14 @@ The force style test programs have a common set of options:
    * - -v
      - verbose output: also print the executed LAMMPS commands
 
+The ``ctest`` tool has no mechanism to directly pass flags to the individual
+test programs, but a workaround has been implemented where these flags can be
+set in an environment variable ``TEST_ARGS``. Example:
+
+.. code-block:: bash
+
+   env TEST_ARGS=-s ctest -V -R BondStyle
+
 To add a test for a style that is not yet covered, it is usually best
 to copy a YAML file for a similar style to a new file, edit the details
 of the style (how to call it, how to set its coefficients) and then
@@ -244,6 +259,16 @@ and working.
      of mis-compiled code (or an undesired large loss of precision due
      to significant reordering of operations and thus less error cancellation).
 
+Tests for other components and utility functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Additional tests that validate utility functions or specific components
+of LAMMPS are implemented as standalone executable which may, or may not
+require creating a suitable LAMMPS instance.  These tests are more specific
+and do not require YAML format input files.  To add a test, either an
+existing source file needs to be extended or a new file added, which in turn
+requires additions to the ``CMakeLists.txt`` file in the source folder.
+
 Collect and visualize code coverage metrics
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -306,3 +331,23 @@ The images below illustrate how the data is presented.
              :target: JPG/coverage-file-branches.png
 
           Source page with branches
+
+Coding style utilities
+----------------------
+
+To aid with enforcing some of the coding style conventions in LAMMPS
+some additional build targets have been added. These require Python 3.5
+or later and will only work on Unix-like operating and file systems.
+The following options are available.
+
+.. code-block:: bash
+
+   make check-whitespace    # generate coverage report in HTML format
+   make fix-whitespace      # generate coverage report in XML format
+   make check-permissions   # delete folder with HTML format coverage report
+   make fix-permissions     # delete all collected coverage data and HTML output
+
+For the code in the ``unittest`` tree we are using the `clang-format`
+tool (Clang version 8.0 or later is required). If available, the source
+code files in the ``unittest`` tree can be updated to conform to the
+formatting settings using ``make format-tests``.

doc/src/Commands_pair.rst

@@ -183,6 +183,7 @@ OPT.
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mliap <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -228,7 +229,6 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
-   * :doc:`snap (k) <pair_snap>`
    * :doc:`soft (go) <pair_soft>`
    * :doc:`sph/heatconduction <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`

doc/src/Packages_details.rst

@@ -44,6 +44,7 @@ page gives those details.
    * :ref:`MC <PKG-MC>`
    * :ref:`MESSAGE <PKG-MESSAGE>`
    * :ref:`MISC <PKG-MISC>`
+   * :ref:`MLIAP <PKG-MLIAP>`
    * :ref:`MOLECULE <PKG-MOLECULE>`
    * :ref:`MPIIO <PKG-MPIIO>`
    * :ref:`MSCG <PKG-MSCG>`
@@ -652,6 +653,29 @@ listing, "ls src/MISC", to see the list of commands.
 
 ----------
 
+.. _PKG-MLIAP:
+
+MLIAP package
+-------------
+
+**Contents:**
+
+A general interface for machine-learning interatomic potentials.
+
+**Install:**
+
+To use this package, also the :ref:`SNAP package<PKG-SNAP>` needs to be installed.
+
+**Author:** Aidan Thompson (Sandia).
+
+**Supporting info:**
+
+* src/MLIAP: filenames -> commands
+* :doc:`pair_style mliap <pair_mliap>`
+* examples/mliap
+
+----------
+
 .. _PKG-MOLECULE:
 
 MOLECULE package

doc/src/Packages_standard.rst

@@ -59,6 +59,8 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MISC <PKG-MISC>`           | miscellaneous single-file commands   | n/a                                                | no                                                   | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`MLIAP <PKG-MLIAP>`         | multiple machine learning potentials | :doc:`pair_style mliap <pair_mliap>`               | mliap                                                | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MOLECULE <PKG-MOLECULE>`   | molecular system force fields        | :doc:`Howto bioFF <Howto_bioFF>`                   | peptide                                              | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MPIIO <PKG-MPIIO>`         | MPI parallel I/O dump and restart    | :doc:`dump <dump>`                                 | n/a                                                  | no      |

doc/src/Speed_gpu.rst

@@ -88,7 +88,7 @@ GPUs/node to 1.
 
 Using the "-pk" switch explicitly allows for setting of the number of
 GPUs/node to use and additional options.  Its syntax is the same as
-same as the "package gpu" command.  See the :doc:`package <package>`
+the "package gpu" command.  See the :doc:`package <package>`
 command doc page for details, including the default values used for
 all its options if it is not specified.
 

doc/src/compute_mesont.rst

@@ -26,23 +26,23 @@ Examples
 Description
 """""""""""
 
-These computes define computations for the stretching (estretch), bending 
-(ebend), and intertube (etube) per-node (atom) and total energies. The 
-evaluated value is selected by a parameter passed to the compute: estretch, 
+These computes define computations for the stretching (estretch), bending
+(ebend), and intertube (etube) per-node (atom) and total energies. The
+evaluated value is selected by a parameter passed to the compute: estretch,
 ebend, etube.
 
 **Output info:**
 
-These computes calculate per-node (per-atom) vectors, which can be accessed by 
-any command that uses per-atom values from a compute as input, and global 
-scalars. See the :doc:`Howto output <Howto_output>` doc page for an overview of 
+These computes calculate per-node (per-atom) vectors, which can be accessed by
+any command that uses per-atom values from a compute as input, and global
+scalars. See the :doc:`Howto output <Howto_output>` doc page for an overview of
 LAMMPS output options.
 
 The computed values are provided in energy :doc:`units <units>`.
 
 Restrictions
 """"""""""""
-These computes are part of the USER-MESONT package. They are only enabled if 
+These computes are part of the USER-MESONT package. They are only enabled if
 LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
 doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
 must be used.

doc/src/compute_orientorder_atom.rst

@@ -26,7 +26,7 @@ Syntax
        *wl* value = yes or no
        *wl/hat* value = yes or no
        *components* value = ldegree
-       *chunksize* value = number of atoms in each pass 
+       *chunksize* value = number of atoms in each pass
 
 Examples
 """"""""
@@ -52,14 +52,17 @@ For each atom, :math:`Q_l` is a real number defined as follows:
    \bar{Y}_{lm} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{lm}( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) ) \\
    Q_l = & \sqrt{\frac{4 \pi}{2 l + 1} \sum_{m = -l}^{m = l} \bar{Y}_{lm} \bar{Y}^*_{lm}}
 
-The first equation defines the spherical harmonic order parameters.
+The first equation defines the local order parameters as averages
+of the spherical harmonics :math:`Y_{lm}` for each neighbor.
 These are complex number components of the 3D analog of the 2D order
 parameter :math:`q_n`, which is implemented as LAMMPS compute
 :doc:`hexorder/atom <compute_hexorder_atom>`.
 The summation is over the *nnn* nearest
 neighbors of the central atom.
-The angles theta and phi are the standard spherical polar angles
+The angles :math:`theta` and :math:`phi` are the standard spherical polar angles
 defining the direction of the bond vector :math:`r_{ij}`.
+The phase and sign of :math:`Y_{lm}` follow the standard conventions, 
+so that :math:`{\rm sign}(Y_{ll}(0,0)) = (-1)^l`.   
 The second equation defines :math:`Q_l`, which is a
 rotationally invariant non-negative amplitude obtained by summing
 over all the components of degree *l*\ .
@@ -102,8 +105,8 @@ structures are given in Table I of :ref:`Steinhardt <Steinhardt>`, and these
 can be reproduced with this keyword.
 
 The optional keyword *components* will output the components of the
-normalized complex vector :math:`\bar{Y}_{lm}` of degree *ldegree*\ , which must be
-explicitly included in the keyword *degrees*\ . This option can be used
+*normalized* complex vector :math:`\hat{Y}_{lm} = \bar{Y}_{lm}/|\bar{Y}_{lm}|` of degree *ldegree*\,
+which must be included in the list of order parameters to be computed. This option can be used
 in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
 calculate the ten Wolde's criterion to identify crystal-like
 particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
@@ -177,11 +180,15 @@ If the keyword *wl/hat* is set to yes, then the :math:`\hat{W}_l`
 values for each atom will be added to the output array, which are real numbers.
 
 If the keyword *components* is set, then the real and imaginary parts
-of each component of (normalized) :math:`\bar{Y}_{lm}` will be added to the
-output array in the following order: :math:`Re(\bar{Y}_{-m}) Im(\bar{Y}_{-m})
-Re(\bar{Y}_{-m+1}) Im(\bar{Y}_{-m+1}) ... Re(\bar{Y}_m) Im(\bar{Y}_m)`.  This
-way, the per-atom array will have a total of *nlvalues*\ +2\*(2\ *l*\ +1)
-columns.
+of each component of *normalized* :math:`\hat{Y}_{lm}` will be added to the
+output array in the following order: :math:`{\rm Re}(\hat{Y}_{-m}), {\rm Im}(\hat{Y}_{-m}), 
+{\rm Re}(\hat{Y}_{-m+1}), {\rm Im}(\hat{Y}_{-m+1}), \dots , {\rm Re}(\hat{Y}_m), {\rm Im}(\hat{Y}_m)`.  
+
+In summary, the per-atom array will contain *nlvalues* columns, followed by
+an additional *nlvalues* columns if *wl* is set to yes, followed by
+an additional *nlvalues* columns if *wl/hat* is set to yes, followed
+by an additional 2\*(2\* *ldegree*\ +1) columns if the *components* 
+keyword is set.
 
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc

doc/src/compute_property_atom.rst

@@ -64,7 +64,7 @@ Syntax
            end12x, end12y, end12z = end points of line segment
            corner123x, corner123y, corner123z = corner points of triangle
            nbonds = number of bonds assigned to an atom
-           buckling = buckling flag used in mesoscopic simulation of nanotubes 
+           buckling = buckling flag used in mesoscopic simulation of nanotubes
 
   .. parsed-literal::
 

doc/src/compute_sna_atom.rst

@@ -30,7 +30,7 @@ Syntax
 * R_1, R_2,... = list of cutoff radii, one for each type (distance units)
 * w_1, w_2,... = list of neighbor weights, one for each type
 * zero or more keyword/value pairs may be appended
-* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag*
+* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag*
 
   .. parsed-literal::
 
@@ -44,6 +44,15 @@ Syntax
        *quadraticflag* value = *0* or *1*
           *0* = do not generate quadratic terms
           *1* = generate quadratic terms
+       *chem* values = *nelements* *elementlist*
+          *nelements* = number of SNAP elements
+          *elementlist* = *ntypes* integers in range [0, *nelements*)
+       *bnormflag* value = *0* or *1*
+          *0* = do not normalize
+          *1* = normalize bispectrum components
+       *wselfallflag* value = *0* or *1*
+          *0* = self-contribution only for element of central atom
+          *1* = self-contribution for all elements
 
 Examples
 """"""""
@@ -54,6 +63,7 @@ Examples
    compute db all sna/atom 1.4 0.95 6 2.0 1.0
    compute vb all sna/atom 1.4 0.95 6 2.0 1.0
    compute snap all snap 1.4 0.95 6 2.0 1.0
+   compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
 
 Description
 """""""""""
@@ -71,27 +81,26 @@ mathematical definition is given in the paper by Thompson et
 al. :ref:`(Thompson) <Thompson20141>`
 
 The position of a neighbor atom *i'* relative to a central atom *i* is
-a point within the 3D ball of radius *R_ii' = rcutfac\*(R_i + R_i')*
+a point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* :math:`(R_i + R_i')`
 
 Bartok et al. :ref:`(Bartok) <Bartok20101>`, proposed mapping this 3D ball
 onto the 3-sphere, the surface of the unit ball in a four-dimensional
-space.  The radial distance *r* within *R_ii'* is mapped on to a third
-polar angle *theta0* defined by,
+space.  The radial distance *r*  within *R_ii'* is mapped on to a third
+polar angle :math:`\theta_0` defined by,
 
 .. math::
 
-  \theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
+  \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
 
 In this way, all possible neighbor positions are mapped on to a subset
-of the 3-sphere.  Points south of the latitude *theta0max=rfac0\*Pi*
+of the 3-sphere.  Points south of the latitude :math:`\theta_0` = *rfac0* :math:`\pi`
 are excluded.
 
-The natural basis for functions on the 3-sphere is formed by the 4D
-hyperspherical harmonics *U\^j_m,m'(theta, phi, theta0).*  These
-functions are better known as *D\^j_m,m',* the elements of the Wigner
+The natural basis for functions on the 3-sphere is formed by the
+representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, \theta_0)`.
+These functions are better known as :math:`D^j_{m,m'}`, the elements of the Wigner
 *D*\ -matrices :ref:`(Meremianin <Meremianin2006>`,
-:ref:`Varshalovich) <Varshalovich1987>`.
-
+:ref:`Varshalovich <Varshalovich1987>`, :ref:`Mason) <Mason2009>`
 The density of neighbors on the 3-sphere can be written as a sum of
 Dirac-delta functions, one for each neighbor, weighted by species and
 radial distance. Expanding this density function as a generalized
@@ -100,20 +109,20 @@ coefficient as
 
 .. math::
 
-  u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
+  u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{\mu_{i'}} U^j_{m,m'}(\theta_0,\theta,\phi)}
 
-The *w_i'* neighbor weights are dimensionless numbers that are chosen
-to distinguish atoms of different types, while the central atom is
-arbitrarily assigned a unit weight.  The function *fc(r)* ensures that
+The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that depend on
+:math:`\mu_{i'}`, the SNAP element of atom *i'*, while the central atom is
+arbitrarily assigned a unit weight.  The function :math:`f_c(r)` ensures that
 the contribution of each neighbor atom goes smoothly to zero at
-*R_ii'*:
+:math:`R_{ii'}`:
 
 .. math::
 
   f_c(r)   = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
            = & 0,  r > R_{ii'}
 
-The expansion coefficients *u\^j_m,m'* are complex-valued and they are
+The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and they are
 not directly useful as descriptors, because they are not invariant
 under rotation of the polar coordinate frame. However, the following
 scalar triple products of expansion coefficients can be shown to be
@@ -128,7 +137,8 @@ real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
         {j_2} {m_2} {m'_2} \end{array}}
         u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
 
-The constants *H\^jmm'_j1m1m1'_j2m2m2'* are coupling coefficients,
+The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}`
+are coupling coefficients,
 analogous to Clebsch-Gordan coefficients for rotations on the
 2-sphere. These invariants are the components of the bispectrum and
 these are the quantities calculated by the compute *sna/atom*\ . They
@@ -136,13 +146,12 @@ characterize the strength of density correlations at three points on
 the 3-sphere. The j2=0 subset form the power spectrum, which
 characterizes the correlations of two points. The lowest-order
 components describe the coarsest features of the density function,
-while higher-order components reflect finer detail.  Note that the
-central atom is included in the expansion, so three point-correlations
-can be either due to three neighbors, or two neighbors and the central
-atom.
+while higher-order components reflect finer detail. Each bispectrum
+component contains terms that depend on the positions of up to 4
+atoms (3 neighbors and the central atom).
 
 Compute *snad/atom* calculates the derivative of the bispectrum components
-summed separately for each atom type:
+summed separately for each LAMMPS atom type:
 
 .. math::
 
@@ -165,7 +174,7 @@ Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
 virial components, each atom type, and each bispectrum component.  See
 section below on output for a detailed explanation.
 
-Compute *snap* calculates a global array contains information related
+Compute *snap* calculates a global array containing information related
 to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
 and *snav/atom*\ . The first row of the array contains the summation of
 *sna/atom* over all atoms, but broken out by type. The last six rows
@@ -201,8 +210,8 @@ The argument *rcutfac* is a scale factor that controls the ratio of
 atomic radius to radial cutoff distance.
 
 The argument *rfac0* and the optional keyword *rmin0* define the
-linear mapping from radial distance to polar angle *theta0* on the
-3-sphere.
+linear mapping from radial distance to polar angle :math:`theta_0` on the
+3-sphere, given above.
 
 The argument *twojmax* defines which
 bispectrum components are generated. See section below on output for a
@@ -210,7 +219,7 @@ detailed explanation of the number of bispectrum components and the
 ordered in which they are listed.
 
 The keyword *switchflag* can be used to turn off the switching
-function.
+function :math:`f_c(r)`.
 
 The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum
 components of an atom with no neighbors, are subtracted from
@@ -219,13 +228,72 @@ normally only affects compute *sna/atom*\ . However, when
 *quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ .
 
 The keyword *quadraticflag* determines whether or not the
-quadratic analogs to the bispectrum quantities are generated.
+quadratic combinations of bispectrum quantities are generated.
 These are formed by taking the outer product of the vector
 of bispectrum components with itself.
 See section below on output for a
 detailed explanation of the number of quadratic terms and the
 ordered in which they are listed.
 
+The keyword *chem* activates the explicit multi-element variant
+of the SNAP bispectrum components. The argument *nelements*
+specifies the number of SNAP elements that will be handled.
+This is followed by *elementlist*, a list of integers of
+length *ntypes*, with values in the range [0, *nelements* ),
+which maps each LAMMPS type to one of the SNAP elements.
+Note that multiple LAMMPS types can be mapped to the same element,
+and some elements may be mapped by no LAMMPS type. However, in typical
+use cases (training SNAP potentials) the mapping from LAMMPS types
+to elements is one-to-one.
+
+The explicit multi-element variant invoked by the *chem* keyword
+partitions the density of neighbors into partial densities
+for each chemical element.  This is described in detail in the
+paper by :ref:`Cusentino et al. <Cusentino2020>`
+The bispectrum components are indexed on
+ordered triplets of elements:
+
+.. math::
+
+   B_{j_1,j_2,j}^{\kappa\lambda\mu} =
+   \sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^{\mu}_{j,m,m'})^*
+   H {\scriptscriptstyle \begin{array}{l} {j} {m} {m'} \\
+        {j_1} {m_1} {m'_1} \\
+        {j_2} {m_2} {m'_2} \end{array}}
+        u^{\kappa}_{j_1,m_1,m'_1} u^{\lambda}_{j_2,m_2,m'_2}
+
+where :math:`u^{\mu}_{j,m,m'}` is an expansion coefficient for the partial density of neighbors
+of element :math:`\mu`
+
+.. math::
+
+  u^{\mu}_{j,m,m'} =  w^{self}_{\mu_{i}\mu} U^{j,m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{\delta_{\mu\mu_{i'}}f_c(r_{ii'}) w_{\mu_{i'}} U^{j,m,m'}(\theta_0,\theta,\phi)}
+
+where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is either 1 or 0
+(see keyword *wselfallflag* below), :math:`\delta_{\mu\mu_{i'}}` indicates
+that the sum is only over neighbor atoms of element :math:`\mu`,
+and all other quantities are the same as those appearing in the
+original equation for :math:`u^j_{m,m'}` given above.
+
+The keyword *wselfallflag* defines the rule used for the self-contribution.
+If *wselfallflag* is on, then :math:`w^{self}_{\mu_{i}\mu}` = 1. If it is
+off then :math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case
+of :math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1.
+When the *chem* keyword is not used, this keyword has no effect.
+
+The keyword *bnormflag* determines whether or not the bispectrum
+component :math:`B_{j_1,j_2,j}` is divided by a factor of :math:`2j+1`.
+This normalization simplifies force calculations because of the
+following symmetry relation
+
+.. math::
+
+ \frac{B_{j_1,j_2,j}}{2j+1} = \frac{B_{j,j_2,j_1}}{2j_1+1} = \frac{B_{j_1,j,j_2}}{2j_2+1}
+
+This option is typically used in conjunction with the *chem* keyword,
+and LAMMPS will generate a warning if both *chem* and *bnormflag*
+are not both set or not both unset.
+
 .. note::
 
    If you have a bonded system, then the settings of
@@ -257,6 +325,8 @@ described by the following piece of python code:
            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
                if (j>=j1): print j1/2.,j2/2.,j/2.
 
+For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramidal number. For odd twojmax = 2 *m*\ -1, :math:`K = m(m+1)(m+2)/3`, twice the *m*\ -th tetrahedral number.
+
 .. note::
 
    the *diagonal* keyword allowing other possible choices
@@ -267,16 +337,15 @@ described by the following piece of python code:
 Compute *snad/atom* evaluates a per-atom array. The columns are
 arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
 block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
-components of the atom position.  Each of these sub-blocks contains
-one column for each bispectrum component, the same as for compute
-*sna/atom*
+components of the atom position.  Each of these sub-blocks contains *K*
+columns for the *K* bispectrum components, the same as for compute *sna/atom*
 
 Compute *snav/atom* evaluates a per-atom array. The columns are
 arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
 block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
 *yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt
-notation.  Each of these sub-blocks contains one column for each
-bispectrum component, the same as for compute *sna/atom*
+notation.  Each of these sub-blocks contains *K*
+columns for the *K* bispectrum components, the same as for compute *sna/atom*
 
 Compute *snap* evaluates a global array.
 The columns are arranged into
@@ -312,6 +381,14 @@ of linear terms i.e. linear and quadratic terms are contiguous.
 So the nesting order from inside to outside is bispectrum component,
 linear then quadratic, vector/tensor component, type.
 
+If the *chem* keyword is used, then the data is arranged into :math:`N_{elem}^3`
+sub-blocks, each sub-block corresponding to a particular chemical labeling
+:math:`\kappa\lambda\mu` with the last label changing fastest.
+Each sub-block contains *K* bispectrum components. For the purposes
+of handling contributions to force, virial, and quadratic combinations,
+these :math:`N_{elem}^3` sub-blocks are treated as a single block
+of :math:`K N_{elem}^3` columns.
+
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
@@ -320,7 +397,8 @@ Restrictions
 """"""""""""
 
 These computes are part of the SNAP package.  They are only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
 
 Related commands
 """"""""""""""""
@@ -332,6 +410,7 @@ Default
 
 The optional keyword defaults are *rmin0* = 0,
 *switchflag* = 1, *bzeroflag* = 1, *quadraticflag* = 0,
+*bnormflag* = 0, *wselfallflag* = 0
 
 ----------
 
@@ -352,3 +431,11 @@ available at `arXiv:1409.3880 <http://arxiv.org/abs/1409.3880>`_
 
 **(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory
 of Angular Momentum, World Scientific, Singapore (1987).
+
+.. _Mason2009:
+
+**(Mason)** J. K. Mason, Acta Cryst A65, 259 (2009).
+
+.. _Cusentino2020:
+
+**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)

doc/src/fix_adapt.rst

@@ -35,7 +35,7 @@ Syntax
          v_name = variable with name that calculates value of aparam
 
 * zero or more keyword/value pairs may be appended
-* keyword = *scale* or *reset*
+* keyword = *scale* or *reset* or *mass*
 
   .. parsed-literal::
 
@@ -45,6 +45,9 @@ Syntax
        *reset* value = *no* or *yes*
          *no* = values will remain altered at the end of a run
          *yes* = reset altered values to their original values at the end of a run
+       *mass* value = *no* or *yes*
+         *no* = mass is not altered by changes in diameter
+         *yes* = mass is altered by changes in diameter
 
 Examples
 """"""""
@@ -53,7 +56,7 @@ Examples
 
    fix 1 all adapt 1 pair soft a 1 1 v_prefactor
    fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
-   fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+   fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 pair coul/cut scale 3 3 v_scale2 scale yes reset yes
    fix 1 all adapt 10 atom diameter v_size
 
    variable ramp_up equal "ramp(0.01,0.5)"
@@ -86,12 +89,13 @@ the end of a simulation.  Even if *reset* is specified as *yes*\ , a
 restart file written during a simulation will contain the modified
 settings.
 
-If the *scale* keyword is set to *no*\ , then the value of the altered
-parameter will be whatever the variable generates.  If the *scale*
-keyword is set to *yes*\ , then the value of the altered parameter will
-be the initial value of that parameter multiplied by whatever the
-variable generates.  I.e. the variable is now a "scale factor" applied
-in (presumably) a time-varying fashion to the parameter.
+If the *scale* keyword is set to *no*\ , which is the default, then
+the value of the altered parameter will be whatever the variable
+generates.  If the *scale* keyword is set to *yes*\ , then the value
+of the altered parameter will be the initial value of that parameter
+multiplied by whatever the variable generates.  I.e. the variable is
+now a "scale factor" applied in (presumably) a time-varying fashion to
+the parameter.
 
 Note that whether scale is *no* or *yes*\ , internally, the parameters
 themselves are actually altered by this fix.  Make sure you use the
@@ -107,16 +111,17 @@ style supports it.  Note that the :doc:`pair_style <pair_style>` and
 to specify these parameters initially; the fix adapt command simply
 overrides the parameters.
 
-The *pstyle* argument is the name of the pair style.  If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
-a sub-style name.  If there are multiple sub-styles using the same
-pair style, then *pstyle* should be specified as "style:N" where N is
-which instance of the pair style you wish to adapt, e.g. the first,
-second, etc.  For example, *pstyle* could be specified as "soft" or
-"lubricate" or "lj/cut:1" or "lj/cut:2".  The *pparam* argument is the
-name of the parameter to change.  This is the current list of pair
-styles and parameters that can be varied by this fix.  See the doc
-pages for individual pair styles and their energy formulas for the
-meaning of these parameters:
+The *pstyle* argument is the name of the pair style.  If
+:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
+*pstyle* should be a sub-style name.  If there are multiple
+sub-styles using the same pair style, then *pstyle* should be specified
+as "style:N" where N is which instance of the pair style you wish to
+adapt, e.g. the first, second, etc.  For example, *pstyle* could be
+specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2".  The
+*pparam* argument is the name of the parameter to change.  This is the
+current list of pair styles and parameters that can be varied by this
+fix.  See the doc pages for individual pair styles and their energy
+formulas for the meaning of these parameters:
 
 +---------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`born <pair_born>`                                             | a,b,c                                            | type pairs  |
@@ -234,31 +239,32 @@ the coefficients for the symmetric J,I interaction to the same values.
 
 A wild-card asterisk can be used in place of or in conjunction with
 the I,J arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
-number of atom types, then an asterisk with no numeric values means
-all types from 1 to N.  A leading asterisk means all types from 1 to n
-(inclusive).  A trailing asterisk means all types from n to N
+types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+the number of atom types, then an asterisk with no numeric values
+means all types from 1 to N.  A leading asterisk means all types from
+1 to n (inclusive).  A trailing asterisk means all types from n to N
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).  Note that only type pairs with I <= J are considered; if
 asterisks imply type pairs where J < I, they are ignored.
 
-IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
-be a sub-style name.  You must specify I,J arguments that correspond
-to type pair values defined (via the :doc:`pair_coeff <pair_coeff>`
-command) for that sub-style.
+IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
+<pair_hybrid>` is being used, then the *pstyle* will be a sub-style
+name.  You must specify I,J arguments that correspond to type pair
+values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
+that sub-style.
 
 The *v_name* argument for keyword *pair* is the name of an
-:doc:`equal-style variable <variable>` which will be evaluated each time
-this fix is invoked to set the parameter to a new value.  It should be
-specified as v_name, where name is the variable name.  Equal-style
-variables can specify formulas with various mathematical functions,
-and include :doc:`thermo_style <thermo_style>` command keywords for the
-simulation box parameters and timestep and elapsed time.  Thus it is
-easy to specify parameters that change as a function of time or span
-consecutive runs in a continuous fashion.  For the latter, see the
-*start* and *stop* keywords of the :doc:`run <run>` command and the
-*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
-details.
+:doc:`equal-style variable <variable>` which will be evaluated each
+time this fix is invoked to set the parameter to a new value.  It
+should be specified as v_name, where name is the variable name.
+Equal-style variables can specify formulas with various mathematical
+functions, and include :doc:`thermo_style <thermo_style>` command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify parameters that change as a function
+of time or span consecutive runs in a continuous fashion.  For the
+latter, see the *start* and *stop* keywords of the :doc:`run <run>`
+command and the *elaplong* keyword of :doc:`thermo_style custom
+<thermo_style>` for details.
 
 For example, these commands would change the prefactor coefficient of
 the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
@@ -319,23 +325,28 @@ The *atom* keyword enables various atom properties to be changed.  The
 current list of atom parameters that can be varied by this fix:
 
 * charge = charge on particle
-* diameter, or, diameter/disc = diameter of particle
+* diameter or diameter/disc = diameter of particle
 
 The *v_name* argument of the *atom* keyword is the name of an
-:doc:`equal-style variable <variable>` which will be evaluated each time
-this fix is invoked to set, or scale the parameter to a new value.
-It should be specified as v_name, where name is the variable name.  See the
-discussion above describing the formulas associated with equal-style
-variables.  The new value is assigned to the corresponding attribute
-for all atoms in the fix group.
+:doc:`equal-style variable <variable>` which will be evaluated each
+time this fix is invoked to set, or scale the parameter to a new
+value.  It should be specified as v_name, where name is the variable
+name.  See the discussion above describing the formulas associated
+with equal-style variables.  The new value is assigned to the
+corresponding attribute for all atoms in the fix group.
 
 If the atom parameter is *diameter* and per-atom density and per-atom
-mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also
-changed when the diameter changes. The mass is set from the particle volume
-for 3d systems (density is assumed to stay constant). For 2d, the default is
-for LAMMPS to model particles with a radius attribute as spheres.
-However, if the atom parameter is *diameter/disc*, then the mass is
-set from the particle area (the density is assumed to be in mass/distance^2 units).
+mass are defined for particles (e.g. :doc:`atom_style granular
+<atom_style>`), then the mass of each particle is, by default, also
+changed when the diameter changes. The mass is set from the particle
+volume for 3d systems (density is assumed to stay constant). For 2d,
+the default is for LAMMPS to model particles with a radius attribute
+as spheres. However, if the atom parameter is *diameter/disc*, then the
+mass is set from the particle area (the density is assumed to be in
+mass/distance^2 units). The mass of the particle may also be kept constant
+if the *mass* keyword is set to *no*. This can be useful to account for
+diameter changes that do not involve mass changes, e.g., thermal expansion.
+
 
 For example, these commands would shrink the diameter of all granular
 particles in the "center" group from 1.0 to 0.1 in a linear fashion
@@ -348,13 +359,63 @@ over the course of a 1000-step simulation:
 
 ----------
 
+This fix can be used in long simulations which are restarted one or
+more times to continuously adapt simulation parameters, but it must be
+done carefully.  There are two issues to consider.  The first is how
+to adapt the parameters in a continuous manner from one simulation to
+the next.  The second is how, if desired, to reset the parameters to
+their original values at the end of the last restarted run.
+
+Note that all the parameters changed by this fix are written into a
+restart file in their current changed state.  A new restarted
+simulation does not know their original time=0 values, unless the
+input script explicitly resets the parameters (after the restart file
+is read), to their original values.
+
+Also note, that the time-dependent variable(s) used in the restart
+script should typically be written as a function of time elapsed since
+the original simulation began.
+
+With this in mind, if the *scale* keyword is set to *no* (the default)
+in a restarted simulation, original parameters are not needed.  The
+adapted parameters should seamlessly continue their variation relative
+to the preceding simulation.
+
+If the *scale* keyword is set to *yes*, then the input script should
+typically reset the parameters being adapted to their original values,
+so that the scaling formula specified by the variable will operate
+correctly.  An exception is if the *atom* keyword is being used with
+*scale yes*.  In this case, information is added to the restart file
+so that per-atom properties in the new run will automatically be
+scaled relative to their original values.  This will only work if the
+fix adapt command specified in the restart script has the same ID as
+the one used in the original script.
+
+In a restarted run, if the *reset* keyword is set to *yes*, and the
+run ends in this script (as opposed to just writing more restart
+files, parameters will be restored to the values they were at the
+beginning of the run command in the restart script.  Which as
+explained above, may or may not be the original values of the
+parameters.  Again, an exception is if the *atom* keyword is being
+used with *reset yes* (in all the runs). In that case, the original
+per-atom parameters are stored in the restart file, and will be
+restored when the restarted run finally completes.
+
+----------
+
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various :doc:`output commands <Howto_output>`.
-No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+If the *atom* keyword is used and the *scale* or *reset* keyword is
+set to *yes*, then this fix writes information to a restart file so
+that in a restarted run scaling can continue in a seamless manner
+and/or the per-atom values can be restored, as explained above.
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to
+this fix.  No global or per-atom quantities are stored by this fix for
+access by various :doc:`output commands <Howto_output>`.  No parameter
+of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command.  This fix is not invoked during :doc:`energy
+minimization <minimize>`.
 
 For :doc:`rRESPA time integration <run_style>`, this fix changes
 parameters on the outermost rRESPA level.
@@ -371,4 +432,4 @@ Related commands
 Default
 """""""
 
-The option defaults are scale = no, reset = no.
+The option defaults are scale = no, reset = no, mass = yes.

doc/src/pair_coeff.rst

@@ -89,14 +89,20 @@ LAMMPS so long as they are in the format LAMMPS expects, as discussed
 on the individual doc pages.  The first line of potential files may
 contain metadata with upper case tags followed their value. These may
 be parsed and used by LAMMPS.  Currently supported are the "DATE:"
-tag and the "UNITS:" tag.  For pair styles that have been programmed
+tag and the ``UNITS:`` tag.  For pair styles that have been programmed
 to support the metadata, the value of the "DATE:" tag is printed to
 the screen and logfile so that the version of a potential file can be
-later identified.  The "UNITS:" tag indicates the :doc:`units <units>`
+later identified.  The ``UNITS:`` tag indicates the :doc:`units <units>`
 setting required for this particular potential file.  If the potential
-file ware created for a different sets of units, LAMMPS will terminate
+file was created for a different sets of units, LAMMPS will terminate
 with an error.  If the potential file does not contain the tag, no
-check will be made.
+check will be made and it is the responsibility of the user to determine
+that the unit style is correct.
+
+In some select cases and for specific combinations of unit styles,
+LAMMPS is capable of automatically converting potential parameters
+from a file. In those cases, a warning message signaling that an
+automatic conversion has happened is printed to the screen.
 
 When a pair_coeff command using a potential file is specified, LAMMPS
 looks for the potential file in 2 places.  First it looks in the

doc/src/pair_eam.rst

@@ -76,7 +76,7 @@ Examples
 
    pair_style eam
    pair_coeff * * cuu3
-   pair_coeff 1*3 1\*3 niu3.eam
+   pair_coeff 1*3 1*3 niu3.eam
 
    pair_style eam/alloy
    pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni

doc/src/pair_eim.rst

@@ -48,7 +48,7 @@ and :math:`sigma_i` are calculated as
    \sigma_i  = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\
    E_i\left(q_i,\sigma_i\right)  = & \frac{1}{2} \cdot q_i \cdot \sigma_i
 
-where :math:`\eta_{ji} is a pairwise function describing electron flow from atom
+where :math:`\eta_{ji}` is a pairwise function describing electron flow from atom
 I to atom J, and :math:`\psi_{ij}` is another pairwise function.  The multi-body
 nature of the EIM potential is a result of the embedding energy term.
 A complete list of all the pair functions used in EIM is summarized
@@ -63,7 +63,7 @@ below
    \right.\\
    \eta_{ji} = & A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) \\
    \psi_{ij}\left(r\right) = & A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) \\
-   f_{c}\left(r,r_p,r_c\right) = & 0.510204 \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204
+   f_{c}\left(r,r_p,r_c\right) = & 0.510204 \cdot \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204
 
 Here :math:`E_b, r_e, r_(c,\phi), \alpha, \beta, A_(\psi), \zeta, r_(s,\psi),
 r_(c,\psi), A_(\eta), r_(s,\eta), r_(c,\eta), \chi,` and pair function type

doc/src/pair_mdf.rst

@@ -85,7 +85,8 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
 
 .. math::
 
-   E(r) = 4\epsilon\biggl[\bigl(\frac{\sigma}{r}\bigr)^{12} - \bigl(\frac{\sigma}{r}\bigr)^6\biggr]
+   E(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
+                            \left(\frac{\sigma}{r}\right)^6 \right]
 
 Either the first two or all of the following coefficients must be
 defined for each pair of atoms types via the pair_coeff command as in
@@ -141,7 +142,7 @@ given or both left out:
 **Mixing, shift, table, tail correction, restart, rRESPA info**\ :
 
 For atom type pairs I,J and I != J, the :math:`\epsilon` and
-:math:`sigma` coefficients and cutoff distances for the lj/mdf pair
+:math:`\sigma` coefficients and cutoff distances for the lj/mdf pair
 style can be mixed.  The default mix value is *geometric*\ .  See the
 "pair_modify" command for details. The other two pair styles buck/mdf
 and lennard/mdf do not support mixing, so all I,J pairs of coefficients

doc/src/pair_mesont_tpm.rst

@@ -9,7 +9,7 @@ Syntax
 
 .. parsed-literal::
 
-   pair_style mesont/tpm cut table_path BendingMode TPMType 
+   pair_style mesont/tpm cut table_path BendingMode TPMType
 
 * cut = the cutoff distance
 * table_path = the path to the potential table
@@ -114,7 +114,7 @@ study the thermal transport properties of carbon nanotube films
 The methods for modeling of
 the mechanical energy dissipation into heat (energy exchange between the
 dynamic degrees of freedom of the mesoscopic model and the energy of atomic
-vibrations that are not explicitly represented in the model) 
+vibrations that are not explicitly represented in the model)
 :ref:`(Zhigilei10) <Zhigilei10>` and mesoscopic description of covalent cross-links
 between nanotubes :ref:`(Banna) <Banna>` have also been developed but are not
 included in this first release of the LAMMPS implementation of the force field.
@@ -144,7 +144,7 @@ pair interactions.
 The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` ,
 where L is the maximum segment length, R is the maximum tube radius, and
 :math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting
-segments. Because of the use of extended chain concept at CNT ends, the recommended 
+segments. Because of the use of extended chain concept at CNT ends, the recommended
 cutoff is 3L.
 
 The MESONT-TABTP_10_10.xrs potential file provided with LAMMPS (see the

doc/src/pair_mliap.rst

@@ -0,0 +1,136 @@
+.. index:: pair_style mliap
+
+pair_style mliap command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style mliap
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor
+   pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor 
+   pair_coeff * * In P
+
+Description
+"""""""""""
+
+Pair style *mliap* provides a general interface to families of 
+machine-learning interatomic potentials. It provides separate 
+definitions of the interatomic potential functional form (*model*)
+and the geometric quantities that characterize the atomic positions
+(*descriptor*). By defining *model* and *descriptor* separately, 
+it is possible to use many different models with a given descriptor,
+or many different descriptors with a given model. Currently, the pair_style 
+supports just two models, *linear* and *quadratic*,
+and one descriptor, *sna*, the SNAP descriptor used by :doc:`pair_style snap <pair_snap>`, including the linear, quadratic,
+and chem variants. Work is currently underway to extend
+the interface to handle neural network energy models,
+and it is also straightforward to add new descriptor styles.
+
+The pair_style *mliap* command must be followed by two keywords
+*model* and *descriptor* in either order. A single
+*pair_coeff* command is also required. The first 2 arguments 
+must be \* \* so as to span all LAMMPS atom types.
+This is followed by a list of N arguments
+that specify the mapping of MLIAP
+element names to LAMMPS atom types, 
+where N is the number of LAMMPS atom types.
+
+The *model* keyword is followed by a model style, currently limited to
+either *linear* or *quadratic*. In both cases,
+this is followed by a single argument specifying the model filename containing the 
+linear or quadratic coefficients for a set of elements. 
+The model filename usually ends in the *.mliap.model* extension.
+It may contain coefficients for many elements. The only requirement is that it
+contain at least those element names appearing in the
+*pair_coeff* command.
+
+The top of the model file can contain any number of blank and comment lines (start with #), 
+but follows a strict format after that. The first non-blank non-comment
+line must contain two integers:
+
+* nelems  = Number of elements
+* ncoeff = Number of coefficients
+
+This is followed by one block for each of the *nelem* elements.
+Each block consists of *ncoeff* coefficients, one per line.
+Note that this format is similar, but not identical to that used
+for the :doc:`pair_style snap <pair_snap>` coefficient file.
+Specifically, the line containing the element weight and radius is omitted, 
+since these are handled by the *descriptor*.
+
+The *descriptor* keyword is followed by a descriptor style, and additional arguments.
+Currently the only descriptor style is *sna*, indicating the bispectrum component 
+descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of 
+:doc:`pair_style snap <pair_snap>`.
+The \'p\' in SNAP is dropped, because keywords that match pair_styles are silently stripped 
+out by the LAMMPS command parser. A single additional argument specifies the descriptor filename 
+containing the parameters and setting used by the SNAP descriptor. 
+The descriptor filename usually ends in the *.mliap.descriptor* extension.
+
+The SNAP descriptor file closely follows the format of the 
+:doc:`pair_style snap <pair_snap>` parameter file. 
+The file can contain blank and comment lines (start
+with #) anywhere. Each non-blank non-comment line must contain one
+keyword/value pair. The required keywords are *rcutfac* and
+*twojmax*\ . There are many optional keywords that are described
+on the :doc:`pair_style snap <pair_snap>` doc page.
+In addition, the SNAP descriptor file must contain
+the *nelems*, *elems*, *radelems*, and *welems* keywords.
+The *nelems* keyword specifies the number of elements
+provided in the other three keywords.
+The *elems* keyword is followed by a list of *nelems* 
+element names that must include the element
+names appearing in the *pair_coeff* command,
+but can contain other names too.
+Similarly, the *radelems* and *welems* keywords are
+followed by lists of *nelems* numbers giving the element radius
+and element weight of each element. Obviously, the order
+in which the elements are listed must be consistent for all
+three keywords.
+
+See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for these *model* and *descriptor* files.
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands 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
+*inner*\ , *middle*\ , *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This style is part of the MLIAP package.  It is only enabled if LAMMPS
+was built with that package. In addition, building LAMMPS with the MLIAP package
+requires building LAMMPS with the SNAP package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style snap  <pair_snap>`,
+
+**Default:** none

doc/src/pair_snap.rst

@@ -24,27 +24,30 @@ Examples
 Description
 """""""""""
 
-Pair style *snap* computes interactions using the spectral
-neighbor analysis potential (SNAP) :ref:`(Thompson) <Thompson20142>`.
-Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
-:ref:`(Bartok2013) <Bartok2013>` which uses bispectrum components
+Pair style *snap* defines the spectral
+neighbor analysis potential (SNAP), a machine-learning 
+interatomic potential :ref:`(Thompson) <Thompson20142>`.
+Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`, 
+SNAP uses bispectrum components
 to characterize the local neighborhood of each atom
 in a very general way. The mathematical definition of the
-bispectrum calculation used by SNAP is identical
-to that used by :doc:`compute sna/atom <compute_sna_atom>`.
+bispectrum calculation and its derivatives w.r.t. atom positions
+is identical to that used by :doc:`compute snap <compute_sna_atom>`,
+which is used to fit SNAP potentials to *ab initio* energy, force,
+and stress data.
 In SNAP, the total energy is decomposed into a sum over
 atom energies. The energy of atom *i* is
 expressed as a weighted sum over bispectrum components.
 
 .. math::
 
-   E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i
+   E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i
 
 where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ ,
-and :math:`\beta_k^{\alpha_i}` is the corresponding linear coefficient
-that depends on :math:\alpha_i`, the SNAP element of atom *i*\ . The
+and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient
+that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The
 number of bispectrum components used and their definitions
-depend on the value of *twojmax*
+depend on the value of *twojmax* and other parameters
 defined in the SNAP parameter file described below.
 The bispectrum calculation is described in more detail
 in :doc:`compute sna/atom <compute_sna_atom>`.
@@ -136,17 +139,51 @@ The SNAP parameter file can contain blank and comment lines (start
 with #) anywhere. Each non-blank non-comment line must contain one
 keyword/value pair. The required keywords are *rcutfac* and
 *twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ ,
-*switchflag*\ , *bzeroflag*\, and *chunksize*\.
+*switchflag*\ , *bzeroflag*\ , *quadraticflag*\ , *chemflag*\ , 
+*bnormflag*\ , *wselfallflag*\ , and *chunksize*\ .
 
 The default values for these keywords are
 
 * *rfac0* = 0.99363
 * *rmin0* = 0.0
-* *switchflag* = 0
+* *switchflag* = 1
 * *bzeroflag* = 1
-* *quadraticflag* = 1
+* *quadraticflag* = 0
+* *chemflag* = 0
+* *bnormflag* = 0
+* *wselfallflag* = 0
 * *chunksize* = 2000
 
+If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms 
+that have been shown to increase the overall accuracy of the potential without much increase
+in computational cost :ref:`(Wood) <Wood20182>`. 
+
+.. math::
+
+   E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i
+
+where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components, 
+:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients 
+for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}` 
+is the symmetric *K* by *K* matrix of quadratic coefficients.
+The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
+for each element, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
+
+If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum
+components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP
+potential to capture energy differences in chemically complex systems, 
+at the expense of a significant increase in computational cost :ref:`(Cusentino) <Cusentino20202>`.
+
+.. math::
+
+   E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i 
+
+where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components 
+for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and 
+:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector 
+of linear coefficients for element :math:`\mu_i`. The SNAP element file should contain 
+a total of :math:`K N_{elem}^3` coefficients for each of the :math:`N_{elem}` elements.
+
 The keyword *chunksize* is only applicable when using the
 pair style *snap* with the KOKKOS package and is ignored otherwise.
 This keyword controls
@@ -159,10 +196,6 @@ into two passes.
 Detailed definitions for all the other keywords
 are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.
 
-If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
-The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
-for each element, the upper-triangular elements of alpha.
-
 .. note::
 
    The previously used *diagonalstyle* keyword was removed in 2019,
@@ -221,7 +254,8 @@ Related commands
 
 :doc:`compute sna/atom <compute_sna_atom>`,
 :doc:`compute snad/atom <compute_sna_atom>`,
-:doc:`compute snav/atom <compute_sna_atom>`
+:doc:`compute snav/atom <compute_sna_atom>`,
+:doc:`compute snap <compute_sna_atom>`
 
 **Default:** none
 
@@ -235,6 +269,10 @@ Related commands
 
 **(Bartok2010)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
-.. _Bartok2013:
+.. _Wood20182:
 
-**(Bartok2013)** Bartok, Gillan, Manby, Csanyi, Phys Rev B 87, 184115 (2013).
+**(Wood)** Wood and Thompson, J Chem Phys, 148, 241721, (2018)
+
+.. _Cusentino20202:
+
+**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)

doc/src/pair_style.rst

@@ -291,6 +291,7 @@ accelerated styles exist.
 * :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
+* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
 * :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
 * :doc:`soft <pair_soft>` - Soft (cosine) potential
 * :doc:`sph/heatconduction <pair_sph_heatconduction>` -

doc/src/pair_tersoff_mod.rst

@@ -74,7 +74,7 @@ formulation of the V_ij term, where it contains an additional c0 term.
 
 .. math::
 
-   V_{ij}  & = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+   V_{ij}  = f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
 
 The modified cutoff function :math:`f_C` proposed by :ref:`(Murty) <Murty>` and
 having a continuous second-order differential is employed. The

doc/src/units.rst

@@ -49,6 +49,15 @@ new units.  And you must correctly convert all output from the new
 units to the old units when comparing to the original results.  That
 is often not simple to do.
 
+Potential or table files may have a ``UNITS:`` tag included in the
+first line indicating the unit style those files were created for.
+If the tag exists, its value will be compared to the chosen unit style
+and LAMMPS will stop with an error message if there is a mismatch.
+In some select cases and for specific combinations of unit styles,
+LAMMPS is capable of automatically converting potential parameters
+from a file. In those cases, a warning message signaling that an
+automatic conversion has happened is printed to the screen.
+
 ----------
 
 For style *lj*\ , all quantities are unitless.  Without loss of

doc/utils/sphinx-config/false_positives.txt

@@ -487,6 +487,7 @@ Critchley
 crossterm
 Crowson
 Crozier
+Cryst
 Crystallogr
 Csanyi
 csh
@@ -510,6 +511,7 @@ CuH
 cuFFT
 Cummins
 Curk
+Cusentino
 customIDs
 cutbond
 cuthi
@@ -1758,6 +1760,7 @@ mem
 memalign
 MEMALIGN
 membered
+memcheck
 Mendelev
 mer
 Meremianin
@@ -1824,6 +1827,7 @@ Mj
 mK
 mkdir
 mkv
+mliap
 mlparks
 Mniszewski
 mnt
@@ -1993,6 +1997,7 @@ Neel
 Neelov
 Negre
 nelem
+nelems
 Nelement
 Nelements
 nemd
@@ -3296,6 +3301,7 @@ xsu
 xtc
 xu
 Xu
+xxxxx
 xy
 xyz
 xz

examples/README

@@ -88,6 +88,7 @@ melt:     rapid melt of 3d LJ system
 message:  client/server coupling of 2 codes
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
+mliap:    examples for using several bundled MLIAP potentials
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style

examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff

@@ -1,66 +0,0 @@
-# Tersoff parameters for various elements and mixtures
-# multiple entries can be added to this file, LAMMPS reads the ones it needs
-# these entries are in LAMMPS "metal" units:
-#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
-#   other quantities are unitless
-
-# Aidan Thompson (athomps at sandia.gov) takes full blame for this
-# file.  It specifies various potentials published by J. Tersoff for
-# silicon, carbon and germanium. Since Tersoff published several
-# different silicon potentials, I refer to them using atom types
-# Si(B), Si(C) and Si(D). The last two are almost almost identical but
-# refer to two different publications. These names should be used in
-# the LAMMPS command when the file is invoked. For example:
-# pair_coeff * * SiCGe.tersoff Si(B).  The Si(D), C and Ge potentials
-# can be used pure silicon, pure carbon, pure germanium, binary SiC,
-# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
-# generate an error if this file is used with any combination
-# involving C and Ge, since there are no entries for the GeC
-# interactions (Tersoff did not publish parameters for this
-# cross-interaction.)
-
-# format of a single entry (one or more lines):
-#   element 1, element 2, element 3, 
-#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
-
-# The original Tersoff potential for Silicon, Si(B)
-# J. Tersoff, PRB, 37, 6991 (1988) 
-
-Si(B)  Si(B)   Si(B)  3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
-             0.33675  1.3258  95.373  3.0  0.2  3.2394  3264.7
-
-# The later Tersoff potential for Silicon, Si(C)
-# J. Tersoff, PRB, 38, 9902 (1988) 
-
-Si(C)  Si(C)   Si(C)  3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
-             1.0999e-6  1.7322  471.18  2.85  0.15  2.4799  1830.8
-
-# The later Tersoff potential for Carbon, Silicon, and Germanium
-# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
-# The Si and C parameters are very close to those in SiC.tersoff
-
-C      C       C         3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7  2.2119  346.74    1.95    0.15   3.4879  1393.6
-Si(D)  Si(D)   Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.7322  471.18    2.85    0.15   2.4799  1830.8
-Ge     Ge      Ge        3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7  1.7047  419.23    2.95    0.15   2.4451  1769.0
-
-C      Si(D)   Si(D)     3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7  1.97205 395.1451  2.3573  0.1527 2.9839  1597.3111
-C      Si(D)   C         3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0        0.0     0.0       1.95    0.15   0.0     0.0
-C      C       Si(D)     3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0        0.0     0.0       2.3573  0.1527 0.0     0.0
-
-Si(D)  C       C         3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.97205 395.1451  2.3573  0.1527 2.9839  1597.3111
-Si(D)  Si(D)   C         3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.3573  0.1527 0.0     0.0
-Si(D)  C       Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.85    0.15   0.0     0.0
- 
-Si(D)  Ge      Ge        3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.71845 444.7177  2.8996  0.1500 2.4625  1799.6347
-Si(D)  Si(D)   Ge        3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.8996  0.1500 0.0     0.0
-Si(D)  Ge      Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.85    0.15   0.0     0.0
- 
-Ge     Si(D)   Si(D)     3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7  1.71845 444.7177  2.8996  0.1500 2.4625  1799.6347
-Ge     Si(D)   Ge        3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0        0.0     0.0       2.95    0.15   0.0     0.0
-Ge     Ge      Si(D)     3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0        0.0     0.0       2.8996  0.1500 0.0     0.0
-
-# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) 
-#   element 1, element 2, element 3, 
-#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
-C(O)    C(O)   C(O)     3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7  2.2119  430.0    1.95    0.15   3.4879  1393.6
-

examples/USER/phonon/dynamical_matrix_command/Silicon/SiCGe.tersoff

@@ -0,0 +1 @@
+../../../../../potentials/SiCGe.tersoff

examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp

@@ -16,4 +16,4 @@ mass ${Si}     28.08550
 ###########################
 
 pair_style      tersoff
-pair_coeff      * *  Si.opt.tersoff Si(D)
+pair_coeff      * * SiCGe.tersoff Si(D)

examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat

@@ -1,192 +1,192 @@
 5409.83472486 3.05075234 0.00000214
--1277.48270695 -863.24917964 -862.95613831
--193.14095266 0.11071645 0.00000015
--1277.48270619 -863.24917934 862.95613793
--193.17613831 0.34066975 -0.00000031
--1276.01088244 861.54715125 -861.62537402
-83.46959051 -0.09801326 0.00000000
--1276.01088167 861.54715064 861.62537387
-3.05073556 5409.83419867 0.00000137
--863.13224993 -1277.34160622 -862.92133430
-0.12865796 -193.14095472 -0.00000023
--863.13224825 -1277.34160485 862.92133392
--0.23661028 83.46934214 -0.00000046
-861.66402909 -1276.15172701 861.66024333
--0.00634065 -193.17585981 -0.00000015
-861.66402909 -1276.15172686 -861.66024394
-0.00000031 0.00000031 5410.11037330
--862.89766079 -862.97973912 -1277.71823542
-0.00000000 -0.00000008 83.84059083
-862.89766018 862.97973851 -1277.71823557
-0.00000015 0.00000015 -193.17558390
--861.60900269 861.52691291 -1276.08157137
--0.00000015 -0.00000031 -193.17573821
-861.60900330 -861.52691284 -1276.08157236
--1277.48271824 -863.13225435 -862.89768596
-5409.83567916 3.04882502 2.82007861
--1277.34161080 -863.24919475 862.97975804
--193.14089260 0.11950100 0.11994134
--1277.52243157 863.24943259 -863.11331046
--193.17597070 0.16713301 -0.02106496
--1274.64156872 859.96385388 860.17328202
-83.46945758 -0.16730525 -0.06100253
--863.24919444 -1277.34161103 -862.97975804
-3.04882666 5409.83567944 -2.82007731
--863.13225496 -1277.48271916 862.89768688
-0.11950094 -193.14089255 -0.11994043
-863.24943320 -1277.52243118 863.11331076
--0.16730522 83.46945778 0.06100314
-859.96385365 -1274.64156819 -860.17328225
-0.16713979 -193.17596607 0.02106008
--862.95611199 -862.92132598 -1277.71824411
-2.82004085 -2.82004013 5410.11000835
-862.92132743 862.95611344 -1277.71824587
--0.11994722 0.11994786 83.84083834
--862.88110757 862.88110699 -1277.34764097
-0.02099713 0.06108924 -193.17561785
-860.25587487 -860.25587502 -1274.81548840
--0.06108897 -0.02099687 -193.17561808
--193.14095465 0.12865765 0.00000015
--1277.34160508 -863.13224794 862.92133361
-5409.83419867 3.05073968 0.00000092
--1277.34160584 -863.13224924 -862.92133483
-83.46934214 -0.23660998 -0.00000076
--1276.15172724 861.66402917 861.66024325
--193.17585988 -0.00634042 -0.00000031
--1276.15172694 861.66402940 -861.66024325
-0.11071645 -193.14095243 0.00000046
--863.24917949 -1277.48270718 862.95613831
-3.05075524 5409.83472478 -0.00000046
--863.24918117 -1277.48270825 -862.95613923
-0.34066922 -193.17613823 0.00000046
-861.54715094 -1276.01088228 -861.62537295
--0.09801303 83.46959035 0.00000015
-861.54713538 -1276.01088145 861.62537387
--0.00000046 -0.00000023 83.84059068
-862.97973867 862.89766010 -1277.71823633
--0.00000214 -0.00000053 5410.11037574
--862.97973943 -862.89766079 -1277.71823633
-0.00000015 0.00000008 -193.17558374
-861.52691291 -861.60900269 -1276.08157198
--0.00000015 -0.00000015 -193.17573814
--861.52691368 861.60900261 -1276.08157243
+-1277.48271855 -863.13225405 -862.89768612
+-193.14095469 0.12865732 0.00000061
 -1277.48271786 -863.13225450 862.89768520
--193.14089232 0.11950085 -0.11994115
--1277.34161255 -863.24919673 -862.97975957
-5409.83568051 3.04882517 -2.82007644
--1277.52243110 863.24943259 863.11330990
-83.46945732 -0.16730494 0.06100319
--1274.64156796 859.96385342 -860.17328103
--193.17597041 0.16713331 0.02106477
--863.24919482 -1277.34161057 862.97975774
-0.11950077 -193.14089270 0.11994160
--863.13225473 -1277.48271839 -862.89768673
-3.04882502 5409.83568081 2.82007903
-863.24943084 -1277.52242966 -863.11330868
-0.16713324 -193.17597064 -0.02106522
-859.96385510 -1274.64156926 860.17328255
--0.16730411 83.46945641 -0.06100350
-862.95611161 862.92132537 -1277.71824365
-0.11994725 -0.11994740 83.84083859
--862.92132606 -862.95611207 -1277.71824548
--2.82003936 2.82004013 5410.11000806
-862.88110509 -862.88110547 -1277.34764015
-0.06108893 0.02099703 -193.17561792
--860.25587388 860.25587441 -1274.81548916
--0.02099726 -0.06108878 -193.17561777
--193.17613465 -0.23660693 0.00000015
--1277.52241409 863.24943328 -862.88111478
-83.46934549 0.34066334 -0.00000015
--1277.52241425 863.24943335 862.88111508
-5404.58897235 -9.71806749 0.00000015
--1273.31333522 -858.38273960 -858.96245956
--193.21062369 -0.11938368 0.00000000
--1273.31333598 -858.38273967 858.96245926
-0.34066342 83.46934572 0.00000015
-863.24943335 -1277.52241402 862.88111478
--0.23660723 -193.17613480 -0.00000046
-863.24943320 -1277.52241425 -862.88111432
--9.71806582 5404.58897135 -0.00000183
--858.38273891 -1273.31333552 -858.96245926
--0.11938338 -193.21062369 0.00000000
--858.38273937 -1273.31333598 858.96245987
--0.00000031 -0.00000008 -193.17559595
--863.11328229 863.11328297 -1277.34763999
-0.00000000 -0.00000015 -193.17559595
-863.11328305 -863.11328282 -1277.34763984
-0.00000122 -0.00000259 5404.30470550
--858.80486827 -858.80486866 -1273.17865241
--0.00000031 0.00000000 83.09905870
-858.80486827 858.80486812 -1273.17865272
+-193.17613450 -0.23660702 0.00000031
 -1276.01089136 861.66402482 -861.60900483
--193.17596134 -0.16730494 0.02099535
--1276.15175745 861.54714988 861.52691337
-83.46947097 0.16714109 0.06108436
--1273.31334651 -858.38273311 -858.80488185
-5404.58493608 -3.04507687 -2.81778617
--1276.19187193 -861.66399965 861.74280750
--193.21058304 -0.11920641 -0.12012575
-861.54714972 -1276.15175730 861.52691337
-0.16714140 83.46947120 0.06108451
-861.66402345 -1276.01089022 -861.60900330
--0.16730487 -193.17596164 0.02099489
--858.38273281 -1273.31334681 -858.80488063
--3.04507603 5404.58493554 -2.81778617
--861.66400079 -1276.19187270 861.74280887
--0.11920511 -193.21058281 -0.12012498
--861.62536929 861.66025668 -1276.08157121
--0.02106026 0.06099877 -193.17561197
-861.66025752 -861.62537051 -1276.08157274
-0.06099923 -0.02106049 -193.17561227
--858.96244980 -858.96244965 -1273.17866523
--2.81780608 -2.81780615 5404.30474272
-861.58531232 861.58531248 -1275.71087663
-0.12013467 0.12013460 83.09915619
-83.46958166 -0.00634218 -0.00000023
--1274.64157002 859.96383191 860.25587098
--193.17585332 -0.09802844 0.00000023
--1274.64157155 859.96383290 -860.25587243
--193.21062064 -0.11939070 -0.00000008
--1276.19189573 -861.66398638 861.58531118
-5404.58377546 3.62403097 0.00000015
--1276.19189558 -861.66398615 -861.58531103
--0.09802859 -193.17585355 -0.00000015
-859.96383206 -1274.64156979 -860.25587113
--0.00634187 83.46958204 -0.00000008
-859.96383282 -1274.64157132 860.25587212
--0.11939055 -193.21062041 0.00000000
--861.66398576 -1276.19189528 861.58531087
-3.62402982 5404.58377698 -0.00000076
--861.66398927 -1276.19189772 -861.58531331
-0.00000000 0.00000000 -193.17573654
-860.17327676 -860.17327637 -1274.81551212
-0.00000031 0.00000023 -193.17573676
--860.17327615 860.17327645 -1274.81551258
-0.00000000 0.00000015 83.09907327
-861.74281299 861.74281299 -1275.71086763
--0.00000046 -0.00000015 5404.30514861
--861.74281406 -861.74281421 -1275.71086938
+83.46958227 -0.00634221 -0.00000026
 -1276.01088968 861.66402284 861.60900330
-83.46947136 0.16714109 -0.06108436
--1276.15175722 861.54714957 -861.52691391
--193.17596141 -0.16730510 -0.02099527
--1273.31334666 -858.38273281 858.80488124
--193.21058304 -0.11920641 0.12012636
--1276.19187285 -861.66400087 -861.74280773
-5404.58493638 -3.04507565 2.81778602
+3.05073556 5409.83419867 0.00000137
+-863.24919414 -1277.34161118 -862.97975804
+0.11071644 -193.14095221 0.00000015
+-863.24919482 -1277.34161057 862.97975774
+0.34066372 83.46934579 0.00000015
+861.54714972 -1276.15175730 861.52691337
+-0.09802844 -193.17585342 -0.00000005
 861.54715133 -1276.15175913 -861.52691490
--0.16730502 -193.17596118 -0.02099497
-861.66402314 -1276.01088976 861.60900383
-0.16714125 83.46947151 -0.06108497
--858.38273296 -1273.31334681 858.80488139
--0.11920686 -193.21058311 0.12012605
--861.66400079 -1276.19187255 -861.74280811
--3.04506703 5404.58493432 2.81779319
+0.00000031 0.00000031 5410.11037330
+-862.95611222 -862.92132598 -1277.71824426
+-0.00000027 -0.00000023 83.84059068
+862.95611161 862.92132537 -1277.71824365
+-0.00000015 0.00000006 -193.17559671
+-861.62536929 861.66025668 -1276.08157121
+0.00000031 -0.00000000 -193.17573662
 861.62536952 -861.66025637 -1276.08157175
+-1277.48270695 -863.24917964 -862.95613831
+5409.83567791 3.04882503 2.82007909
+-1277.34160500 -863.13224794 862.92133361
+-193.14089232 0.11950085 -0.11994115
+-1277.52241409 863.24943335 -862.88111478
+-193.17596134 -0.16730494 0.02099535
+-1274.64156987 859.96383191 860.25587098
+83.46947136 0.16714109 -0.06108436
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examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon

@@ -1,7 +1,7 @@
-LAMMPS (16 Jul 2018)
+LAMMPS (15 Jun 2020)
 Reading data file ...
-  orthogonal box = (0 0 0) to (5.431 5.431 5.431)
-  1 by 2 by 2 MPI processor grid
+  orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431)
+  1 by 1 by 1 MPI processor grid
   reading atoms ...
   8 atoms
 Finding 1-2 1-3 1-4 neighbors ...
@@ -11,6 +11,9 @@ Finding 1-2 1-3 1-4 neighbors ...
   0 = max # of 1-3 neighbors
   0 = max # of 1-4 neighbors
   1 = max # of special neighbors
+  special bonds CPU = 4.2e-05 secs
+  read_data CPU = 0.002 secs
+Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -23,36 +26,40 @@ Neighbor list info ...
       pair build: full/bin
       stencil: full/bin/3d
       bin: standard
-Calculating Dynamical Matrix...
-Dynamical Matrix calculation took 0.001183 seconds
+Calculating Dynamical Matrix ...
+  Total # of atoms = 8
+  Atoms in group = 8
+  Total dynamical matrix elements = 576
+ 10% 20% 30% 50% 60% 70% 80%
 Finished Calculating Dynamical Matrix
-Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms
+Loop time of 0.000775099 on 1 procs for 48 steps with 8 atoms
 
-0.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5350.544 ns/day, 0.004 hours/ns, 61927.589 timesteps/s
+91.3% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.00016781 | 0.00041345 | 0.00051464 |   0.0 |  0.00
-Bond    | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 |   0.0 |  0.00
+Pair    | 0.00074148 | 0.00074148 | 0.00074148 |   0.0 | 95.66
+Bond    | 3.8147e-06 | 3.8147e-06 | 3.8147e-06 |   0.0 |  0.49
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00056143 | 0.00066602 | 0.00090865 |   0.0 |  0.00
+Comm    | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 |   0.0 |  1.02
 Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.224e+06  |            |       |100.00
+Modify  | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 |   0.0 |  0.12
+Other   |            | 2.098e-05  |            |       |  2.71
 
-Nlocal:    2 ave 3 max 1 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Nghost:    56 ave 57 max 55 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
+Nlocal:    8 ave 8 max 8 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    86 ave 86 max 86 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  32 ave 48 max 16 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 128
 Ave neighs/atom = 16
 Ave special neighs/atom = 0
-Neighbor list builds = 0
+Neighbor list builds = 1
 Dangerous builds = 0
 Total wall time: 0:00:00

examples/USER/phonon/dynamical_matrix_command/python/SiCGe.tersoff

@@ -0,0 +1 @@
+../../../../../potentials/SiCGe.tersoff

examples/USER/phonon/dynamical_matrix_command/python/dynmat.py

@@ -38,5 +38,5 @@ dynmat = dynmat.reshape((dynlen, dynlen))
 eigvals, eigvecs = np.linalg.eig(dynmat)
 
 # frequencies in THz
-omegas = np.sqrt(np.abs(eigvals))
+omegas = np.sqrt(np.abs(eigvals))/2/np.pi
 print(omegas)

examples/USER/phonon/dynamical_matrix_command/python/ff-silicon.lmp

@@ -0,0 +1 @@
+../Silicon/ff-silicon.lmp

examples/USER/phonon/dynamical_matrix_command/python/results/dynmat.dat

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+-0.00634065 -193.17585981 -0.00000015
+859.96385345 -1274.64156845 -860.17328227
+-0.09801307 83.46959066 0.00000092
+859.96385342 -1274.64156728 860.17328103
+-0.11938399 -193.21062370 0.00000031
+-861.66399988 -1276.19187163 861.74280780
+3.62403013 5404.58377402 0.00000142
+-861.66400079 -1276.19187255 -861.74280803
+-0.00000031 -0.00000038 -193.17573821
+860.25587448 -860.25587441 -1274.81548871
+0.00000000 -0.00000026 -193.17573875
+-860.25587388 860.25587456 -1274.81548916
+0.00000015 -0.00000009 83.09905855
+861.58531164 861.58531156 -1275.71087571
+0.00000046 0.00000089 5404.30514766
+-861.58531232 -861.58531217 -1275.71087655
+-1276.01088198 861.54713523 861.62537356
+83.46945674 -0.16730402 -0.06100344
+-1276.15172688 861.66402939 -861.66024402
+-193.17596584 0.16713972 0.02106034
+-1273.31333552 -858.38273940 858.96245956
+-193.21058227 -0.11920503 -0.12012498
+-1276.19189573 -861.66398605 -861.58531085
+5404.58493188 -3.04506924 2.81779059
+861.66402925 -1276.15172686 -861.66024394
+0.16713982 -193.17596610 0.02106041
+861.54713537 -1276.01088130 861.62537448
+-0.16730426 83.46945625 -0.06100350
+-858.38273967 -1273.31333570 858.96245987
+-0.11920511 -193.21058281 -0.12012514
+-861.66398958 -1276.19189780 -861.58531314
+-3.04506687 5404.58493417 2.81779303
+861.60900299 -861.52691253 -1276.08157236
+-0.06108885 -0.02099714 -193.17561830
+-861.52691343 861.60900260 -1276.08157198
+-0.02099726 -0.06108848 -193.17561792
+858.80486782 858.80486829 -1273.17865256
+0.12013467 0.12013460 83.09915604
+-861.74281406 -861.74281426 -1275.71086942
+2.81780737 2.81780737 5404.30474524

examples/USER/phonon/dynamical_matrix_command/python/results/out.dynamt

@@ -0,0 +1,71 @@
+LAMMPS (15 Jun 2020)
+Reading data file ...
+  orthogonal box = (0.0 0.0 0.0) to (5.431 5.431 5.431)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 4.2e-05 secs
+  read_data CPU = 0.001 secs
+Reading potential file ../../../../../potentials/SiCGe.tersoff with DATE: 2009-03-18
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4
+  ghost atom cutoff = 4
+  binsize = 2, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Calculating Dynamical Matrix ...
+  Total # of atoms = 8
+  Atoms in group = 8
+  Total dynamical matrix elements = 576
+ 10% 20% 30% 50% 60% 70% 80%[3.34264870e-05 6.09176101e-05 1.72068597e-04 1.60807822e+01
+ 1.60807027e+01 1.60806903e+01 1.48964054e+01 1.49012648e+01
+ 1.49129598e+01 1.49081641e+01 1.48999471e+01 1.49095175e+01
+ 1.21983946e+01 1.21957091e+01 1.22010862e+01 1.22037817e+01
+ 1.22037910e+01 1.22037868e+01 6.89648276e+00 6.89524412e+00
+ 6.89619622e+00 6.89553366e+00 6.89615471e+00 6.89557491e+00]
+
+Finished Calculating Dynamical Matrix
+Loop time of 0.000677109 on 1 procs for 48 steps with 8 atoms
+
+Performance: 6124.865 ns/day, 0.004 hours/ns, 70889.645 timesteps/s
+91.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00064349 | 0.00064349 | 0.00064349 |   0.0 | 95.04
+Bond    | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 |   0.0 |  0.14
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.1683e-05 | 1.1683e-05 | 1.1683e-05 |   0.0 |  1.73
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 |   0.0 |  0.14
+Other   |            | 2.003e-05  |            |       |  2.96
+
+Nlocal:    8 ave 8 max 8 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    86 ave 86 max 86 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Ave special neighs/atom = 0
+Neighbor list builds = 1
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/phonon/dynamical_matrix_command/python/silicon_input_file.lmp

@@ -0,0 +1 @@
+../Silicon/silicon_input_file.lmp

examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_potential.mod

@@ -1,15 +1,15 @@
 #This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
 
 #Pair Potentials
-pair_style		hybrid/overlay buck/coul/long ${cut_off} table linear 39901
-pair_coeff		1 1 buck/coul/long 0.0 1.0 0.0								#No interactions between Si atoms 
-pair_coeff		1 2 buck/coul/long 18003.757200 0.205205 133.538100	
-pair_coeff		2 2 buck/coul/long 1388.773000  0.362319 175.000000					#BKS interaction in PRL 64 1955 (1990)
-pair_modify		shift yes
-pair_coeff		1 2 table potential_SiO2.TPF Si-O ${cut_off}
-pair_coeff		2 2 table potential_SiO2.TPF O-O ${cut_off}						#See the potential file for more information
-kspace_style		pppm 1.0e-4 
+pair_style              hybrid/overlay buck/coul/long ${cut_off} table linear 39901
+pair_coeff              1 1 buck/coul/long 0.0 1.0 0.0                                                          #No interactions between Si atoms
+pair_coeff              1 2 buck/coul/long 18003.757200 0.205205 133.538100
+pair_coeff              2 2 buck/coul/long 1388.773000  0.362319 175.000000                                     #BKS interaction in PRL 64 1955 (1990)
+pair_modify             shift yes
+pair_coeff              1 2 table potential_SiO2.TPF Si-O ${cut_off}
+pair_coeff              2 2 table potential_SiO2.TPF O-O ${cut_off}                                             #See the potential file for more information
+kspace_style            pppm 1.0e-4
 
 #Neighbor style
-neighbor		2.0 bin
-neigh_modify		check yes every 1 delay 0 page 100000 one 2000
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000

examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qbmsst.in

@@ -1,55 +0,0 @@
-## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
-variable		x_rep equal 2	#plot is made with x_rep = 8						#x-direction replication number
-variable		y_rep equal 1	#plot is made with y_rep = 5						#y-direction replication number
-variable		z_rep equal 4	#plot is made with z_rep = 15						#z-direction replication number
-variable		cut_off equal 10.0									#Cut-off distance for the Buckingham term (Angstrom in metal units)
-variable		pressure equal 1.03125									#Initial state pressure (bar in metal units)
-variable		temperature equal 300.0									#Initial state quantum temperature (K in metal units)
-variable		delta_t equal 1.0e-3									#MD timestep length (ps in metal units)
-variable		damp_qtb equal 1									#1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
-variable		v_msst equal 78.0									#Shock velocity (Angstrom/ps in metal units)
-variable		q_msst equal 40.0									#Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
-variable		tscale_msst equal 0.05									#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)
-
-
-## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
-include			alpha_quartz_qtb.mod
-
-
-## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation. 
-## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
-#Compression restart 1
-reset_timestep		0
-#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
-fix			shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 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}
-run			1000
-write_restart		restart.1000
-
-#Compression restart 2
-#Read restart file and load potential again
-clear
-read_restart		restart.1000
-include			alpha_quartz_potential.mod
-#Use the same fix id and add no tscale if the system is already compressed
-fix			shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 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			10000 											#10 ps

examples/USER/qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod

@@ -3,60 +3,60 @@
 
 ## This part defines units, alpha-quartz crystal, and atomic information
 #General
-units			metal
-dimension		3
-boundary		p p p
-atom_style		charge
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
 
 #Lattice
-lattice			custom 1.0 &
-			a1	4.916000 0.000000 0.000000 &
-			a2	-2.45800 4.257381 0.000000 &
-			a3	0.000000 0.000000 5.405400 &
-			&		
-			basis	0.469700 0.000000 0.000000 &
-			basis	0.000000 0.469700 0.666667 &
-			basis	0.530300 0.530300 0.333333 &
-			&
-			basis	0.413500 0.266900 0.119100 &
-			basis	0.266900 0.413500 0.547567 &
-			basis	0.733100 0.146600 0.785767 &
-			basis	0.586500 0.853400 0.214233 &
-			basis	0.853400 0.586500 0.452433 &
-			basis	0.146600 0.733100 0.880900							#American Mineralogist 65 920 1980 (Space Group 154)
+lattice                 custom 1.0 &
+                        a1      4.916000 0.000000 0.000000 &
+                        a2      -2.45800 4.257381 0.000000 &
+                        a3      0.000000 0.000000 5.405400 &
+                        &
+                        basis   0.469700 0.000000 0.000000 &
+                        basis   0.000000 0.469700 0.666667 &
+                        basis   0.530300 0.530300 0.333333 &
+                        &
+                        basis   0.413500 0.266900 0.119100 &
+                        basis   0.266900 0.413500 0.547567 &
+                        basis   0.733100 0.146600 0.785767 &
+                        basis   0.586500 0.853400 0.214233 &
+                        basis   0.853400 0.586500 0.452433 &
+                        basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
 
 #Computational Cell
-region			orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box 
-create_box		2 orthorhombic_unit_cell  
-create_atoms		1 box &
-			basis	1 1 &
-			basis	2 1 &
-			basis	3 1 &
-			basis	4 2 &
-			basis	5 2 &
-			basis	6 2 &
-			basis	7 2 &
-			basis	8 2 &
-			basis	9 2 
-replicate		${x_rep} ${y_rep} ${z_rep}
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+create_atoms            1 box &
+                        basis   1 1 &
+                        basis   2 1 &
+                        basis   3 1 &
+                        basis   4 2 &
+                        basis   5 2 &
+                        basis   6 2 &
+                        basis   7 2 &
+                        basis   8 2 &
+                        basis   9 2
+replicate               ${x_rep} ${y_rep} ${z_rep}
 
 #Atomic Information
-mass			1 28.085500
-mass			2 15.999400
-set			type 1 charge +2.4 
-set			type 2 charge -1.2
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+set                     type 2 charge -1.2
 
 
 ## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
-include			alpha_quartz_potential.mod
+include                 alpha_quartz_potential.mod
 
 
 ## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
-variable		p_damp equal ${delta_t}*1000								#Recommended pressure damping parameter in fix nph
-fix			scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp}				#NPH does the time integration
-fix			quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100	#Change f_max (THz) if your Debye frequency is higher
-thermo_style		custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
-thermo			100
-run			2000											# 2 ps
-unfix			quartz_qtb
-unfix			scapegoat_qtb
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  200
+run                     2000                                                                                    # 2 ps
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb

examples/USER/qtb/alpha_quartz_qbmsst/in.alpha_quartz_qbmsst

@@ -0,0 +1,55 @@
+## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
+variable                x_rep equal 2   #plot is made with x_rep = 8                                            #x-direction replication number
+variable                y_rep equal 1   #plot is made with y_rep = 5                                            #y-direction replication number
+variable                z_rep equal 4   #plot is made with z_rep = 15                                           #z-direction replication number
+variable                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+variable                v_msst equal 78.0                                                                       #Shock velocity (Angstrom/ps in metal units)
+variable                q_msst equal 40.0                                                                       #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
+variable                tscale_msst equal 0.05                                                                  #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)
+
+
+## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
+include                 alpha_quartz_qtb.mod
+
+
+## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
+## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
+#Compression restart 1
+reset_timestep          0
+#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 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                  200
+timestep                ${delta_t}
+run                     1000
+write_restart           restart.1000
+
+#Compression restart 2
+#Read restart file and load potential again
+clear
+read_restart            restart.1000
+include                 alpha_quartz_potential.mod
+#Use the same fix id and add no tscale if the system is already compressed
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 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                  500
+timestep                ${delta_t}
+restart                 1000 restart
+run                     10000                                                                                   #10 ps

examples/USER/qtb/alpha_quartz_qbmsst/log.15Jun20.alpha_quartz_qbmsst.g++.1

@@ -0,0 +1,430 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
+variable                x_rep equal 2   #plot is made with x_rep = 8                                            #x-direction replication number
+variable                y_rep equal 1   #plot is made with y_rep = 5                                            #y-direction replication number
+variable                z_rep equal 4   #plot is made with z_rep = 15                                           #z-direction replication number
+variable                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+variable                v_msst equal 78.0                                                                       #Shock velocity (Angstrom/ps in metal units)
+variable                q_msst equal 40.0                                                                       #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
+variable                tscale_msst equal 0.05                                                                  #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)
+
+
+## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
+include                 alpha_quartz_qtb.mod
+## This script first constructs an alpha quartz 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, alpha-quartz crystal, and atomic information
+#General
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
+
+#Lattice
+lattice                 custom 1.0                         a1      4.916000 0.000000 0.000000                         a2      -2.45800 4.257381 0.000000                         a3      0.000000 0.000000 5.405400                                                 basis   0.469700 0.000000 0.000000                         basis   0.000000 0.469700 0.666667                         basis   0.530300 0.530300 0.333333                                                 basis   0.413500 0.266900 0.119100                         basis   0.266900 0.413500 0.547567                         basis   0.733100 0.146600 0.785767                         basis   0.586500 0.853400 0.214233                         basis   0.853400 0.586500 0.452433                         basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
+Lattice spacing in x,y,z = 7.374 4.25738 5.4054
+
+#Computational Cell
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
+  1 by 1 by 1 MPI processor grid
+create_atoms            1 box                         basis   1 1                         basis   2 1                         basis   3 1                         basis   4 2                         basis   5 2                         basis   6 2                         basis   7 2                         basis   8 2                         basis   9 2
+Created 18 atoms
+  create_atoms CPU = 0.000 seconds
+replicate               ${x_rep} ${y_rep} ${z_rep}
+replicate               2 ${y_rep} ${z_rep}
+replicate               2 1 ${z_rep}
+replicate               2 1 4
+  orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
+  1 by 1 by 1 MPI processor grid
+  144 atoms
+  replicate CPU = 0.000271082 secs
+
+#Atomic Information
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+  48 settings made for charge
+set                     type 2 charge -1.2
+  96 settings made for charge
+
+
+## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
+include                 alpha_quartz_potential.mod
+#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
+
+#Pair Potentials
+pair_style              hybrid/overlay buck/coul/long ${cut_off} table linear 39901
+pair_style              hybrid/overlay buck/coul/long 10 table linear 39901
+pair_coeff              1 1 buck/coul/long 0.0 1.0 0.0                                                          #No interactions between Si atoms
+pair_coeff              1 2 buck/coul/long 18003.757200 0.205205 133.538100
+pair_coeff              2 2 buck/coul/long 1388.773000  0.362319 175.000000                                     #BKS interaction in PRL 64 1955 (1990)
+pair_modify             shift yes
+pair_coeff              1 2 table potential_SiO2.TPF Si-O ${cut_off}
+pair_coeff              1 2 table potential_SiO2.TPF Si-O 10
+pair_coeff              2 2 table potential_SiO2.TPF O-O ${cut_off}                                             #See the potential file for more information
+pair_coeff              2 2 table potential_SiO2.TPF O-O 10                                             
+WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (src/pair_table.cpp:471)
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+
+
+## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+variable                p_damp equal 0.001*1000                                                            
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300                                
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+fix                     quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 
+fix                     quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100 
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  200
+run                     2000                                                                                    # 2 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.301598
+  grid = 9 8 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00117056
+  estimated relative force accuracy = 8.12908e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 5280 1080
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 80.09 | 80.09 | 80.09 Mbytes
+Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz 
+       0            0   -34026.791   -2793.6042    1810.0985        9.832     8.514762      21.6216   -37470.578   -37470.432   -27139.363 -6.4345368e-12   0.94245783 4.2212262e-10 
+     200     170.7381    43248.332   -2790.8398     1879.164    9.9554912    8.6217086     21.89317    39337.624    42979.126    47428.246    324.91326    454.85872   -2034.6053 
+     400    258.09921     -28257.8   -2788.3487    1856.1432    9.9146707    8.5863569    21.803402   -19478.873   -29571.375   -35723.152    4633.9026    8487.8103   -626.12005 
+     600    277.77032   -22751.351   -2786.2715    1866.9783    9.9339253    8.6030319    21.845744   -21727.335   -29200.027   -17326.692   -4327.8571   -8218.4965    252.30681 
+     800     349.8665    30508.003   -2784.2204    1873.4953    9.9454706    8.6130304    21.871134    29929.055    33562.672    28032.281   -3188.5605    12329.482    7558.5678 
+    1000    373.67651   -18839.569   -2783.2178    1855.5937    9.9136922    8.5855095     21.80125   -18063.486   -22288.321   -16166.902   -416.09547   -10368.975    9030.4208 
+    1200     423.3474    6846.9905   -2781.9271    1896.2131    9.9855083    8.6477041    21.959181    2147.3938    11765.857    6627.7202   -7627.6782   -1297.6517   -4758.4746 
+    1400    418.54527   -6416.7506   -2781.4358    1834.2719    9.8755745    8.5524986    21.717425    5693.0543   -19487.901    -5455.405    827.66513    -523.1508   -3890.9919 
+    1600    429.42796    3939.8836   -2780.5861    1895.8859     9.984934    8.6472068    21.957918    3755.6959   -1326.4343    9390.3893    1948.1153    4489.8629    1466.0914 
+    1800     447.7623   -8344.6306   -2780.1071    1858.4925    9.9188518    8.5899779    21.812596   -17549.498    3336.8135   -10821.208    1643.4226   -644.56065   -8935.9666 
+    2000     438.1306   -6691.4691   -2780.7407    1871.3547    9.9416812    8.6097487    21.862801   -6959.2196   -8486.8466    -4628.341   -1019.9006    443.03694    -2751.917 
+Loop time of 2.46815 on 1 procs for 2000 steps with 144 atoms
+
+Performance: 70.012 ns/day, 0.343 hours/ns, 810.323 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    | 2.0003     | 2.0003     | 2.0003     |   0.0 | 81.04
+Kspace  | 0.20006    | 0.20006    | 0.20006    |   0.0 |  8.11
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.023753   | 0.023753   | 0.023753   |   0.0 |  0.96
+Output  | 0.0001986  | 0.0001986  | 0.0001986  |   0.0 |  0.01
+Modify  | 0.23896    | 0.23896    | 0.23896    |   0.0 |  9.68
+Other   |            | 0.004907   |            |       |  0.20
+
+Nlocal:    144 ave 144 max 144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3943 ave 3943 max 3943 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    41952 ave 41952 max 41952 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 41952
+Ave neighs/atom = 291.333
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb
+
+
+## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
+## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
+#Compression restart 1
+reset_timestep          0
+#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
+QBMSST parameters:
+  Shock in z direction
+  Cell mass-like parameter qmass (units of mass^2/length^4) =  4.00000e+01
+  Shock velocity =  7.80000e+01
+  Artificial viscosity (units of mass/length/time) =  0.00000e+00
+  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                  200
+timestep                ${delta_t}
+timestep                0.001
+run                     1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.303132
+  grid = 9 8 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00104699
+  estimated relative force accuracy = 7.27093e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 5520 1152
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Fix QBMSST v0 =  1.87135e+03
+Fix QBMSST p0 = -4.62948e+03
+Fix QBMSST e0 = to be -2.78074e+03
+Fix QBMSST initial strain rate of -4.01096e-01 established by reducing temperature by factor of  5.00000e-02
+Per MPI rank memory allocation (min/avg/max) = 80.1 | 80.1 | 80.1 Mbytes
+Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos 
+       0          300   -6922.9433   -2780.7394    1871.3547    9.9416812    8.6097487    21.862801   -4819.9907    10.953265   -190.51273            0            0 
+     200    294.95797    54876.416   -2779.2988    1723.7621    9.9416812    8.6097487    20.138495    108897.19   -29.773973   -9271.7281    6.1518102   -15.057867 
+     400     288.3711    139521.03   -2778.7321    1628.5574    9.9416812    8.6097487    19.026231    222107.71    8.0682073    24727.575    10.120041   -28.714693 
+     600    280.56521    98070.281   -2779.8934    1687.2434    9.9416812    8.6097487    19.711852    164558.51    2.6076928    16005.656    7.6739491   -42.705007 
+     800    274.94701    106060.26   -2779.2916    1651.0723    9.9416812    8.6097487    19.289269     176842.6   -39.645354   -1804.9466    9.1815975   -56.628078 
+    1000    268.47106    189695.34   -2779.4951    1492.6355    9.9416812    8.6097487    17.438272     277351.5   -84.834482   -33116.996    15.785409   -69.870519 
+Loop time of 2.05219 on 1 procs for 1000 steps with 144 atoms
+
+Performance: 42.101 ns/day, 0.570 hours/ns, 487.284 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    | 1.6815     | 1.6815     | 1.6815     |   0.0 | 81.94
+Kspace  | 0.10373    | 0.10373    | 0.10373    |   0.0 |  5.05
+Neigh   | 0.0061183  | 0.0061183  | 0.0061183  |   0.0 |  0.30
+Comm    | 0.012444   | 0.012444   | 0.012444   |   0.0 |  0.61
+Output  | 0.00014687 | 0.00014687 | 0.00014687 |   0.0 |  0.01
+Modify  | 0.24529    | 0.24529    | 0.24529    |   0.0 | 11.95
+Other   |            | 0.002948   |            |       |  0.14
+
+Nlocal:    144 ave 144 max 144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    4243 ave 4243 max 4243 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    48210 ave 48210 max 48210 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 48210
+Ave neighs/atom = 334.792
+Neighbor list builds = 8
+Dangerous builds = 0
+write_restart           restart.1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.306435
+  grid = 9 8 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000955688
+  estimated relative force accuracy = 6.63689e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 5280 1080
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 3
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+
+#Compression restart 2
+#Read restart file and load potential again
+clear
+  using 1 OpenMP thread(s) per MPI task
+read_restart            restart.1000
+  restoring atom style charge from restart
+  orthogonal box = (-0.05484062286382799 -0.04749337384227555 2.0916641327653274) to (9.886840622863804 8.562255373842252 19.52993586723476)
+  1 by 1 by 1 MPI processor grid
+  restoring pair style hybrid/overlay from restart
+  144 atoms
+  read_restart CPU = 0.0002563 secs
+include                 alpha_quartz_potential.mod
+#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
+
+#Pair Potentials
+pair_style              hybrid/overlay buck/coul/long ${cut_off} table linear 39901
+pair_style              hybrid/overlay buck/coul/long 10 table linear 39901
+pair_coeff              1 1 buck/coul/long 0.0 1.0 0.0                                                          #No interactions between Si atoms
+pair_coeff              1 2 buck/coul/long 18003.757200 0.205205 133.538100
+pair_coeff              2 2 buck/coul/long 1388.773000  0.362319 175.000000                                     #BKS interaction in PRL 64 1955 (1990)
+pair_modify             shift yes
+pair_coeff              1 2 table potential_SiO2.TPF Si-O ${cut_off}
+pair_coeff              1 2 table potential_SiO2.TPF Si-O 10
+pair_coeff              2 2 table potential_SiO2.TPF O-O ${cut_off}                                             #See the potential file for more information
+pair_coeff              2 2 table potential_SiO2.TPF O-O 10                                             
+WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (src/pair_table.cpp:471)
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+#Use the same fix id and add no tscale if the system is already compressed
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
+QBMSST parameters:
+  Shock in z direction
+  Cell mass-like parameter qmass (units of mass^2/length^4) =  4.00000e+01
+  Shock velocity =  7.80000e+01
+  Artificial viscosity (units of mass/length/time) =  0.00000e+00
+  Initial pressure calculated on first step
+  Initial volume calculated on first step
+  Initial energy calculated on first step
+Resetting global fix info from restart file:
+  fix style: qbmsst, fix ID: shock
+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                  500
+timestep                ${delta_t}
+timestep                0.001
+restart                 1000 restart
+run                     10000                                                                                   #10 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.306435
+  grid = 9 8 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000955688
+  estimated relative force accuracy = 6.63689e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 5280 1080
+All restart file global fix info was re-assigned
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 3
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 80.12 | 80.12 | 80.12 Mbytes
+Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos 
+    1000    268.47106    189686.77   -2781.5194    1492.6355    9.9416812    8.6097487    17.438272    277378.37   -84.692548   -33090.129    15.785409            0 
+    1500    362.13476    692245.96   -2800.9352    1011.2037    9.9416812    8.6097487    11.813766    661095.53    188.71833   -49928.712    35.851981    -24.11484 
+    2000    860.78914     714816.8    -2830.893    997.64749    9.9416812    8.6097487     11.65539    653537.64    852.68158   -68765.537     36.41702   -44.978484 
+    2500    1620.8281    709511.19   -2840.8217    1000.3425    9.9416812    8.6097487    11.686875    660030.01    1184.3105   -60030.892    36.304689    -65.69966 
+    3000    2395.6824    649526.84   -2832.6859    995.56591    9.9416812    8.6097487    11.631071    660984.37    939.07209   -63050.693    36.503782   -86.383242 
+    3500    3034.6774    715794.56   -2822.6098     995.8622    9.9416812    8.6097487    11.634532    712849.74    1055.7295   -10938.816    36.491433   -106.99315 
+    4000    3487.9039    736791.25   -2804.1216    994.13867    9.9416812    8.6097487    11.614397    765817.85    943.15747    40595.305    36.563271   -127.76315 
+    4500    3718.6279     813775.8   -2788.1942    995.82514    9.9416812    8.6097487    11.634099    881961.06    1370.5559    158141.68    36.492977   -148.68649 
+    5000    3691.4947    750146.58   -2770.5541    1018.4785    9.9416812    8.6097487    11.898756    770500.36     196.2793    65528.786    35.548762    -169.8589 
+    5500    3585.8602    831522.51   -2766.0198    1005.6834    9.9416812    8.6097487    11.749273    916093.67    1088.1987    200476.48    36.082073   -190.89436 
+    6000    3431.6405    749891.94   -2771.6404    1011.9077    9.9416812    8.6097487     11.82199    781321.11    268.24344     70882.55     35.82264   -212.20913 
+    6500    3350.2876    666113.16   -2780.4124    1028.8353    9.9416812    8.6097487    12.019753    749294.32    371.38231    52939.676    35.117081   -233.59556 
+    7000    3339.2397     675783.2   -2782.7559    1022.6541    9.9416812    8.6097487    11.947539    690109.39   -26.949124   -11388.054    35.374719   -254.95868 
+    7500     3395.582    726601.74   -2784.7652    1018.1439    9.9416812    8.6097487    11.894846    759167.86     506.5811    53917.852     35.56271   -276.24361 
+    8000    3393.2372    625141.93   -2771.6398    1035.4915    9.9416812    8.6097487    12.097517    598674.46   -895.80046   -92142.112    34.839641   -297.61681 
+    8500    3272.9752    659367.77    -2776.608    1031.8188    9.9416812    8.6097487    12.054609    688358.42   -142.30814   -5513.8593    34.992722   -318.94541 
+    9000    3277.8848    724828.76   -2777.6502    1017.6314    9.9416812    8.6097487    11.888859    724452.11    58.574942    18775.738     35.58407    -340.1718 
+    9500    3273.7854    620652.38   -2780.0794    1023.5922    9.9416812    8.6097487    11.958499    747175.42     317.3826    46458.505    35.335617   -361.41643 
+   10000    3329.1766    668606.38   -2786.3493    1022.9534    9.9416812    8.6097487    11.951035    703351.81    168.14538      2103.38    35.362244   -382.64609 
+   10500    3398.9956    642919.16   -2784.2833    1016.2587    9.9416812    8.6097487    11.872822    661298.16   -230.03577    -45520.34    35.641287   -403.78721 
+   11000    3418.7053    675754.06   -2782.6318    1005.7483    9.9416812    8.6097487     11.75003    689789.84   -136.97148   -25773.422    36.079372   -424.97556 
+Loop time of 32.4277 on 1 procs for 10000 steps with 144 atoms
+
+Performance: 26.644 ns/day, 0.901 hours/ns, 308.378 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 28.397     | 28.397     | 28.397     |   0.0 | 87.57
+Kspace  | 1.0225     | 1.0225     | 1.0225     |   0.0 |  3.15
+Neigh   | 0.27594    | 0.27594    | 0.27594    |   0.0 |  0.85
+Comm    | 0.1797     | 0.1797     | 0.1797     |   0.0 |  0.55
+Output  | 0.10409    | 0.10409    | 0.10409    |   0.0 |  0.32
+Modify  | 2.4112     | 2.4112     | 2.4112     |   0.0 |  7.44
+Other   |            | 0.03707    |            |       |  0.11
+
+Nlocal:    144 ave 144 max 144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5541 ave 5541 max 5541 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    74662 ave 74662 max 74662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 74662
+Ave neighs/atom = 518.486
+Neighbor list builds = 207
+Dangerous builds = 0
+Total wall time: 0:00:37

examples/USER/qtb/alpha_quartz_qbmsst/log.15Jun20.alpha_quartz_qbmsst.g++.4

@@ -0,0 +1,430 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+## This script first uses fix qtb to equilibrate alpha quartz structure to an initial state with quantum nuclear correction and then simulate shock induced phase transition through the quantum thermal bath multi-scale shock technique
+variable                x_rep equal 2   #plot is made with x_rep = 8                                            #x-direction replication number
+variable                y_rep equal 1   #plot is made with y_rep = 5                                            #y-direction replication number
+variable                z_rep equal 4   #plot is made with z_rep = 15                                           #z-direction replication number
+variable                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+variable                v_msst equal 78.0                                                                       #Shock velocity (Angstrom/ps in metal units)
+variable                q_msst equal 40.0                                                                       #Box mass-like parameter in the MSST (mass^2/length^4, where mass=grams/mole and length=Angstrom in metal units)
+variable                tscale_msst equal 0.05                                                                  #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)
+
+
+## This part uses fix qtb to prepare alpha-quartz with quantum nuclear correction of the initial state
+include                 alpha_quartz_qtb.mod
+## This script first constructs an alpha quartz 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, alpha-quartz crystal, and atomic information
+#General
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
+
+#Lattice
+lattice                 custom 1.0                         a1      4.916000 0.000000 0.000000                         a2      -2.45800 4.257381 0.000000                         a3      0.000000 0.000000 5.405400                                                 basis   0.469700 0.000000 0.000000                         basis   0.000000 0.469700 0.666667                         basis   0.530300 0.530300 0.333333                                                 basis   0.413500 0.266900 0.119100                         basis   0.266900 0.413500 0.547567                         basis   0.733100 0.146600 0.785767                         basis   0.586500 0.853400 0.214233                         basis   0.853400 0.586500 0.452433                         basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
+Lattice spacing in x,y,z = 7.374 4.25738 5.4054
+
+#Computational Cell
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
+  1 by 2 by 2 MPI processor grid
+create_atoms            1 box                         basis   1 1                         basis   2 1                         basis   3 1                         basis   4 2                         basis   5 2                         basis   6 2                         basis   7 2                         basis   8 2                         basis   9 2
+Created 18 atoms
+  create_atoms CPU = 0.000 seconds
+replicate               ${x_rep} ${y_rep} ${z_rep}
+replicate               2 ${y_rep} ${z_rep}
+replicate               2 1 ${z_rep}
+replicate               2 1 4
+  orthogonal box = (0.0 0.0 0.0) to (9.832 8.514762 21.6216)
+  1 by 1 by 4 MPI processor grid
+  144 atoms
+  replicate CPU = 0.000225782 secs
+
+#Atomic Information
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+  48 settings made for charge
+set                     type 2 charge -1.2
+  96 settings made for charge
+
+
+## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
+include                 alpha_quartz_potential.mod
+#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
+
+#Pair Potentials
+pair_style              hybrid/overlay buck/coul/long ${cut_off} table linear 39901
+pair_style              hybrid/overlay buck/coul/long 10 table linear 39901
+pair_coeff              1 1 buck/coul/long 0.0 1.0 0.0                                                          #No interactions between Si atoms
+pair_coeff              1 2 buck/coul/long 18003.757200 0.205205 133.538100
+pair_coeff              2 2 buck/coul/long 1388.773000  0.362319 175.000000                                     #BKS interaction in PRL 64 1955 (1990)
+pair_modify             shift yes
+pair_coeff              1 2 table potential_SiO2.TPF Si-O ${cut_off}
+pair_coeff              1 2 table potential_SiO2.TPF Si-O 10
+pair_coeff              2 2 table potential_SiO2.TPF O-O ${cut_off}                                             #See the potential file for more information
+pair_coeff              2 2 table potential_SiO2.TPF O-O 10                                             
+WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (src/pair_table.cpp:471)
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+
+
+## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+variable                p_damp equal 0.001*1000                                                            
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300                                
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+fix                     quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 
+fix                     quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100 
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  200
+run                     2000                                                                                    # 2 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.301598
+  grid = 9 8 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00117056
+  estimated relative force accuracy = 8.12908e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2400 288
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
+Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz 
+       0            0   -34026.791   -2793.6042    1810.0985        9.832     8.514762      21.6216   -37470.578   -37470.432   -27139.363 1.0530512e-10   0.94245783 4.0087238e-10 
+     200    153.57631    45538.205   -2790.8177    1873.0866    9.9447472     8.612404    21.869543    41721.016    44095.248    50798.351   -3961.4596     1223.325     2871.656 
+     400    234.74785   -34404.175   -2789.0189    1850.2127       9.9041    8.5772024    21.780156   -28329.333   -39376.313    -35506.88   -1154.5043   -5411.1071    2246.6749 
+     600    265.24833   -20905.145   -2786.2727    1874.9981     9.948129    8.6153326     21.87698   -22753.886   -21091.083   -18870.468   -4645.5548    2968.2945    1415.0311 
+     800    297.79035     32990.58   -2784.8247    1853.6946     9.910309    8.5825796     21.79381    30061.364     35359.18    33551.195   -3092.2971      1525.52   -6461.0249 
+    1000    367.71884   -27539.239   -2783.0102    1864.7161    9.9299114    8.5995557    21.836917   -20273.387   -38720.429   -23623.901    7639.0334   -866.35665    543.52723 
+    1200    399.77109    3807.7814    -2781.511    1893.4978    9.9807399    8.6435745    21.948695    1625.8226    7441.2236     2356.298   -4057.1674    3814.9305    1528.4567 
+    1400    466.57962    -4148.235   -2780.1546    1851.5925    9.9065614    8.5793341    21.785568    -10883.19     1816.768   -3378.2828    896.25296    -7208.541   -42.253127 
+    1600    497.86539     14505.31   -2778.9409    1882.2616    9.9609584    8.6264432    21.905193    8268.1103    20614.738    14633.082   -2690.5669    6807.3187    11995.878 
+    1800    557.31182   -108.04462   -2778.1875     1875.514    9.9490413    8.6161228    21.878986    948.68308   -1929.7575    656.94053   -1628.2172   -6594.5909   -4423.4368 
+    2000    480.39449   -8852.2243   -2778.4963    1862.9552    9.9267847     8.596848    21.830042   -18274.307    3038.8369   -11321.203   -5002.1016    12023.282    6845.2769 
+Loop time of 1.42181 on 4 procs for 2000 steps with 144 atoms
+
+Performance: 121.535 ns/day, 0.197 hours/ns, 1406.656 timesteps/s
+87.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.72578    | 0.80093    | 0.87518    |   6.1 | 56.33
+Kspace  | 0.33737    | 0.41245    | 0.48642    |   8.4 | 29.01
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.066098   | 0.071334   | 0.076039   |   1.6 |  5.02
+Output  | 0.00021172 | 0.00039291 | 0.00093484 |   0.0 |  0.03
+Modify  | 0.090105   | 0.1077     | 0.11384    |   3.1 |  7.58
+Other   |            | 0.029      |            |       |  2.04
+
+Nlocal:    36 ave 36 max 36 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    2614 ave 2614 max 2614 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    10488 ave 11326 max 9404 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+
+Total # of neighbors = 41952
+Ave neighs/atom = 291.333
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb
+
+
+## This part demonstrates how to retart fix qbmsst during any stage of the shock simulation.
+## PPPM may break down when compression ratio becomes extremely large. One can always use this restart technique to resume the shock simulation.
+#Compression restart 1
+reset_timestep          0
+#Beta is the number of time steps between each update of the quantum bath temperature. Setting a larger beta can reduce thermal flactuations.
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q ${q_msst} tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale ${tscale_msst} damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.05 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
+QBMSST parameters:
+  Shock in z direction
+  Cell mass-like parameter qmass (units of mass^2/length^4) =  4.00000e+01
+  Shock velocity =  7.80000e+01
+  Artificial viscosity (units of mass/length/time) =  0.00000e+00
+  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                  200
+timestep                ${delta_t}
+timestep                0.001
+run                     1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.30088
+  grid = 9 8 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00120534
+  estimated relative force accuracy = 8.37062e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2400 288
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Fix QBMSST v0 =  1.86296e+03
+Fix QBMSST p0 = -1.13219e+04
+Fix QBMSST e0 = to be -2.77850e+03
+Fix QBMSST initial strain rate of -4.21890e-01 established by reducing temperature by factor of  5.00000e-02
+Per MPI rank memory allocation (min/avg/max) = 79.7 | 79.7 | 79.7 Mbytes
+Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos 
+       0          300    -9106.318   -2778.4963    1862.9552    9.9267847     8.596848    21.830042   -11562.002    12.009862    -240.0699            0            0 
+     200    296.47213    25984.111   -2777.5178    1770.2164    9.9267847     8.596848    20.743332    64970.204   -25.305765   -1564.7673    3.8828772    -15.16768 
+     400    291.06707    69977.517   -2777.6325     1684.893    9.9267847     8.596848    19.743515    144833.82   -12.184734     6667.384    7.4552796   -29.607028 
+     600    287.21118    39706.699   -2778.0322    1716.9533    9.9267847     8.596848    20.119196    87971.152   -38.593844   -23279.741    6.1129484   -43.751298 
+     800    284.33611    18833.281   -2778.1637    1792.7576    9.9267847     8.596848    21.007468    43725.433   -8.1267799   -3885.5802    2.9391022   -58.454556 
+    1000    281.98328   -6030.6935   -2778.3314    1881.8369    9.9267847     8.596848    22.051297   -14118.602    1.3183874    13055.078  -0.79055793   -73.780965 
+Loop time of 1.25215 on 4 procs for 1000 steps with 144 atoms
+
+Performance: 69.001 ns/day, 0.348 hours/ns, 798.628 timesteps/s
+90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.67979    | 0.73665    | 0.8091     |   5.4 | 58.83
+Kspace  | 0.18687    | 0.25893    | 0.31544    |   9.1 | 20.68
+Neigh   | 0.0011306  | 0.0012404  | 0.0013735  |   0.3 |  0.10
+Comm    | 0.040339   | 0.041345   | 0.042296   |   0.4 |  3.30
+Output  | 0.00020051 | 0.00035506 | 0.00081801 |   0.0 |  0.03
+Modify  | 0.19595    | 0.2007     | 0.20253    |   0.6 | 16.03
+Other   |            | 0.01292    |            |       |  1.03
+
+Nlocal:    36 ave 38 max 34 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    2527.75 ave 2547 max 2518 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Neighs:    10194.8 ave 11177 max 9437 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 40779
+Ave neighs/atom = 283.188
+Neighbor list builds = 6
+Dangerous builds = 0
+write_restart           restart.1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.302953
+  grid = 9 8 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00105569
+  estimated relative force accuracy = 7.33134e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2640 288
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+
+#Compression restart 2
+#Read restart file and load potential again
+clear
+  using 1 OpenMP thread(s) per MPI task
+read_restart            restart.1000
+  restoring atom style charge from restart
+  orthogonal box = (-0.04739235907204603 -0.041042988010289584 -0.21484841641189512) to (9.879392359072014 8.555804988010294 21.83644841641206)
+  1 by 1 by 4 MPI processor grid
+  restoring pair style hybrid/overlay from restart
+  144 atoms
+  read_restart CPU = 0.000472307 secs
+include                 alpha_quartz_potential.mod
+#This script implements the BKS pair potential for various silicon dioxide compounds. Inner part is fixed with a harmonic potential. Long range Coulomb interactions are evaluated with the pppm method.
+
+#Pair Potentials
+pair_style              hybrid/overlay buck/coul/long ${cut_off} table linear 39901
+pair_style              hybrid/overlay buck/coul/long 10 table linear 39901
+pair_coeff              1 1 buck/coul/long 0.0 1.0 0.0                                                          #No interactions between Si atoms
+pair_coeff              1 2 buck/coul/long 18003.757200 0.205205 133.538100
+pair_coeff              2 2 buck/coul/long 1388.773000  0.362319 175.000000                                     #BKS interaction in PRL 64 1955 (1990)
+pair_modify             shift yes
+pair_coeff              1 2 table potential_SiO2.TPF Si-O ${cut_off}
+pair_coeff              1 2 table potential_SiO2.TPF Si-O 10
+pair_coeff              2 2 table potential_SiO2.TPF O-O ${cut_off}                                             #See the potential file for more information
+pair_coeff              2 2 table potential_SiO2.TPF O-O 10                                             
+WARNING: 1 of 39901 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (src/pair_table.cpp:471)
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+#Use the same fix id and add no tscale if the system is already compressed
+fix                     shock all qbmsst z ${v_msst} q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q ${q_msst} tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp ${damp_qtb} f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta ${eta_qbmsst} beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init ${temperature}
+fix                     shock all qbmsst z 78 q 40 tscale 0.0 damp 1 f_max 120 N_f 100 seed 35082 eta 1 beta 5 T_init 300
+QBMSST parameters:
+  Shock in z direction
+  Cell mass-like parameter qmass (units of mass^2/length^4) =  4.00000e+01
+  Shock velocity =  7.80000e+01
+  Artificial viscosity (units of mass/length/time) =  0.00000e+00
+  Initial pressure calculated on first step
+  Initial volume calculated on first step
+  Initial energy calculated on first step
+Resetting global fix info from restart file:
+  fix style: qbmsst, fix ID: shock
+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                  500
+timestep                ${delta_t}
+timestep                0.001
+restart                 1000 restart
+run                     10000                                                                                   #10 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.302953
+  grid = 9 8 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00105569
+  estimated relative force accuracy = 7.33134e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2640 288
+All restart file global fix info was re-assigned
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 2 4
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair table, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 79.71 | 79.71 | 79.71 Mbytes
+Step v_T_qm Press TotEng Volume Lx Ly Lz Pzz v_dhug v_dray v_lgr_vel v_lgr_pos 
+    1000    281.98328   -6031.2395   -2778.6227    1881.8369    9.9267847     8.596848    22.051297   -14113.621    1.3373278    13060.059  -0.79055793            0 
+    1500    266.12746    44405.573   -2777.9815    1739.6543    9.9267847     8.596848    20.385206    92590.239    -12.06041    397.47049    5.1624821   -37.823748 
+    2000    255.79411    17620.408   -2777.9685    1785.7619    9.9267847     8.596848    20.925494    48670.364   -16.082827   -4813.6764    3.2320016   -73.974437 
+    2500     256.8887    40153.833   -2778.4337    1752.9461    9.9267847     8.596848    20.540959    79665.002    7.7413878   -1368.8927    4.6059671   -112.35254 
+    3000    261.55251    5315.4799   -2779.0755    1834.3375    9.9267847     8.596848      21.4947    15896.368    22.588205     3192.882    1.1981949   -148.36068 
+    3500    261.57101    57911.809   -2778.1223    1713.3956    9.9267847     8.596848    20.077507     110996.8   -9.4471543   -3240.9018    6.2619064   -186.41261 
+    4000    254.88665     13952.95   -2778.4816    1818.2782    9.9267847     8.596848    21.306518    26833.588    2.2818412    647.88057    1.8705799   -222.72504 
+    4500    240.08908    73322.997   -2776.7382    1668.6666    9.9267847     8.596848    19.553375    151978.11   -43.917346     189.1572    8.1346613   -260.52885 
+    5000    214.49084    1925.2557   -2777.0657    1890.0985    9.9267847     8.596848    22.148106   -5218.7292     -44.5537    28890.787   -1.1364617   -297.26329 
+    5500     194.6515    71804.842   -2777.3417    1669.7297    9.9267847     8.596848    19.565832    146911.42   -34.911593   -3985.0635    8.0901523    -334.1879 
+    6000    186.23814    10196.007   -2777.1394    1837.3793    9.9267847     8.596848    21.530344    23550.907   -18.381207    13401.096    1.0708382    -371.9208 
+    6500    172.53603    5474.3725   -2777.4502    1818.0038    9.9267847     8.596848    21.303303    18389.825    -22.65951   -8026.2088    1.8820667   -407.83084 
+    7000    160.91186    107908.64   -2777.6746    1621.7378    9.9267847     8.596848    19.003464    196841.27   -8.6606903    5654.1938    10.099523    -444.9925 
+    7500    146.01905    147030.69   -2777.2543    1539.7536    9.9267847     8.596848    18.042777    253089.02   -43.928324   -6926.1018    13.532114   -478.63113 
+    8000    207.17758     837859.1   -2796.8957    989.32874    9.9267847     8.596848    11.592918    811765.11    1172.3778    89652.363    36.577833   -503.41923 
+    8500    725.15657    853732.89   -2832.3144    974.18299    9.9267847     8.596848    11.415441    773926.64    1749.5702    39098.598     37.21197   -524.17835 
+    9000    1554.6089    807867.74   -2843.0063    990.10922    9.9267847     8.596848    11.602064    749697.22    1959.0322     28239.71    36.545155   -544.77354 
+    9500    2440.1194    748145.05   -2839.2364    992.38871    9.9267847     8.596848    11.628775    691503.58    1437.0708   -28040.223    36.449715   -565.41198 
+   10000    3112.1817    823862.43   -2820.0495    982.35471    9.9267847     8.596848    11.511197    754954.89    1330.6807    26987.244    36.869828   -586.12357 
+   10500    3550.0273    868916.79   -2803.7678    983.70386    9.9267847     8.596848    11.527006    867368.45    1727.9058    140533.46    36.813341   -607.00946 
+   11000    3839.7527    830581.55   -2795.3804    995.31485    9.9267847     8.596848    11.663063       811740    1150.0462    94652.768    36.327201   -628.02229 
+Loop time of 15.1476 on 4 procs for 10000 steps with 144 atoms
+
+Performance: 57.039 ns/day, 0.421 hours/ns, 660.171 timesteps/s
+91.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7228     | 9.085      | 10.626     |  36.0 | 59.98
+Kspace  | 1.6343     | 3.1795     | 4.5467     |  61.0 | 20.99
+Neigh   | 0.02063    | 0.027076   | 0.034395   |   3.1 |  0.18
+Comm    | 0.54719    | 0.57781    | 0.60468    |   2.8 |  3.81
+Output  | 0.10128    | 0.1019     | 0.10373    |   0.3 |  0.67
+Modify  | 2.0819     | 2.1159     | 2.1495     |   1.8 | 13.97
+Other   |            | 0.06035    |            |       |  0.40
+
+Nlocal:    36 ave 38 max 33 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    4267 ave 4304 max 4239 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:    18859.2 ave 25108 max 12333 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 75437
+Ave neighs/atom = 523.868
+Neighbor list builds = 95
+Dangerous builds = 0
+Total wall time: 0:00:17

examples/USER/qtb/alpha_quartz_qbmsst/potential_SiO2.TPF

@@ -1,4 +1,4 @@
-#Potential between O,Si atoms. r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
+#Potential between O,Si atoms. UNITS: metal  r ranges from 0.1 to 20.0. This file+BKS(with no shift)=alpha*(r-rs)^2(0.1<r<rs);BKS(20.0>r>rs). alpha=100, rsOO=1.43869, rsSiO=1.19362. All with metal units.
 
 Si-O
 N 39901

examples/USER/qtb/alpha_quartz_qtb/alpha_quartz_qtb.in

@@ -1,79 +0,0 @@
-## This script first constructs an alpha quartz 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		cut_off equal 10.0									#Cut-off distance for the Buckingham term (Angstrom in metal units)
-variable		pressure equal 1.03125									#Initial state pressure (bar in metal units)
-variable		temperature equal 300.0									#Initial state quantum temperature (K in metal units)
-variable		delta_t equal 1.0e-3									#MD timestep length (ps in metal units)
-variable		damp_qtb equal 1									#1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
-
-## This part defines units, alpha-quartz crystal, and atomic information
-#General
-units			metal
-dimension		3
-boundary		p p p
-atom_style		charge
-
-#Lattice
-lattice			custom 1.0 &
-			a1	4.916000 0.000000 0.000000 &
-			a2	-2.45800 4.257381 0.000000 &
-			a3	0.000000 0.000000 5.405400 &
-			&		
-			basis	0.469700 0.000000 0.000000 &
-			basis	0.000000 0.469700 0.666667 &
-			basis	0.530300 0.530300 0.333333 &
-			&
-			basis	0.413500 0.266900 0.119100 &
-			basis	0.266900 0.413500 0.547567 &
-			basis	0.733100 0.146600 0.785767 &
-			basis	0.586500 0.853400 0.214233 &
-			basis	0.853400 0.586500 0.452433 &
-			basis	0.146600 0.733100 0.880900							#American Mineralogist 65 920 1980 (Space Group 154)
-
-#Computational Cell
-region			orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box 
-create_box		2 orthorhombic_unit_cell  
-create_atoms		1 box &
-			basis	1 1 &
-			basis	2 1 &
-			basis	3 1 &
-			basis	4 2 &
-			basis	5 2 &
-			basis	6 2 &
-			basis	7 2 &
-			basis	8 2 &
-			basis	9 2 
-replicate		${x_rep} ${y_rep} ${z_rep}
-
-#Atomic Information
-mass			1 28.085500
-mass			2 15.999400
-set			type 1 charge +2.4 
-set			type 2 charge -1.2
-
-
-## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
-#Pair Potentials
-pair_style		buck/coul/long ${cut_off}								#BKS interaction, PRL 64 1955 (1990)
-pair_coeff		1 1 0.0 1.0 0.0 
-pair_coeff		1 2 18003.757200 0.205205 133.538100
-pair_coeff		2 2 1388.773000  0.362319 175.000000
-pair_modify		shift yes
-kspace_style		pppm 1.0e-4 
-
-#Neighbor style
-neighbor		2.0 bin
-neigh_modify		check yes every 1 delay 0 page 100000 one 2000
-
-
-## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
-variable		p_damp equal ${delta_t}*1000								#Recommended pressure damping parameter in fix nph
-fix			scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp}				#NPH does the time integration
-fix			quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100	#Change f_max (THz) if your Debye frequency is higher
-thermo_style		custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
-thermo			100
-run			20000											# 20 ps
-unfix			quartz_qtb
-unfix			scapegoat_qtb

examples/USER/qtb/alpha_quartz_qtb/in.alpha_quartz_qtb

@@ -0,0 +1,79 @@
+## This script first constructs an alpha quartz 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                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+
+## This part defines units, alpha-quartz crystal, and atomic information
+#General
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
+
+#Lattice
+lattice                 custom 1.0 &
+                        a1      4.916000 0.000000 0.000000 &
+                        a2      -2.45800 4.257381 0.000000 &
+                        a3      0.000000 0.000000 5.405400 &
+                        &
+                        basis   0.469700 0.000000 0.000000 &
+                        basis   0.000000 0.469700 0.666667 &
+                        basis   0.530300 0.530300 0.333333 &
+                        &
+                        basis   0.413500 0.266900 0.119100 &
+                        basis   0.266900 0.413500 0.547567 &
+                        basis   0.733100 0.146600 0.785767 &
+                        basis   0.586500 0.853400 0.214233 &
+                        basis   0.853400 0.586500 0.452433 &
+                        basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
+
+#Computational Cell
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+create_atoms            1 box &
+                        basis   1 1 &
+                        basis   2 1 &
+                        basis   3 1 &
+                        basis   4 2 &
+                        basis   5 2 &
+                        basis   6 2 &
+                        basis   7 2 &
+                        basis   8 2 &
+                        basis   9 2
+replicate               ${x_rep} ${y_rep} ${z_rep}
+
+#Atomic Information
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+set                     type 2 charge -1.2
+
+
+## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
+#Pair Potentials
+pair_style              buck/coul/long ${cut_off}                                                               #BKS interaction, PRL 64 1955 (1990)
+pair_coeff              1 1 0.0 1.0 0.0
+pair_coeff              1 2 18003.757200 0.205205 133.538100
+pair_coeff              2 2 1388.773000  0.362319 175.000000
+pair_modify             shift yes
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+
+
+## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  500
+run                     10000                                                                                   # 20 ps
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb

examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.1

@@ -0,0 +1,152 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+## This script first constructs an alpha quartz 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                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+
+## This part defines units, alpha-quartz crystal, and atomic information
+#General
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
+
+#Lattice
+lattice                 custom 1.0                         a1      4.916000 0.000000 0.000000                         a2      -2.45800 4.257381 0.000000                         a3      0.000000 0.000000 5.405400                                                 basis   0.469700 0.000000 0.000000                         basis   0.000000 0.469700 0.666667                         basis   0.530300 0.530300 0.333333                                                 basis   0.413500 0.266900 0.119100                         basis   0.266900 0.413500 0.547567                         basis   0.733100 0.146600 0.785767                         basis   0.586500 0.853400 0.214233                         basis   0.853400 0.586500 0.452433                         basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
+Lattice spacing in x,y,z = 7.374 4.25738 5.4054
+
+#Computational Cell
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
+  1 by 1 by 1 MPI processor grid
+create_atoms            1 box                         basis   1 1                         basis   2 1                         basis   3 1                         basis   4 2                         basis   5 2                         basis   6 2                         basis   7 2                         basis   8 2                         basis   9 2
+Created 18 atoms
+  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
+  orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
+  1 by 1 by 1 MPI processor grid
+  144 atoms
+  replicate CPU = 0.000219584 secs
+
+#Atomic Information
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+  48 settings made for charge
+set                     type 2 charge -1.2
+  96 settings made for charge
+
+
+## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
+#Pair Potentials
+pair_style              buck/coul/long ${cut_off}                                                               #BKS interaction, PRL 64 1955 (1990)
+pair_style              buck/coul/long 10                                                               
+pair_coeff              1 1 0.0 1.0 0.0
+pair_coeff              1 2 18003.757200 0.205205 133.538100
+pair_coeff              2 2 1388.773000  0.362319 175.000000
+pair_modify             shift yes
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+
+
+## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+variable                p_damp equal 0.001*1000                                                            
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300                                
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+fix                     quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 
+fix                     quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100 
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  500
+run                     10000                                                                                   # 20 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.307414
+  grid = 9 15 10
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000822922
+  estimated relative force accuracy = 5.71487e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 5984 1350
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 3 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 79.54 | 79.54 | 79.54 Mbytes
+Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz 
+       0            0   -34025.794   -2793.6041    1810.0985        9.832    17.029524      10.8108   -37478.502   -37477.413   -27121.466 -1.3649088e-10    1.3388978 5.8209479e-10 
+     500    281.29079   -40385.348   -2786.6755    1844.5575     9.893999    17.136909    10.878971   -44649.574   -45631.516   -30874.953   -5970.3691    3630.1324    5208.8966 
+    1000    405.39848   -15491.657   -2783.3315    1874.0851    9.9465141    17.227868    10.936714   -7770.4561   -21469.887   -17234.627   -4706.5632   -8313.9522   -5109.7918 
+    1500    428.98568   -12118.951   -2781.3232    1874.1627    9.9466513    17.228106    10.936865   -11239.135   -11740.052   -13377.666   -3778.9317   -6220.1431    12775.412 
+    2000    522.11905    -6687.482   -2779.2181    1855.9626     9.914349    17.172157    10.901347   -8016.0133    -10737.23   -1309.2028   -4980.3805    5270.2674    5848.5479 
+    2500    496.74376    4264.2623   -2778.9979    1849.3244    9.9025147    17.151659    10.888335    -477.1374      3487.19    9782.7343   -4961.2016    2380.6522    4736.0758 
+    3000    456.49628     2320.781   -2779.3844    1853.2925    9.9095923    17.163918    10.896117    5479.6232   -2954.3023     4437.022    3719.9287    4445.0723   -3278.5058 
+    3500    485.20722   -7480.1789   -2778.6062    1859.6305     9.920876    17.183462    10.908524   -9340.6334   -6129.8494   -6970.0541   -7379.3507    1772.8159    334.33057 
+    4000    527.61216    -13499.73   -2777.3433    1889.9405    9.9744857    17.276316     10.96747   -16483.038   -7465.2297   -16550.923     -2517.02    -1863.063     3314.927 
+    4500    519.94117    721.60614   -2777.8506    1879.6562    9.9563603    17.244922    10.947541    -913.2791   -1765.7541    4843.8516    4466.5704   -14141.087   -6439.5669 
+    5000    505.27757   -6278.3805   -2777.3641    1881.2931    9.9592497    17.249927    10.950718   -14254.233   -2653.6233   -1927.2858    1838.1568    5767.9267    597.47761 
+    5500    500.70903    11303.821   -2777.8881    1871.0076    9.9410666    17.218433    10.930724   -6452.7947    24876.967     15487.29    522.01171    10473.257     9780.893 
+    6000    526.65329    7991.2419    -2777.172    1856.9227    9.9160583    17.175117    10.903227   -68.823156    11005.468    13037.081    1253.9214    10039.559    1053.0486 
+    6500    485.30026    12811.546   -2777.5866      1845.31    9.8953442    17.139239     10.88045    10063.921    20215.037    8155.6798    -3886.954    2249.2807    4855.0011 
+    7000    507.85472    2649.7919   -2777.3359    1861.2877     9.923822    17.188564    10.911763   -4214.7779    6995.1472    5169.0064    -2188.489    6157.0955    533.65478 
+    7500     528.5729    3161.4629   -2779.0851    1855.7946    9.9140499    17.171639    10.901018     2935.365   -2873.1363    9422.1601     771.1885   -4360.9131    4939.8209 
+    8000    533.77283     4534.849   -2777.6538    1858.4772    9.9188246    17.179909    10.906268   -1187.9433    15739.396   -946.90551   -5187.8588    2446.5059    8079.2032 
+    8500    518.71765    1108.9877   -2777.7019    1866.6125    9.9332765     17.20494    10.922159    8720.4976   -8234.9325    2841.3979    5148.5004   -2125.3524   -4127.7468 
+    9000    536.71495   -496.88283   -2778.0262    1877.7099    9.9529227    17.238968    10.943761   -3481.5874   -4611.6246    6602.5634   -2788.5111   -13323.148     4338.813 
+    9500    527.06773   -236.09043   -2778.1125    1895.9227    9.9849986    17.294525     10.97903   -12233.409    7578.0514    3947.0863   -6399.0254    995.22838    8590.7109 
+   10000    526.77335   -4480.6866   -2777.7171    1886.8998    9.9691335    17.267046    10.961585    -3139.961     1336.993   -11639.092    13496.371   -11543.676   -6180.9262 
+Loop time of 8.86837 on 1 procs for 10000 steps with 144 atoms
+
+Performance: 97.425 ns/day, 0.246 hours/ns, 1127.603 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    | 6.1503     | 6.1503     | 6.1503     |   0.0 | 69.35
+Kspace  | 1.1522     | 1.1522     | 1.1522     |   0.0 | 12.99
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11705    | 0.11705    | 0.11705    |   0.0 |  1.32
+Output  | 0.00035834 | 0.00035834 | 0.00035834 |   0.0 |  0.00
+Modify  | 1.4245     | 1.4245     | 1.4245     |   0.0 | 16.06
+Other   |            | 0.02397    |            |       |  0.27
+
+Nlocal:    144 ave 144 max 144 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3804 ave 3804 max 3804 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    41952 ave 41952 max 41952 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 41952
+Ave neighs/atom = 291.333
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb
+Total wall time: 0:00:08

examples/USER/qtb/alpha_quartz_qtb/log.15Jun20.alpha_quartz_qtb.g++.4

@@ -0,0 +1,152 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+## This script first constructs an alpha quartz 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                cut_off equal 10.0                                                                      #Cut-off distance for the Buckingham term (Angstrom in metal units)
+variable                pressure equal 1.03125                                                                  #Initial state pressure (bar in metal units)
+variable                temperature equal 300.0                                                                 #Initial state quantum temperature (K in metal units)
+variable                delta_t equal 1.0e-3                                                                    #MD timestep length (ps in metal units)
+variable                damp_qtb equal 1                                                                        #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
+
+## This part defines units, alpha-quartz crystal, and atomic information
+#General
+units                   metal
+dimension               3
+boundary                p p p
+atom_style              charge
+
+#Lattice
+lattice                 custom 1.0                         a1      4.916000 0.000000 0.000000                         a2      -2.45800 4.257381 0.000000                         a3      0.000000 0.000000 5.405400                                                 basis   0.469700 0.000000 0.000000                         basis   0.000000 0.469700 0.666667                         basis   0.530300 0.530300 0.333333                                                 basis   0.413500 0.266900 0.119100                         basis   0.266900 0.413500 0.547567                         basis   0.733100 0.146600 0.785767                         basis   0.586500 0.853400 0.214233                         basis   0.853400 0.586500 0.452433                         basis   0.146600 0.733100 0.880900                                                      #American Mineralogist 65 920 1980 (Space Group 154)
+Lattice spacing in x,y,z = 7.374 4.25738 5.4054
+
+#Computational Cell
+region                  orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
+create_box              2 orthorhombic_unit_cell
+Created orthogonal box = (0.0 0.0 0.0) to (4.916 8.514762 5.4054)
+  1 by 2 by 2 MPI processor grid
+create_atoms            1 box                         basis   1 1                         basis   2 1                         basis   3 1                         basis   4 2                         basis   5 2                         basis   6 2                         basis   7 2                         basis   8 2                         basis   9 2
+Created 18 atoms
+  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
+  orthogonal box = (0.0 0.0 0.0) to (9.832 17.029524 10.8108)
+  1 by 2 by 2 MPI processor grid
+  144 atoms
+  replicate CPU = 0.000231981 secs
+
+#Atomic Information
+mass                    1 28.085500
+mass                    2 15.999400
+set                     type 1 charge +2.4
+  48 settings made for charge
+set                     type 2 charge -1.2
+  96 settings made for charge
+
+
+## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
+#Pair Potentials
+pair_style              buck/coul/long ${cut_off}                                                               #BKS interaction, PRL 64 1955 (1990)
+pair_style              buck/coul/long 10                                                               
+pair_coeff              1 1 0.0 1.0 0.0
+pair_coeff              1 2 18003.757200 0.205205 133.538100
+pair_coeff              2 2 1388.773000  0.362319 175.000000
+pair_modify             shift yes
+kspace_style            pppm 1.0e-4
+
+#Neighbor style
+neighbor                2.0 bin
+neigh_modify            check yes every 1 delay 0 page 100000 one 2000
+
+
+## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
+variable                p_damp equal ${delta_t}*1000                                                            #Recommended pressure damping parameter in fix nph
+variable                p_damp equal 0.001*1000                                                            
+fix                     scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} ptemp ${temperature}                                #NPH does the time integration
+fix                     scapegoat_qtb all nph iso 1.03125 ${pressure} ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 ${p_damp} ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp ${temperature}                                
+fix                     scapegoat_qtb all nph iso 1.03125 1.03125 1 ptemp 300                                
+fix                     quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
+fix                     quartz_qtb all qtb temp 300 damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 
+fix                     quartz_qtb all qtb temp 300 damp 1 seed 35082 f_max 120.00 N_f 100 
+thermo_style            custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
+thermo                  500
+run                     10000                                                                                   # 20 ps
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.307414
+  grid = 9 15 10
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000822922
+  estimated relative force accuracy = 5.71487e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2688 405
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 2 3 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair buck/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 79.08 | 79.08 | 79.09 Mbytes
+Step Temp Press TotEng Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pyz Pxz 
+       0            0   -34025.794   -2793.6041    1810.0985        9.832    17.029524      10.8108   -37478.502   -37477.413   -27121.466 -5.9958847e-10    1.3388978 7.2750373e-10 
+     500    222.04947   -50221.579   -2787.6677    1851.5661    9.9065143    17.158586    10.892732   -61493.697   -53512.432    -35658.61    4973.9976    7095.5481   -2041.6341 
+    1000    361.92367    -14345.85   -2783.1509    1861.0579    9.9234137    17.187857    10.911314   -4145.4149   -28701.195   -10190.939    7896.3934   -3901.2874   -490.57107 
+    1500    457.97039   -4934.8727   -2779.8321    1860.2254    9.9219337    17.185294    10.909687   -3680.7192   -3045.0707   -8078.8283    456.70383   -4705.3346   -2175.8144 
+    2000    523.52684    -9516.755   -2778.5181    1866.3577    9.9328244    17.204157    10.921662   -11042.489   -7777.5634   -9730.2127   -2016.3336     6027.001   -4150.3656 
+    2500    489.58881   -4968.5157   -2777.3948    1864.0745    9.9287723    17.197139    10.917206   -13652.344    -2823.514    1570.3111   -7481.9537   -1150.3548    10502.368 
+    3000    559.52782   -2882.7076   -2777.5527    1883.2223    9.9626528    17.255821     10.95446    3061.1755   -10570.656    -1138.642   -12045.354   -856.20951    16292.443 
+    3500    521.67929    9974.5929   -2776.7752    1880.5936    9.9580152    17.247789     10.94936    15358.559    7855.8683    6709.3509    7292.9372   -9848.9204   -523.61056 
+    4000    497.90872   -2012.9259   -2776.5554    1862.1703    9.9253904    17.191281    10.913488   -1154.5123    4270.0275   -9154.2927    971.94826   -10157.618    4694.0509 
+    4500    533.64016   -7218.9278   -2775.8789    1883.3041     9.962797    17.256071    10.954618   -18299.547    -5497.566    2140.3296   -1335.6063    -10353.21    5703.7506 
+    5000    551.61416    1590.9702   -2777.6093    1866.2047    9.9325531    17.203687    10.921363     -4600.02       6535.3    2837.6306    3412.3383      9492.18    1017.5742 
+    5500    499.36075    188.82067   -2777.9872    1863.2925    9.9273838    17.194734     10.91568    -3238.914     1143.013     2662.363    4193.7623   -11565.423    2575.9361 
+    6000      478.563    4064.8319    -2778.946    1867.7185     9.935238    17.208337    10.924316    1947.7246    3346.7411    6900.0301   -6339.9554    4133.6942    -4555.406 
+    6500    512.63865    10227.461   -2778.8476    1855.5323    9.9135828     17.17083    10.900505    7423.8967    7558.2024    15700.285    -621.4585   -2620.4837   -3256.7524 
+    7000     489.9889    13037.303   -2778.8793    1856.2469    9.9148553    17.173034    10.901904    10690.345    16770.786    11650.779   -4056.5527   -5023.8847    469.21909 
+    7500    495.52187    1320.5068   -2778.1189    1871.7467    9.9423755      17.2207    10.932164    1978.2905    738.78041    1244.4496    1826.0923   -7829.3563    1873.2713 
+    8000    474.60945   -4203.2068   -2778.8915    1866.5966    9.9332482    17.204891    10.922128   -1480.6896   -12516.261    1387.3306    2731.4462   -1292.9741    10743.939 
+    8500    473.16225   -6266.1992    -2778.594    1872.9075    9.9444304    17.224259    10.934423   -12680.492   -2832.6603   -3285.4455    7226.9632    3762.6841   -5834.9064 
+    9000     486.6579    2843.7947   -2778.0388    1877.3735    9.9523282    17.237939    10.943107    805.23659    6213.7247    1512.4228    2685.2063   -3517.5266   -17054.035 
+    9500    549.35112   -1028.3899   -2776.8124    1880.7965    9.9583733    17.248409    10.949754   -1817.8413    2754.8459   -4022.1743   -3101.1463    8397.2345   -8608.1342 
+   10000    562.27081     12885.53   -2775.7435    1850.2864    9.9042316    17.154633    10.890222    15758.218    9989.5121    12908.859   -25.724137   -16691.374    267.85371 
+Loop time of 3.80648 on 4 procs for 10000 steps with 144 atoms
+
+Performance: 226.981 ns/day, 0.106 hours/ns, 2627.100 timesteps/s
+94.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3526     | 1.6581     | 1.9634     |  21.3 | 43.56
+Kspace  | 0.92143    | 1.2222     | 1.5232     |  24.7 | 32.11
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.31886    | 0.32256    | 0.32604    |   0.5 |  8.47
+Output  | 0.0003643  | 0.00083923 | 0.0022533  |   0.0 |  0.02
+Modify  | 0.39166    | 0.45985    | 0.52607    |   8.9 | 12.08
+Other   |            | 0.143      |            |       |  3.76
+
+Nlocal:    36 ave 36 max 36 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    2614 ave 2614 max 2614 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    10488 ave 12570 max 8406 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 41952
+Ave neighs/atom = 291.333
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix                   quartz_qtb
+unfix                   scapegoat_qtb
+Total wall time: 0:00:03

examples/mliap/InP_JCPA2020.mliap

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.mliap

examples/mliap/InP_JCPA2020.mliap.descriptor

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.mliap.descriptor

examples/mliap/InP_JCPA2020.mliap.model

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.mliap.model

examples/mliap/Ta06A.mliap

@@ -0,0 +1 @@
+../../potentials/Ta06A.mliap

examples/mliap/Ta06A.mliap.descriptor

@@ -0,0 +1 @@
+../../potentials/Ta06A.mliap.descriptor

examples/mliap/Ta06A.mliap.model

@@ -0,0 +1 @@
+../../potentials/Ta06A.mliap.model

examples/mliap/W.quadratic.mliap

@@ -0,0 +1 @@
+../../potentials/W.quadratic.mliap

examples/mliap/W.quadratic.mliap.descriptor

@@ -0,0 +1 @@
+../../potentials/W.quadratic.mliap.descriptor

examples/mliap/W.quadratic.mliap.model

@@ -0,0 +1 @@
+../../potentials/W.quadratic.mliap.model

examples/mliap/WBe_Wood_PRB2019.mliap

@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.mliap

examples/mliap/WBe_Wood_PRB2019.mliap.descriptor

@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.mliap.descriptor

examples/mliap/WBe_Wood_PRB2019.mliap.model

@@ -0,0 +1 @@
+../../potentials/WBe_Wood_PRB2019.mliap.model

examples/mliap/in.mliap.snap.Ta06A

@@ -0,0 +1,53 @@
+# Demonstrate MLIAP interface to kinear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/in.mliap.snap.WBe.PRB2019

@@ -0,0 +1,56 @@
+# Demonstrate MLIAP interface to SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      2 box
+create_atoms    1 box
+mass 1 183.84
+mass 2 9.012182
+
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+group   tungsten         type 1
+group   beryllium        type 2
+# choose potential
+
+include WBe_Wood_PRB2019.mliap
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/in.mliap.snap.chem

@@ -0,0 +1,46 @@
+# Demonstrate MLIAP interface to ChemSNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         diamond $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      2 box
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.mliap
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/in.mliap.snap.quadratic

@@ -0,0 +1,55 @@
+
+# Demonstrate MLIAP interface to quadratic SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	1 box
+create_atoms	1 box
+displace_atoms  all random 0.01 0.01 0.01 12345
+
+mass 1 183.84
+
+# choose potential
+
+include W.quadratic.mliap
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check no
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.1

@@ -0,0 +1,156 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to kinear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.316
+Lattice spacing in x,y,z = 3.316 3.316 3.316
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap
+# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+
+# Definition of SNAP potential Ta_Cand06A
+# Assumes 1 LAMMPS atom type
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+Reading potential file Ta06A.mliap.model with DATE: 2014-09-05
+Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems Ta 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 0 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * mliap Ta
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.592 | 6.592 | 6.592 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300    -11.85157    -11.85157   -11.813095    2717.1661   -2717.1661 
+      10    296.01467   -11.851059   -11.851059   -11.813095    2697.4796   -2697.4796 
+      20    284.53666   -11.849587   -11.849587   -11.813095    2289.1527   -2289.1527 
+      30    266.51577   -11.847275   -11.847275   -11.813095    1851.7131   -1851.7131 
+      40    243.05007   -11.844266   -11.844266   -11.813095     1570.684    -1570.684 
+      50    215.51032   -11.840734   -11.840734   -11.813094    1468.1899   -1468.1899 
+      60    185.48331   -11.836883   -11.836883   -11.813094    1524.8757   -1524.8757 
+      70     154.6736   -11.832931   -11.832931   -11.813094    1698.3351   -1698.3351 
+      80    124.79303   -11.829099   -11.829099   -11.813094    1947.0715   -1947.0715 
+      90    97.448054   -11.825592   -11.825592   -11.813094    2231.9563   -2231.9563 
+     100    74.035418   -11.822589   -11.822589   -11.813094    2515.8526   -2515.8526 
+Loop time of 0.931876 on 1 procs for 100 steps with 128 atoms
+
+Performance: 4.636 ns/day, 5.177 hours/ns, 107.310 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.93067    | 0.93067    | 0.93067    |   0.0 | 99.87
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.000377   | 0.000377   | 0.000377   |   0.0 |  0.04
+Output  | 0.000467   | 0.000467   | 0.000467   |   0.0 |  0.05
+Modify  | 0.000162   | 0.000162   | 0.000162   |   0.0 |  0.02
+Other   |            | 0.000196   |            |       |  0.02
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00

examples/mliap/log.21Jun20.mliap.snap.Ta06A.g++.4

@@ -0,0 +1,156 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to kinear SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.316
+Lattice spacing in x,y,z = 3.316 3.316 3.316
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.mliap
+# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+
+# Definition of SNAP potential Ta_Cand06A
+# Assumes 1 LAMMPS atom type
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
+Reading potential file Ta06A.mliap.model with DATE: 2014-09-05
+Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems Ta 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 0 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * mliap Ta
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.528 | 6.528 | 6.528 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300    -11.85157    -11.85157   -11.813095    2717.1661   -2717.1661 
+      10    296.01467   -11.851059   -11.851059   -11.813095    2697.4796   -2697.4796 
+      20    284.53666   -11.849587   -11.849587   -11.813095    2289.1527   -2289.1527 
+      30    266.51577   -11.847275   -11.847275   -11.813095    1851.7131   -1851.7131 
+      40    243.05007   -11.844266   -11.844266   -11.813095     1570.684    -1570.684 
+      50    215.51032   -11.840734   -11.840734   -11.813094    1468.1899   -1468.1899 
+      60    185.48331   -11.836883   -11.836883   -11.813094    1524.8757   -1524.8757 
+      70     154.6736   -11.832931   -11.832931   -11.813094    1698.3351   -1698.3351 
+      80    124.79303   -11.829099   -11.829099   -11.813094    1947.0715   -1947.0715 
+      90    97.448054   -11.825592   -11.825592   -11.813094    2231.9563   -2231.9563 
+     100    74.035418   -11.822589   -11.822589   -11.813094    2515.8526   -2515.8526 
+Loop time of 0.256886 on 4 procs for 100 steps with 128 atoms
+
+Performance: 16.817 ns/day, 1.427 hours/ns, 389.278 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24436    | 0.24636    | 0.25027    |   0.5 | 95.90
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.005652   | 0.0095395  | 0.01154    |   2.4 |  3.71
+Output  | 0.000472   | 0.0005085  | 0.000617   |   0.0 |  0.20
+Modify  | 6.2e-05    | 6.75e-05   | 7.3e-05    |   0.0 |  0.03
+Other   |            | 0.0004105  |            |       |  0.16
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    928 ave 928 max 928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00

examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.1

@@ -0,0 +1,165 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+mass 1 183.84
+mass 2 9.012182
+
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fractiongroup   tungsten         type 1
+123 atoms in group tungsten
+group   beryllium        type 2
+5 atoms in group beryllium
+# choose potential
+
+include WBe_Wood_PRB2019.mliap
+# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz1 equal 74
+variable zblz2 equal 4
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+Reading potential file WBe_Wood_PRB2019.mliap.model with DATE: 2019-09-18
+Reading potential file WBe_Wood_PRB2019.mliap.descriptor with DATE: 2019-09-18
+SNAP keyword rcutfac 4.8123 
+SNAP keyword twojmax 8 
+SNAP keyword nelems 2 
+SNAP keyword elems W 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 74 ${zblz1}
+pair_coeff 1 1 zbl 74 74
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 74 ${zblz2}
+pair_coeff 1 2 zbl 74 4
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 4 ${zblz2}
+pair_coeff 2 2 zbl 4 4
+pair_coeff * * mliap   W Be
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8123
+  ghost atom cutoff = 5.8123
+  binsize = 2.90615, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300   -8.5980876   -8.5980876   -8.5596125   -35284.855    35284.855 
+      10    296.32664   -8.5976164   -8.5976164   -8.5596124   -35188.339    35188.339 
+      20    282.41417    -8.595832    -8.595832   -8.5596123   -34782.293    34782.293 
+      30    259.69014   -8.5929175   -8.5929175   -8.5596121   -34113.316    34113.316 
+      40    230.50415   -8.5891741   -8.5891741   -8.5596119   -33260.777    33260.777 
+      50    197.88816   -8.5849908   -8.5849908   -8.5596116   -32309.975    32309.975 
+      60    165.27259   -8.5808076   -8.5808076   -8.5596113   -31365.766    31365.766 
+      70    136.15697   -8.5770733   -8.5770733   -8.5596111   -30542.657    30542.657 
+      80    113.58947   -8.5741788   -8.5741788   -8.5596109    -29939.23     29939.23 
+      90    99.477916    -8.572369    -8.572369   -8.5596109   -29619.939    29619.939 
+     100    94.121939   -8.5716822   -8.5716822    -8.559611   -29598.002    29598.002 
+Loop time of 2.95019 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.464 ns/day, 16.390 hours/ns, 33.896 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9486     | 2.9486     | 2.9486     |   0.0 | 99.95
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.000379   | 0.000379   | 0.000379   |   0.0 |  0.01
+Output  | 0.000633   | 0.000633   | 0.000633   |   0.0 |  0.02
+Modify  | 0.000207   | 0.000207   | 0.000207   |   0.0 |  0.01
+Other   |            | 0.000341   |            |       |  0.01
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4

@@ -0,0 +1,165 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to SNAP W-Be potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+mass 1 183.84
+mass 2 9.012182
+
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fractiongroup   tungsten         type 1
+123 atoms in group tungsten
+group   beryllium        type 2
+5 atoms in group beryllium
+# choose potential
+
+include WBe_Wood_PRB2019.mliap
+# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz1 equal 74
+variable zblz2 equal 4
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
+Reading potential file WBe_Wood_PRB2019.mliap.model with DATE: 2019-09-18
+Reading potential file WBe_Wood_PRB2019.mliap.descriptor with DATE: 2019-09-18
+SNAP keyword rcutfac 4.8123 
+SNAP keyword twojmax 8 
+SNAP keyword nelems 2 
+SNAP keyword elems W 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 74 ${zblz1}
+pair_coeff 1 1 zbl 74 74
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 74 ${zblz2}
+pair_coeff 1 2 zbl 74 4
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 4 ${zblz2}
+pair_coeff 2 2 zbl 4 4
+pair_coeff * * mliap   W Be
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8123
+  ghost atom cutoff = 5.8123
+  binsize = 2.90615, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.793 | 6.793 | 6.793 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300   -8.5980876   -8.5980876   -8.5596125   -35284.855    35284.855 
+      10    296.32664   -8.5976164   -8.5976164   -8.5596124   -35188.339    35188.339 
+      20    282.41417    -8.595832    -8.595832   -8.5596123   -34782.293    34782.293 
+      30    259.69014   -8.5929175   -8.5929175   -8.5596121   -34113.316    34113.316 
+      40    230.50415   -8.5891741   -8.5891741   -8.5596119   -33260.777    33260.777 
+      50    197.88816   -8.5849908   -8.5849908   -8.5596116   -32309.975    32309.975 
+      60    165.27259   -8.5808076   -8.5808076   -8.5596113   -31365.766    31365.766 
+      70    136.15697   -8.5770733   -8.5770733   -8.5596111   -30542.657    30542.657 
+      80    113.58947   -8.5741788   -8.5741788   -8.5596109    -29939.23     29939.23 
+      90    99.477916    -8.572369    -8.572369   -8.5596109   -29619.939    29619.939 
+     100    94.121939   -8.5716822   -8.5716822    -8.559611   -29598.002    29598.002 
+Loop time of 0.897476 on 4 procs for 100 steps with 128 atoms
+
+Performance: 4.813 ns/day, 4.986 hours/ns, 111.424 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.84854    | 0.85737    | 0.87512    |   1.1 | 95.53
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.021045   | 0.038782   | 0.047601   |   5.3 |  4.32
+Output  | 0.00061    | 0.0006525  | 0.000774   |   0.0 |  0.07
+Modify  | 0.00011    | 0.00011375 | 0.000117   |   0.0 |  0.01
+Other   |            | 0.0005625  |            |       |  0.06
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    928 ave 928 max 928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00

examples/mliap/log.21Jun20.mliap.snap.chem.g++.1

@@ -0,0 +1,158 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to ChemSNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         diamond $a
+lattice         diamond 5.83
+Lattice spacing in x,y,z = 5.83 5.83 5.83
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+Created 512 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.mliap
+# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
+
+# Definition of SNAP+ZBL potential.
+
+variable zblcutinner index 4
+variable zblcutouter index 4.2
+variable zblz1 index 49
+variable zblz2 index 15
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01
+Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01
+SNAP keyword rcutfac 1.0 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 2 
+SNAP keyword elems In 
+SNAP keyword radelems 3.81205 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0.0 
+SNAP keyword bzeroflag 1 
+SNAP keyword wselfallflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 49 ${zblz1}
+pair_coeff 1 1 zbl 49 49
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 49 ${zblz2}
+pair_coeff 1 2 zbl 49 15
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 15 ${zblz2}
+pair_coeff 2 2 zbl 15 15
+pair_coeff * * mliap   In P
+
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.6589
+  ghost atom cutoff = 8.6589
+  binsize = 4.32945, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.03 | 6.03 | 6.03 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -3.4805794            0   -3.4418771    1353.5968 
+      10    285.84677   -3.4787531            0   -3.4418766    1611.7131 
+      20    248.14649   -3.4738884            0   -3.4418756    2312.0308 
+      30    198.94136   -3.4675394            0   -3.4418744    3168.1543 
+      40    152.74831   -3.4615791            0   -3.4418734    3903.5749 
+      50     121.9796   -3.4576091            0   -3.4418728    4387.1254 
+      60    113.27555   -3.4564863            0   -3.4418729    4556.3003 
+      70    125.68089   -3.4580873            0   -3.4418735    4431.2083 
+      80    151.47475   -3.4614159            0   -3.4418745    4107.2369 
+      90    179.18708   -3.4649919            0   -3.4418754    3739.5881 
+     100    197.50662   -3.4673559            0    -3.441876    3492.7778 
+Loop time of 16.748 on 1 procs for 100 steps with 512 atoms
+
+Performance: 0.258 ns/day, 93.045 hours/ns, 5.971 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 16.746     | 16.746     | 16.746     |   0.0 | 99.99
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.001033   | 0.001033   | 0.001033   |   0.0 |  0.01
+Output  | 0.000235   | 0.000235   | 0.000235   |   0.0 |  0.00
+Modify  | 0.000688   | 0.000688   | 0.000688   |   0.0 |  0.00
+Other   |            | 0.000497   |            |       |  0.00
+
+Nlocal:    512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1959 ave 1959 max 1959 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    31232 ave 31232 max 31232 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  62464 ave 62464 max 62464 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 62464
+Ave neighs/atom = 122
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:17

examples/mliap/log.21Jun20.mliap.snap.chem.g++.4

@@ -0,0 +1,158 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to ChemSNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         diamond $a
+lattice         diamond 5.83
+Lattice spacing in x,y,z = 5.83 5.83 5.83
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+Created 512 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.mliap
+# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
+
+# Definition of SNAP+ZBL potential.
+
+variable zblcutinner index 4
+variable zblcutouter index 4.2
+variable zblz1 index 49
+variable zblz2 index 15
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
+Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01
+Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01
+SNAP keyword rcutfac 1.0 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 2 
+SNAP keyword elems In 
+SNAP keyword radelems 3.81205 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0.0 
+SNAP keyword bzeroflag 1 
+SNAP keyword wselfallflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 49 ${zblz1}
+pair_coeff 1 1 zbl 49 49
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 49 ${zblz2}
+pair_coeff 1 2 zbl 49 15
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 15 ${zblz2}
+pair_coeff 2 2 zbl 15 15
+pair_coeff * * mliap   In P
+
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.6589
+  ghost atom cutoff = 8.6589
+  binsize = 4.32945, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -3.4805794            0   -3.4418771    1353.5968 
+      10    285.84677   -3.4787531            0   -3.4418766    1611.7131 
+      20    248.14649   -3.4738884            0   -3.4418756    2312.0308 
+      30    198.94136   -3.4675394            0   -3.4418744    3168.1543 
+      40    152.74831   -3.4615791            0   -3.4418734    3903.5749 
+      50     121.9796   -3.4576091            0   -3.4418728    4387.1254 
+      60    113.27555   -3.4564863            0   -3.4418729    4556.3003 
+      70    125.68089   -3.4580873            0   -3.4418735    4431.2083 
+      80    151.47475   -3.4614159            0   -3.4418745    4107.2369 
+      90    179.18708   -3.4649919            0   -3.4418754    3739.5881 
+     100    197.50662   -3.4673559            0    -3.441876    3492.7778 
+Loop time of 5.01913 on 4 procs for 100 steps with 512 atoms
+
+Performance: 0.861 ns/day, 27.884 hours/ns, 19.924 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.9328     | 4.9409     | 4.952      |   0.3 | 98.44
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.065669   | 0.076754   | 0.084728   |   2.5 |  1.53
+Output  | 0.000173   | 0.00028775 | 0.000617   |   0.0 |  0.01
+Modify  | 0.000256   | 0.00026675 | 0.000281   |   0.0 |  0.01
+Other   |            | 0.0009633  |            |       |  0.02
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    7808 ave 7808 max 7808 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  15616 ave 15616 max 15616 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 62464
+Ave neighs/atom = 122
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:05

examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.1

@@ -0,0 +1,151 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to quadratic SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+displace_atoms  all random 0.01 0.01 0.01 12345
+
+mass 1 183.84
+
+# choose potential
+
+include W.quadratic.mliap
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems W 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 74 ${zblz}
+pair_coeff 1 1 zbl 74 74
+pair_coeff * * mliap W
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check no
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.093 | 6.093 | 6.093 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300   -1.1602728   -1.1602728   -1.1217977     600047.3    -600047.3 
+      10    288.46387   -1.1587932   -1.1587932   -1.1217976    600359.75   -600359.75 
+      20    268.69718   -1.1562579   -1.1562579   -1.1217974    600870.22   -600870.22 
+      30    243.19855   -1.1529874   -1.1529874   -1.1217971     601511.5    -601511.5 
+      40    215.13122   -1.1493875   -1.1493875   -1.1217969    602202.36   -602202.36 
+      50    187.82673   -1.1458855   -1.1458855   -1.1217966    602860.26   -602860.26 
+      60    164.26822   -1.1428639   -1.1428639   -1.1217965    603413.25   -603413.25 
+      70    146.65179   -1.1406045   -1.1406045   -1.1217964    603809.35   -603809.35 
+      80    136.10769   -1.1392522   -1.1392522   -1.1217964    604022.32   -604022.32 
+      90    132.62756    -1.138806    -1.138806   -1.1217964    604053.33   -604053.33 
+     100    135.19841   -1.1391358   -1.1391358   -1.1217966    603928.48   -603928.48 
+Loop time of 1.69996 on 1 procs for 100 steps with 128 atoms
+
+Performance: 2.541 ns/day, 9.444 hours/ns, 58.825 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6676     | 1.6676     | 1.6676     |   0.0 | 98.09
+Neigh   | 0.03029    | 0.03029    | 0.03029    |   0.0 |  1.78
+Comm    | 0.001238   | 0.001238   | 0.001238   |   0.0 |  0.07
+Output  | 0.000452   | 0.000452   | 0.000452   |   0.0 |  0.03
+Modify  | 0.000175   | 0.000175   | 0.000175   |   0.0 |  0.01
+Other   |            | 0.000241   |            |       |  0.01
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Total wall time: 0:00:01

examples/mliap/log.21Jun20.mliap.snap.quadratic.g++.4

@@ -0,0 +1,151 @@
+LAMMPS (15 Jun 2020)
+# Demonstrate MLIAP interface to quadratic SNAP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+  create_atoms CPU = 0.000 seconds
+displace_atoms  all random 0.01 0.01 0.01 12345
+
+mass 1 183.84
+
+# choose potential
+
+include W.quadratic.mliap
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 6 
+SNAP keyword nelems 1 
+SNAP keyword elems W 
+SNAP keyword radelems 0.5 
+SNAP keyword welems 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 1 
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 74 ${zblz}
+pair_coeff 1 1 zbl 74 74
+pair_coeff * * mliap W
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check no
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair mliap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.031 | 6.032 | 6.033 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300   -1.1602728   -1.1602728   -1.1217977     600047.3    -600047.3 
+      10    288.46387   -1.1587932   -1.1587932   -1.1217976    600359.75   -600359.75 
+      20    268.69718   -1.1562579   -1.1562579   -1.1217974    600870.22   -600870.22 
+      30    243.19855   -1.1529874   -1.1529874   -1.1217971     601511.5    -601511.5 
+      40    215.13122   -1.1493875   -1.1493875   -1.1217969    602202.36   -602202.36 
+      50    187.82673   -1.1458855   -1.1458855   -1.1217966    602860.26   -602860.26 
+      60    164.26822   -1.1428639   -1.1428639   -1.1217965    603413.25   -603413.25 
+      70    146.65179   -1.1406045   -1.1406045   -1.1217964    603809.35   -603809.35 
+      80    136.10769   -1.1392522   -1.1392522   -1.1217964    604022.32   -604022.32 
+      90    132.62756    -1.138806    -1.138806   -1.1217964    604053.33   -604053.33 
+     100    135.19841   -1.1391358   -1.1391358   -1.1217966    603928.48   -603928.48 
+Loop time of 0.520935 on 4 procs for 100 steps with 128 atoms
+
+Performance: 8.293 ns/day, 2.894 hours/ns, 191.963 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.4001     | 0.44784    | 0.49877    |   6.8 | 85.97
+Neigh   | 0.00728    | 0.0080255  | 0.008793   |   0.8 |  1.54
+Comm    | 0.012664   | 0.064342   | 0.11287    |  18.2 | 12.35
+Output  | 0.000511   | 0.00053725 | 0.000613   |   0.0 |  0.10
+Modify  | 7.3e-05    | 7.925e-05  | 8.3e-05    |   0.0 |  0.02
+Other   |            | 0.0001087  |            |       |  0.02
+
+Nlocal:    32 ave 35 max 29 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    431 ave 434 max 428 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    928 ave 1019 max 837 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:  1856 ave 2030 max 1682 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 100
+Dangerous builds not checked
+
+Total wall time: 0:00:00

examples/mliap/log.snap.Ta06A.ref

@@ -0,0 +1,154 @@
+LAMMPS (19 Mar 2020)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.316
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.316
+Lattice spacing in x,y,z = 3.316 3.316 3.316
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  create_atoms CPU = 0.000254 secs
+
+mass 1 180.88
+
+# choose potential
+
+include Ta06A.snap
+# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+
+# Definition of SNAP potential Ta_Cand06A
+# Assumes 1 LAMMPS atom type
+
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 73
+
+# Specify hybrid with SNAP, ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 73 ${zblz}
+pair_coeff 1 1 zbl 73 73
+pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
+Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
+SNAP Element = Ta, Radius 0.5, Weight 1 
+Reading potential file Ta06A.snapparam with DATE: 2014-09-05
+SNAP keyword rcutfac 4.67637 
+SNAP keyword twojmax 6 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword bzeroflag 0 
+SNAP keyword quadraticflag 0 
+
+
+# Setup output
+
+compute  eatom all pe/atom
+compute  energy all reduce sum c_eatom
+
+compute  satom all stress/atom NULL
+compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
+
+thermo_style    custom step temp epair c_energy etotal press v_press
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes
+Step Temp E_pair c_energy TotEng Press v_press 
+       0          300    -11.85157    -11.85157   -11.813095    2717.1661   -2717.1661 
+      10    295.96579   -11.851053   -11.851053   -11.813095    2696.1559   -2696.1559 
+      20    284.32535    -11.84956    -11.84956   -11.813095    2301.3713   -2301.3713 
+      30    266.04602   -11.847215   -11.847215   -11.813095    1832.1745   -1832.1745 
+      40     242.2862   -11.844168   -11.844168   -11.813095    1492.6765   -1492.6765 
+      50    214.48968   -11.840603   -11.840603   -11.813094    1312.8908   -1312.8908 
+      60    184.32523   -11.836734   -11.836734   -11.813094     1284.582    -1284.582 
+      70    153.58055   -11.832791   -11.832791   -11.813094    1374.4457   -1374.4457 
+      80    124.04276   -11.829003   -11.829003   -11.813094     1537.703    -1537.703 
+      90     97.37622   -11.825582   -11.825582   -11.813094    1734.9662   -1734.9662 
+     100    75.007873   -11.822714   -11.822714   -11.813094    1930.8005   -1930.8005 
+Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms
+
+Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.99426    | 0.99426    | 0.99426    |   0.0 | 99.89
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.000305   | 0.000305   | 0.000305   |   0.0 |  0.03
+Output  | 0.000413   | 0.000413   | 0.000413   |   0.0 |  0.04
+Modify  | 0.000159   | 0.000159   | 0.000159   |   0.0 |  0.02
+Other   |            | 0.000191   |            |       |  0.02
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:01

examples/snap/InP_JCPA2020.snap

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.snap

examples/snap/InP_JCPA2020.snapcoeff

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.snapcoeff

examples/snap/InP_JCPA2020.snapparam

@@ -0,0 +1 @@
+../../potentials/InP_JCPA2020.snapparam

examples/snap/in.snap.InP.JCPA2020

@@ -0,0 +1,46 @@
+# Demonstrate SNAP InP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         diamond $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      2 box
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.snap
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+

examples/snap/in.snap.Mo_Chen

@@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 

examples/snap/in.snap.Ta06A

@@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 

examples/snap/in.snap.W.2940

@@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 

examples/snap/in.snap.WBe.PRB2019

@@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 

examples/snap/in.snap.hybrid.WSNAP.HePair

@@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 

examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.1

@@ -0,0 +1,157 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP InP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         diamond $a
+lattice         diamond 5.83
+Lattice spacing in x,y,z = 5.83 5.83 5.83
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+Created 512 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.snap
+# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
+
+# Definition of SNAP+ZBL potential.
+
+variable zblcutinner index 4
+variable zblcutouter index 4.2
+variable zblz1 index 49
+variable zblz2 index 15
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.2 snap
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 49 ${zblz1}
+pair_coeff 1 1 zbl 49 49
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 49 ${zblz2}
+pair_coeff 1 2 zbl 49 15
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 15 ${zblz2}
+pair_coeff 2 2 zbl 15 15
+pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
+Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01
+SNAP Element = In, Radius 3.81205, Weight 1 
+SNAP Element = P, Radius 3.82945, Weight 0.929316 
+Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01
+SNAP keyword rcutfac 1.0 
+SNAP keyword twojmax 6 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0.0 
+SNAP keyword bzeroflag 1 
+SNAP keyword quadraticflag 0 
+SNAP keyword wselfallflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.6589
+  ghost atom cutoff = 8.6589
+  binsize = 4.32945, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -3.4805794            0   -3.4418771    1353.5968 
+      10    285.84677   -3.4787531            0   -3.4418766    1611.7131 
+      20    248.14649   -3.4738884            0   -3.4418756    2312.0308 
+      30    198.94136   -3.4675394            0   -3.4418744    3168.1543 
+      40    152.74831   -3.4615791            0   -3.4418734    3903.5749 
+      50     121.9796   -3.4576091            0   -3.4418728    4387.1254 
+      60    113.27555   -3.4564863            0   -3.4418729    4556.3003 
+      70    125.68089   -3.4580873            0   -3.4418735    4431.2083 
+      80    151.47475   -3.4614159            0   -3.4418745    4107.2369 
+      90    179.18708   -3.4649919            0   -3.4418754    3739.5881 
+     100    197.50662   -3.4673559            0    -3.441876    3492.7778 
+Loop time of 13.3103 on 1 procs for 100 steps with 512 atoms
+
+Performance: 0.325 ns/day, 73.946 hours/ns, 7.513 timesteps/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    | 13.309     | 13.309     | 13.309     |   0.0 | 99.99
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00068474 | 0.00068474 | 0.00068474 |   0.0 |  0.01
+Output  | 0.00020504 | 0.00020504 | 0.00020504 |   0.0 |  0.00
+Modify  | 0.0003829  | 0.0003829  | 0.0003829  |   0.0 |  0.00
+Other   |            | 0.0004075  |            |       |  0.00
+
+Nlocal:    512 ave 512 max 512 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1959 ave 1959 max 1959 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    31232 ave 31232 max 31232 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  62464 ave 62464 max 62464 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 62464
+Ave neighs/atom = 122
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:13

examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.4

@@ -0,0 +1,157 @@
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate SNAP InP potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 5.83
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary        p p p
+
+lattice         diamond $a
+lattice         diamond 5.83
+Lattice spacing in x,y,z = 5.83 5.83 5.83
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
+Created 512 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass 1 114.76
+mass 2 30.98
+
+# choose potential
+
+include InP_JCPA2020.snap
+# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
+
+# Definition of SNAP+ZBL potential.
+
+variable zblcutinner index 4
+variable zblcutouter index 4.2
+variable zblz1 index 49
+variable zblz2 index 15
+
+# Specify hybrid with SNAP and ZBL
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.2 snap
+pair_coeff 1 1 zbl ${zblz1} ${zblz1}
+pair_coeff 1 1 zbl 49 ${zblz1}
+pair_coeff 1 1 zbl 49 49
+pair_coeff 1 2 zbl ${zblz1} ${zblz2}
+pair_coeff 1 2 zbl 49 ${zblz2}
+pair_coeff 1 2 zbl 49 15
+pair_coeff 2 2 zbl ${zblz2} ${zblz2}
+pair_coeff 2 2 zbl 15 ${zblz2}
+pair_coeff 2 2 zbl 15 15
+pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
+Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01
+SNAP Element = In, Radius 3.81205, Weight 1 
+SNAP Element = P, Radius 3.82945, Weight 0.929316 
+Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01
+SNAP keyword rcutfac 1.0 
+SNAP keyword twojmax 6 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0.0 
+SNAP keyword bzeroflag 1 
+SNAP keyword quadraticflag 0 
+SNAP keyword wselfallflag 1 
+SNAP keyword chemflag 1 
+SNAP keyword bnormflag 1 
+
+# Setup output
+
+thermo          10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.6589
+  ghost atom cutoff = 8.6589
+  binsize = 4.32945, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.587 | 4.587 | 4.587 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -3.4805794            0   -3.4418771    1353.5968 
+      10    285.84677   -3.4787531            0   -3.4418766    1611.7131 
+      20    248.14649   -3.4738884            0   -3.4418756    2312.0308 
+      30    198.94136   -3.4675394            0   -3.4418744    3168.1543 
+      40    152.74831   -3.4615791            0   -3.4418734    3903.5749 
+      50     121.9796   -3.4576091            0   -3.4418728    4387.1254 
+      60    113.27555   -3.4564863            0   -3.4418729    4556.3003 
+      70    125.68089   -3.4580873            0   -3.4418735    4431.2083 
+      80    151.47475   -3.4614159            0   -3.4418745    4107.2369 
+      90    179.18708   -3.4649919            0   -3.4418754    3739.5881 
+     100    197.50662   -3.4673559            0    -3.441876    3492.7778 
+Loop time of 3.73974 on 4 procs for 100 steps with 512 atoms
+
+Performance: 1.155 ns/day, 20.776 hours/ns, 26.740 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.4687     | 3.5182     | 3.5985     |   2.7 | 94.07
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.13897    | 0.21952    | 0.26888    |  10.7 |  5.87
+Output  | 0.00018191 | 0.00047094 | 0.0012944  |   0.0 |  0.01
+Modify  | 0.00013065 | 0.00013524 | 0.00014186 |   0.0 |  0.00
+Other   |            | 0.001456   |            |       |  0.04
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    7808 ave 7808 max 7808 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  15616 ave 15616 max 15616 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 62464
+Ave neighs/atom = 122
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/snap/log.15Jun20.snap.Mo_Chen.g++.1

@@ -1,13 +1,13 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP Mo potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.160
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,21 +18,21 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.16
 Lattice spacing in x,y,z = 3.16 3.16 3.16
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
   1 by 1 by 1 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.00029707 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 183.84
 
@@ -40,11 +40,11 @@ mass 1 183.84
 
 include Mo_Chen_PRM2017.snap
 
-# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
 # Generated by Materials Virtual Lab
 # Definition of SNAP potential.
 pair_style snap
-pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
 Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
 SNAP Element = Mo, Radius 0.5, Weight 1 
 Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
@@ -54,7 +54,7 @@ SNAP keyword twojmax 6
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -81,33 +81,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.335 | 3.335 | 3.335 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -22.405975            0     -22.3675    2575.7657 
-      10    294.77555   -22.405305            0     -22.3675    2756.6894 
-      20    279.53011    -22.40335            0     -22.3675    3285.8272 
-      30    255.52174    -22.40027            0     -22.3675    4122.8933 
-      40     224.7299   -22.396321            0   -22.367499    5204.3499 
-      50    189.67529   -22.391825            0   -22.367499    6449.1308 
-      60    153.18862   -22.387145            0   -22.367499     7765.911 
-      70    118.14998   -22.382652            0   -22.367499    9061.1616 
-      80    87.224916   -22.378685            0   -22.367499     10247.68 
-      90    62.623892    -22.37553            0   -22.367498    11250.067 
-     100      45.9103   -22.373386            0   -22.367498    12011.726 
-Loop time of 7.00873 on 1 procs for 100 steps with 128 atoms
+      10     294.8148    -22.40531            0     -22.3675    2762.0942 
+      20    279.68628    -22.40337            0     -22.3675    3306.7656 
+      30    255.84798   -22.400312            0     -22.3675    4168.2979 
+      40    225.22346   -22.396384            0   -22.367499    5281.9537 
+      50    190.25143   -22.391899            0   -22.367499    6565.6626 
+      60    153.66642   -22.387207            0   -22.367499    7927.3186 
+      70    118.25575   -22.382665            0   -22.367499    9271.9554 
+      80    86.616338   -22.378607            0   -22.367499    10510.959 
+      90    60.935787   -22.375314            0   -22.367498    11568.261 
+     100    42.815823    -22.37299            0   -22.367498    12385.433 
+Loop time of 0.897752 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.616 ns/day, 38.937 hours/ns, 14.268 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 4.812 ns/day, 4.988 hours/ns, 111.389 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.0068     | 7.0068     | 7.0068     |   0.0 | 99.97
+Pair    | 0.89711    | 0.89711    | 0.89711    |   0.0 | 99.93
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00083661 | 0.00083661 | 0.00083661 |   0.0 |  0.01
-Output  | 0.00025535 | 0.00025535 | 0.00025535 |   0.0 |  0.00
-Modify  | 0.00034285 | 0.00034285 | 0.00034285 |   0.0 |  0.00
-Other   |            | 0.0005035  |            |       |  0.01
+Comm    | 0.0002501  | 0.0002501  | 0.0002501  |   0.0 |  0.03
+Output  | 0.00013161 | 0.00013161 | 0.00013161 |   0.0 |  0.01
+Modify  | 0.00010276 | 0.00010276 | 0.00010276 |   0.0 |  0.01
+Other   |            | 0.0001559  |            |       |  0.02
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -123,4 +123,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:07
+Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.Mo_Chen.g++.4

@@ -1,13 +1,13 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP Mo potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.160
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,21 +18,21 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.16
 Lattice spacing in x,y,z = 3.16 3.16 3.16
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
   1 by 2 by 2 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000289917 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 183.84
 
@@ -40,11 +40,11 @@ mass 1 183.84
 
 include Mo_Chen_PRM2017.snap
 
-# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
 # Generated by Materials Virtual Lab
 # Definition of SNAP potential.
 pair_style snap
-pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
 Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
 SNAP Element = Mo, Radius 0.5, Weight 1 
 Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
@@ -54,7 +54,7 @@ SNAP keyword twojmax 6
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -81,33 +81,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.271 | 3.271 | 3.271 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -22.405975            0     -22.3675    2575.7657 
-      10    294.63153   -22.405286            0     -22.3675    2753.4662 
-      20    278.98535    -22.40328            0     -22.3675     3272.416 
-      30    254.38916   -22.400125            0     -22.3675    4091.8933 
-      40    222.91191   -22.396088            0   -22.367499    5148.5505 
-      50    187.16984   -22.391504            0   -22.367499    6362.2454 
-      60    150.08253   -22.386747            0   -22.367499    7643.2732 
-      70    114.60307   -22.382197            0   -22.367499    8900.2448 
-      80    83.449257   -22.378201            0   -22.367499    10047.619 
-      90    58.862643   -22.375048            0   -22.367498    11012.233 
-     100     42.41931   -22.372939            0   -22.367498    11740.641 
-Loop time of 2.15419 on 4 procs for 100 steps with 128 atoms
+      10     294.8148    -22.40531            0     -22.3675    2762.0942 
+      20    279.68628    -22.40337            0     -22.3675    3306.7656 
+      30    255.84798   -22.400312            0     -22.3675    4168.2979 
+      40    225.22346   -22.396384            0   -22.367499    5281.9537 
+      50    190.25143   -22.391899            0   -22.367499    6565.6626 
+      60    153.66642   -22.387207            0   -22.367499    7927.3186 
+      70    118.25575   -22.382665            0   -22.367499    9271.9554 
+      80    86.616338   -22.378607            0   -22.367499    10510.959 
+      90    60.935787   -22.375314            0   -22.367498    11568.261 
+     100    42.815823    -22.37299            0   -22.367498    12385.433 
+Loop time of 0.260783 on 4 procs for 100 steps with 128 atoms
 
-Performance: 2.005 ns/day, 11.968 hours/ns, 46.421 timesteps/s
-92.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 16.566 ns/day, 1.449 hours/ns, 383.461 timesteps/s
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.7677     | 1.9028     | 1.9897     |   6.2 | 88.33
+Pair    | 0.23045    | 0.23744    | 0.24455    |   1.2 | 91.05
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.15367    | 0.24295    | 0.38029    |  17.6 | 11.28
-Output  | 0.00034404 | 0.0012512  | 0.0017219  |   1.6 |  0.06
-Modify  | 0.00018859 | 0.00021273 | 0.00023699 |   0.0 |  0.01
-Other   |            | 0.007011   |            |       |  0.33
+Comm    | 0.014524   | 0.021267   | 0.027713   |   3.7 |  8.15
+Output  | 0.00014997 | 0.00040495 | 0.0011623  |   0.0 |  0.16
+Modify  | 4.2439e-05 | 4.6909e-05 | 5.0068e-05 |   0.0 |  0.02
+Other   |            | 0.00162    |            |       |  0.62
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -123,4 +123,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:02
+Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.Ta06A.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
@@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.316
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,28 +18,28 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.316
 Lattice spacing in x,y,z = 3.316 3.316 3.316
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
   1 by 1 by 1 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000350714 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 180.88
 
 # choose potential
 
 include Ta06A.snap
-# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
 
 # Definition of SNAP potential Ta_Cand06A
 # Assumes 1 LAMMPS atom type
@@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 73 ${zblz}
 pair_coeff 1 1 zbl 73 73
-pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
+pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
 SNAP Element = Ta, Radius 0.5, Weight 1 
 Reading potential file Ta06A.snapparam with DATE: 2014-09-05
@@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
 SNAP keyword twojmax 6 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
-SNAP keyword diagonalstyle 3 
 SNAP keyword bzeroflag 0 
 SNAP keyword quadraticflag 0 
 
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -103,33 +102,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.967 | 3.967 | 3.967 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300    -11.85157            0   -11.813095    2717.1661 
-      10    295.96579   -11.851053            0   -11.813095    2696.1559 
-      20    284.32535    -11.84956            0   -11.813095    2301.3713 
-      30    266.04602   -11.847215            0   -11.813095    1832.1745 
-      40     242.2862   -11.844168            0   -11.813095    1492.6765 
-      50    214.48968   -11.840603            0   -11.813094    1312.8908 
-      60    184.32523   -11.836734            0   -11.813094     1284.582 
-      70    153.58055   -11.832791            0   -11.813094    1374.4457 
-      80    124.04276   -11.829003            0   -11.813094     1537.703 
-      90     97.37622   -11.825582            0   -11.813094    1734.9662 
-     100    75.007873   -11.822714            0   -11.813094    1930.8005 
-Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms
+      10    296.01467   -11.851059            0   -11.813095    2697.4796 
+      20    284.53666   -11.849587            0   -11.813095    2289.1527 
+      30    266.51577   -11.847275            0   -11.813095    1851.7131 
+      40    243.05007   -11.844266            0   -11.813095     1570.684 
+      50    215.51032   -11.840734            0   -11.813094    1468.1899 
+      60    185.48331   -11.836883            0   -11.813094    1524.8757 
+      70     154.6736   -11.832931            0   -11.813094    1698.3351 
+      80    124.79303   -11.829099            0   -11.813094    1947.0715 
+      90    97.448054   -11.825592            0   -11.813094    2231.9563 
+     100    74.035418   -11.822589            0   -11.813094    2515.8526 
+Loop time of 0.702618 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 6.148 ns/day, 3.903 hours/ns, 142.325 timesteps/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    | 5.0308     | 5.0308     | 5.0308     |   0.0 | 99.97
+Pair    | 0.70188    | 0.70188    | 0.70188    |   0.0 | 99.90
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00070858 | 0.00070858 | 0.00070858 |   0.0 |  0.01
-Output  | 0.00024676 | 0.00024676 | 0.00024676 |   0.0 |  0.00
-Modify  | 0.0002749  | 0.0002749  | 0.0002749  |   0.0 |  0.01
-Other   |            | 0.0004299  |            |       |  0.01
+Comm    | 0.00025487 | 0.00025487 | 0.00025487 |   0.0 |  0.04
+Output  | 0.00015402 | 0.00015402 | 0.00015402 |   0.0 |  0.02
+Modify  | 0.00011039 | 0.00011039 | 0.00011039 |   0.0 |  0.02
+Other   |            | 0.000217   |            |       |  0.03
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -145,4 +144,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:05
+Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.Ta06A.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP Ta potential
 
@@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.316
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,28 +18,28 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.316
 Lattice spacing in x,y,z = 3.316 3.316 3.316
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
   1 by 2 by 2 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000299692 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 180.88
 
 # choose potential
 
 include Ta06A.snap
-# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
+# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
 
 # Definition of SNAP potential Ta_Cand06A
 # Assumes 1 LAMMPS atom type
@@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 73 ${zblz}
 pair_coeff 1 1 zbl 73 73
-pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
+pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
 SNAP Element = Ta, Radius 0.5, Weight 1 
 Reading potential file Ta06A.snapparam with DATE: 2014-09-05
@@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
 SNAP keyword twojmax 6 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
-SNAP keyword diagonalstyle 3 
 SNAP keyword bzeroflag 0 
 SNAP keyword quadraticflag 0 
 
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -103,33 +102,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.903 | 3.903 | 3.903 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300    -11.85157            0   -11.813095    2717.1661 
-      10     295.8664    -11.85104            0   -11.813095     2702.935 
-      20    283.95868   -11.849513            0   -11.813095    2301.3242 
-      30    265.29535   -11.847119            0   -11.813095    1870.3173 
-      40    241.09337   -11.844015            0   -11.813095    1568.1549 
-      50    212.86732   -11.840395            0   -11.813094    1409.2092 
-      60    182.35256   -11.836481            0   -11.813094    1389.0527 
-      70    151.38968    -11.83251            0   -11.813094    1474.9232 
-      80    121.80051   -11.828715            0   -11.813094    1627.6911 
-      90    95.262635   -11.825311            0   -11.813094    1812.9327 
-     100    73.194645   -11.822481            0   -11.813094    1995.2199 
-Loop time of 1.4959 on 4 procs for 100 steps with 128 atoms
+      10    296.01467   -11.851059            0   -11.813095    2697.4796 
+      20    284.53666   -11.849587            0   -11.813095    2289.1527 
+      30    266.51577   -11.847275            0   -11.813095    1851.7131 
+      40    243.05007   -11.844266            0   -11.813095     1570.684 
+      50    215.51032   -11.840734            0   -11.813094    1468.1899 
+      60    185.48331   -11.836883            0   -11.813094    1524.8757 
+      70     154.6736   -11.832931            0   -11.813094    1698.3351 
+      80    124.79303   -11.829099            0   -11.813094    1947.0715 
+      90    97.448054   -11.825592            0   -11.813094    2231.9563 
+     100    74.035418   -11.822589            0   -11.813094    2515.8526 
+Loop time of 0.230164 on 4 procs for 100 steps with 128 atoms
 
-Performance: 2.888 ns/day, 8.311 hours/ns, 66.850 timesteps/s
-94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 18.769 ns/day, 1.279 hours/ns, 434.473 timesteps/s
+93.5% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 1.2973     | 1.3263     | 1.3444     |   1.6 | 88.66
+Pair    | 0.1824     | 0.19154    | 0.21822    |   3.5 | 83.22
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.14155    | 0.16475    | 0.19518    |   5.0 | 11.01
-Output  | 0.00055361 | 0.0006234  | 0.00078511 |   0.0 |  0.04
-Modify  | 0.00016427 | 0.00020635 | 0.00032949 |   0.0 |  0.01
-Other   |            | 0.004009   |            |       |  0.27
+Comm    | 0.010843   | 0.037176   | 0.046129   |   7.9 | 16.15
+Output  | 0.00014973 | 0.00028926 | 0.00070024 |   0.0 |  0.13
+Modify  | 5.3883e-05 | 5.6803e-05 | 6.1989e-05 |   0.0 |  0.02
+Other   |            | 0.001104   |            |       |  0.48
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -145,4 +144,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:01
+Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.W.2940.g++.1

@@ -1,13 +1,13 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP W potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,28 +18,28 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.1803
 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
   1 by 1 by 1 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000316143 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 183.84
 
 # choose potential
 
 include W_2940_2017_2.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
+# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
@@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 74 ${zblz}
 pair_coeff 1 1 zbl 74 74
-pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
 Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
 SNAP Element = W, Radius 0.5, Weight 1 
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
 SNAP keyword twojmax 8 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
-SNAP keyword diagonalstyle 3 
 SNAP keyword bzeroflag 0 
 SNAP keyword quadraticflag 0 
 
@@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -102,33 +101,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -11.028325            0    -10.98985     3010.497 
-      10    293.40666   -11.027479            0   -10.989849    3246.0559 
-      20    274.27375   -11.025025            0   -10.989849    3927.9497 
-      30    244.50457   -11.021207            0   -10.989849    4983.5484 
-      40     207.0784   -11.016407            0   -10.989849    6299.9473 
-      50    165.74442   -11.011105            0   -10.989848    7736.5123 
-      60    124.62181   -11.005831            0   -10.989848    9140.8587 
-      70    87.744792   -11.001101            0   -10.989848    10366.489 
-      80    58.605244   -10.997364            0   -10.989848    11289.914 
-      90    39.754503   -10.994946            0   -10.989848    11824.945 
-     100    32.524085   -10.994019            0   -10.989848    11932.118 
-Loop time of 18.7678 on 1 procs for 100 steps with 128 atoms
+      10    293.10848   -11.027441            0   -10.989849    3259.9445 
+      20    273.14727   -11.024881            0   -10.989849    3979.8968 
+      30    242.20285   -11.020912            0   -10.989849    5089.0797 
+      40    203.51992    -11.01595            0   -10.989849    6462.9419 
+      50    161.14556   -11.010515            0   -10.989848    7948.1798 
+      60    119.47232    -11.00517            0   -10.989848    9380.8543 
+      70    82.729175   -11.000458            0   -10.989848    10606.025 
+      80    54.483648   -10.996835            0   -10.989848    11496.424 
+      90    37.225263   -10.994622            0   -10.989847    11967.579 
+     100    32.094224   -10.993964            0   -10.989847    11987.181 
+Loop time of 2.29953 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.230 ns/day, 104.265 hours/ns, 5.328 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 1.879 ns/day, 12.775 hours/ns, 43.487 timesteps/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    | 18.766     | 18.766     | 18.766     |   0.0 | 99.99
+Pair    | 2.2988     | 2.2988     | 2.2988     |   0.0 | 99.97
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00081968 | 0.00081968 | 0.00081968 |   0.0 |  0.00
-Output  | 0.00028563 | 0.00028563 | 0.00028563 |   0.0 |  0.00
-Modify  | 0.0003283  | 0.0003283  | 0.0003283  |   0.0 |  0.00
-Other   |            | 0.0005233  |            |       |  0.00
+Comm    | 0.00027108 | 0.00027108 | 0.00027108 |   0.0 |  0.01
+Output  | 0.00014758 | 0.00014758 | 0.00014758 |   0.0 |  0.01
+Modify  | 0.00010991 | 0.00010991 | 0.00010991 |   0.0 |  0.00
+Other   |            | 0.0001643  |            |       |  0.01
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -144,4 +143,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:18
+Total wall time: 0:00:02

examples/snap/log.15Jun20.snap.W.2940.g++.4

@@ -1,13 +1,13 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP W potential
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,28 +18,28 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.1803
 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	1 box
-Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
   1 by 2 by 2 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000297546 secs
+  create_atoms CPU = 0.000 seconds
 
 mass 1 183.84
 
 # choose potential
 
 include W_2940_2017_2.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
+# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
@@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
 pair_coeff 1 1 zbl ${zblz} ${zblz}
 pair_coeff 1 1 zbl 74 ${zblz}
 pair_coeff 1 1 zbl 74 74
-pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
 Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
 SNAP Element = W, Radius 0.5, Weight 1 
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
 SNAP keyword twojmax 8 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
-SNAP keyword diagonalstyle 3 
 SNAP keyword bzeroflag 0 
 SNAP keyword quadraticflag 0 
 
@@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -102,33 +101,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -11.028325            0    -10.98985     3010.497 
-      10    293.22504   -11.027456            0   -10.989849     3258.275 
-      20    273.60084   -11.024939            0   -10.989849    3973.9038 
-      30    243.15327   -11.021034            0   -10.989849    5077.9172 
-      40    205.01905   -11.016142            0   -10.989849    6448.4941 
-      50    163.10914   -11.010767            0   -10.989848    7935.6835 
-      60    121.67854   -11.005453            0   -10.989848    9378.9959 
-      70    84.846972   -11.000729            0   -10.989848    10626.301 
-      80    56.127265   -10.997046            0   -10.989848    11551.687 
-      90    38.025013   -10.994724            0   -10.989847    12069.936 
-     100    31.768127   -10.993922            0   -10.989847    12145.648 
-Loop time of 5.38055 on 4 procs for 100 steps with 128 atoms
+      10    293.10848   -11.027441            0   -10.989849    3259.9445 
+      20    273.14727   -11.024881            0   -10.989849    3979.8968 
+      30    242.20285   -11.020912            0   -10.989849    5089.0797 
+      40    203.51992    -11.01595            0   -10.989849    6462.9419 
+      50    161.14556   -11.010515            0   -10.989848    7948.1798 
+      60    119.47232    -11.00517            0   -10.989848    9380.8543 
+      70    82.729175   -11.000458            0   -10.989848    10606.025 
+      80    54.483648   -10.996835            0   -10.989848    11496.424 
+      90    37.225263   -10.994622            0   -10.989847    11967.579 
+     100    32.094224   -10.993964            0   -10.989847    11987.181 
+Loop time of 0.700403 on 4 procs for 100 steps with 128 atoms
 
-Performance: 0.803 ns/day, 29.892 hours/ns, 18.585 timesteps/s
-96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 6.168 ns/day, 3.891 hours/ns, 142.775 timesteps/s
+95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 4.8254     | 5.0245     | 5.2817     |   7.7 | 93.38
+Pair    | 0.59296    | 0.62019    | 0.6504     |   2.8 | 88.55
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.093845   | 0.34915    | 0.5466     |  29.1 |  6.49
-Output  | 0.00032616 | 0.0011846  | 0.0037167  |   4.2 |  0.02
-Modify  | 0.00022507 | 0.00025326 | 0.0002687  |   0.0 |  0.00
-Other   |            | 0.005432   |            |       |  0.10
+Comm    | 0.048731   | 0.078938   | 0.10647    |   7.8 | 11.27
+Output  | 0.00015879 | 0.00024194 | 0.00048518 |   0.0 |  0.03
+Modify  | 6.4373e-05 | 6.9439e-05 | 7.7963e-05 |   0.0 |  0.01
+Other   |            | 0.0009654  |            |       |  0.14
 
 Nlocal:    32 ave 32 max 32 min
 Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -144,4 +143,4 @@ Ave neighs/atom = 58
 Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:05
+Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.WBe.PRB2019.g++.1

@@ -1,4 +1,5 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP W-Be potential
 
 # Initialize simulation
@@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -17,33 +18,33 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.1803
 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	2 box
-Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
   1 by 1 by 1 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  create_atoms CPU = 0.000234842 secs
+  create_atoms CPU = 0.000 seconds
 mass 1 183.84
 mass 2 9.012182
 
-set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
-  5 settings made for type/fraction
-group	tungsten 	 type 1
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fractiongroup   tungsten         type 1
 123 atoms in group tungsten
-group	beryllium	 type 2
+group   beryllium        type 2
 5 atoms in group beryllium
 # choose potential
 
 include WBe_Wood_PRB2019.snap
+# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
@@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -112,43 +113,43 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -8.5980876            0   -8.5596125   -35284.855 
-      10    299.29029   -8.5979965            0   -8.5596125   -35299.259 
-      20    288.99334   -8.5966759            0   -8.5596124   -35004.093 
-      30    269.91027   -8.5942284            0   -8.5596123   -34447.077 
-      40    243.57361   -8.5908505            0   -8.5596121   -33687.105 
-      50    212.21385   -8.5868284            0   -8.5596119   -32821.864 
-      60    178.77144   -8.5825391            0   -8.5596116    -31971.17 
-      70    146.71854    -8.578428            0   -8.5596113    -31245.51 
-      80    119.50956   -8.5749383            0   -8.5596111   -30724.137 
-      90    99.872785   -8.5724197            0    -8.559611   -30440.244 
-     100    89.604584   -8.5711027            0   -8.5596109   -30392.805 
-Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
+      10    296.32664   -8.5976164            0   -8.5596124   -35188.339 
+      20    282.41417    -8.595832            0   -8.5596123   -34782.293 
+      30    259.69014   -8.5929175            0   -8.5596121   -34113.316 
+      40    230.50415   -8.5891741            0   -8.5596119   -33260.777 
+      50    197.88816   -8.5849908            0   -8.5596116   -32309.975 
+      60    165.27259   -8.5808076            0   -8.5596113   -31365.766 
+      70    136.15697   -8.5770733            0   -8.5596111   -30542.657 
+      80    113.58947   -8.5741788            0   -8.5596109    -29939.23 
+      90    99.477916    -8.572369            0   -8.5596109   -29619.939 
+     100    94.121939   -8.5716822            0    -8.559611   -29598.002 
+Loop time of 2.26616 on 1 procs for 100 steps with 128 atoms
 
-Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
-199.5% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.906 ns/day, 12.590 hours/ns, 44.128 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 3.1672     | 3.1672     | 3.1672     |   0.0 | 99.97
-Neigh   | 0.00030208 | 0.00030208 | 0.00030208 |   0.0 |  0.01
-Comm    | 0.00029612 | 0.00029612 | 0.00029612 |   0.0 |  0.01
-Output  | 0.00019813 | 0.00019813 | 0.00019813 |   0.0 |  0.01
-Modify  | 0.00014448 | 0.00014448 | 0.00014448 |   0.0 |  0.00
-Other   |            | 0.0001433  |            |       |  0.00
+Pair    | 2.2531     | 2.2531     | 2.2531     |   0.0 | 99.42
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0002594  | 0.0002594  | 0.0002594  |   0.0 |  0.01
+Output  | 0.012544   | 0.012544   | 0.012544   |   0.0 |  0.55
+Modify  | 0.00010347 | 0.00010347 | 0.00010347 |   0.0 |  0.00
+Other   |            | 0.0001583  |            |       |  0.01
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 Nghost:    727 ave 727 max 727 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    3710 ave 3710 max 3710 min
+Neighs:    3712 ave 3712 max 3712 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  7420 ave 7420 max 7420 min
+FullNghs:  7424 ave 7424 max 7424 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 7420
-Ave neighs/atom = 57.9688
-Neighbor list builds = 1
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
 Dangerous builds = 0
 
-Total wall time: 0:00:03
+Total wall time: 0:00:02

examples/snap/log.15Jun20.snap.WBe.PRB2019.g++.4

@@ -1,4 +1,5 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (15 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
 # Demonstrate SNAP W-Be potential
 
 # Initialize simulation
@@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -17,33 +18,33 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.1803
 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	2 box
-Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
   1 by 2 by 2 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  create_atoms CPU = 0.000317097 secs
+  create_atoms CPU = 0.000 seconds
 mass 1 183.84
 mass 2 9.012182
 
-set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
-  5 settings made for type/fraction
-group	tungsten 	 type 1
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fractiongroup   tungsten         type 1
 123 atoms in group tungsten
-group	beryllium	 type 2
+group   beryllium        type 2
 5 atoms in group beryllium
 # choose potential
 
 include WBe_Wood_PRB2019.snap
+# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
 # Definition of SNAP+ZBL potential.
 variable zblcutinner equal 4
 variable zblcutouter equal 4.8
@@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -112,43 +113,43 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -8.5980876            0   -8.5596125   -35284.855 
-      10    296.24946   -8.5976065            0   -8.5596124    -35140.29 
-      20    282.27904   -8.5958147            0   -8.5596123     -34710.3 
-      30    259.54978   -8.5928995            0   -8.5596121    -34060.43 
-      40    230.41412   -8.5891626            0   -8.5596119   -33258.275 
-      50    197.85135   -8.5849861            0   -8.5596116   -32389.527 
-      60    165.21732   -8.5808005            0   -8.5596113   -31550.426 
-      70    135.94024   -8.5770455            0   -8.5596111   -30839.006 
-      80    113.06617   -8.5741117            0   -8.5596109   -30339.177 
-      90    98.542347    -8.572249            0   -8.5596109    -30094.29 
-     100    92.524343   -8.5714774            0   -8.5596111   -30091.988 
-Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
+      10    296.32664   -8.5976164            0   -8.5596124   -35188.339 
+      20    282.41417    -8.595832            0   -8.5596123   -34782.293 
+      30    259.69014   -8.5929175            0   -8.5596121   -34113.316 
+      40    230.50415   -8.5891741            0   -8.5596119   -33260.777 
+      50    197.88816   -8.5849908            0   -8.5596116   -32309.975 
+      60    165.27259   -8.5808076            0   -8.5596113   -31365.766 
+      70    136.15697   -8.5770733            0   -8.5596111   -30542.657 
+      80    113.58947   -8.5741788            0   -8.5596109    -29939.23 
+      90    99.477916    -8.572369            0   -8.5596109   -29619.939 
+     100    94.121939   -8.5716822            0    -8.559611   -29598.002 
+Loop time of 0.668977 on 4 procs for 100 steps with 128 atoms
 
-Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 6.458 ns/day, 3.717 hours/ns, 149.482 timesteps/s
+97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.79079    | 0.79788    | 0.80888    |   0.8 | 98.06
-Neigh   | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 |   0.0 |  0.01
-Comm    | 0.0041246  | 0.01515    | 0.022235   |   5.5 |  1.86
-Output  | 0.000144   | 0.00017095 | 0.00024796 |   0.0 |  0.02
-Modify  | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 |   0.0 |  0.01
-Other   |            | 0.000338   |            |       |  0.04
+Pair    | 0.57811    | 0.60637    | 0.63609    |   2.6 | 90.64
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.031571   | 0.061612   | 0.090021   |   8.3 |  9.21
+Output  | 0.00015521 | 0.00021636 | 0.00038552 |   0.0 |  0.03
+Modify  | 5.4836e-05 | 6.1393e-05 | 7.2956e-05 |   0.0 |  0.01
+Other   |            | 0.0007139  |            |       |  0.11
 
-Nlocal:    32 ave 37 max 28 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-Nghost:    431 ave 435 max 426 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Neighs:    927 ave 1071 max 821 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-FullNghs:  1854 ave 2144 max 1624 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    928 ave 928 max 928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 7416
-Ave neighs/atom = 57.9375
-Neighbor list builds = 1
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
 Dangerous builds = 0
 
 Total wall time: 0:00:00

examples/snap/log.15Jun20.snap.hybrid.WSNAP.HePair.g++.1

@@ -1,13 +1,13 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (15 Jun 2020)
   using 1 OpenMP thread(s) per MPI task
-# Demonstrate SNAP Ta potential
+# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
 
 # Initialize simulation
 
 variable nsteps index 100
 variable nrep equal 4
 variable a equal 3.1803
-units		metal
+units           metal
 
 # generate the box and atom positions using a BCC lattice
 
@@ -18,34 +18,33 @@ variable ny equal 4
 variable nz equal ${nrep}
 variable nz equal 4
 
-boundary	p p p
+boundary        p p p
 
 lattice         bcc $a
 lattice         bcc 3.1803
 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
-region		box block 0 ${nx} 0 ${ny} 0 ${nz}
-region		box block 0 4 0 ${ny} 0 ${nz}
-region		box block 0 4 0 4 0 ${nz}
-region		box block 0 4 0 4 0 4
-create_box	2 box
-Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      2 box
+Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
   1 by 1 by 1 MPI processor grid
-create_atoms	1 box
+create_atoms    1 box
 Created 128 atoms
-  Time spent = 0.000426054 secs
+  create_atoms CPU = 0.001 seconds
 mass 1 183.84
 mass 2 4.0026
 
-set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
-  5 settings made for type/fraction
-group	tungsten type 1
+set     group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fractiongroup   tungsten type 1
 123 atoms in group tungsten
-group	helium	type 2
+group   helium  type 2
 5 atoms in group helium
 # choose potential
 
 include W_2940_2017_2_He_JW2013.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
+# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
 #
 # Definition of SNAP+ZBL+Tabulated potential.
 variable zblcutinner equal 4
@@ -60,7 +59,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
 pair_coeff 	1 1 zbl ${zblz} ${zblz}
 pair_coeff 	1 1 zbl 74 ${zblz}
 pair_coeff 	1 1 zbl 74 74
-pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
+pair_coeff 	* * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
 Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
 SNAP Element = W, Radius 0.5, Weight 1 
 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
@@ -68,24 +67,23 @@ SNAP keyword rcutfac 4.73442
 SNAP keyword twojmax 8 
 SNAP keyword rfac0 0.99363 
 SNAP keyword rmin0 0 
-SNAP keyword diagonalstyle 3 
 SNAP keyword bzeroflag 0 
 SNAP keyword quadraticflag 0 
 pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
 Reading potential file He_He_JW2013.table with DATE: 2017-02-20
 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (src/pair_table.cpp:481)
+  Should only be flagged at inflection points (src/pair_table.cpp:467)
 pair_coeff      1 2 table 2 W_He_JW2013.table WHe
 Reading potential file W_He_JW2013.table with DATE: 2017-02-20
 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (src/pair_table.cpp:481)
+  Should only be flagged at inflection points (src/pair_table.cpp:467)
 #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
 #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
 
 
 # Setup output
 
-thermo		10
+thermo          10
 thermo_modify norm yes
 
 # Set up NVE run
@@ -96,7 +94,7 @@ neigh_modify once no every 1 delay 0 check yes
 
 # Run MD
 
-velocity all create 300.0 4928459
+velocity all create 300.0 4928459 loop geom
 fix 1 all nve
 run             ${nsteps}
 run             100
@@ -137,33 +135,33 @@ Neighbor list info ...
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 6.789 | 6.789 | 6.789 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          300   -10.438105            0    -10.39963   -5445.2808 
-      10    290.48923   -10.436885            0   -10.399629   -5646.4813 
-      20    271.18868   -10.434409            0   -10.399629   -5654.4646 
-      30     246.2601   -10.431212            0   -10.399629   -5281.8873 
-      40    218.69918   -10.427677            0   -10.399629   -4343.3636 
-      50    189.12519   -10.423885            0   -10.399629   -2903.1138 
-      60    155.55701   -10.419579            0   -10.399629   -1402.2278 
-      70    118.83581   -10.414869            0   -10.399629   -146.36141 
-      80    85.903126   -10.410645            0   -10.399628    857.74986 
-      90    65.223651   -10.407993            0   -10.399628    1494.2746 
-     100    59.833542   -10.407302            0   -10.399628    1938.9164 
-Loop time of 17.6435 on 1 procs for 100 steps with 128 atoms
+      10    292.90716   -10.437195            0    -10.39963   -5400.8323 
+      20    275.59696   -10.434975            0   -10.399629    -5055.199 
+      30    250.28699   -10.431729            0   -10.399629   -4317.4619 
+      40    218.58148   -10.427662            0   -10.399629   -3069.0256 
+      50    182.80754   -10.423074            0   -10.399629   -1514.9501 
+      60    144.77789   -10.418197            0   -10.399629     134.6083 
+      70    108.06164   -10.413487            0   -10.399628    1747.8913 
+      80    79.630821   -10.409841            0   -10.399628    2913.2733 
+      90    62.795831   -10.407682            0   -10.399628    3646.2528 
+     100    57.450965   -10.406996            0   -10.399628    4022.2665 
+Loop time of 2.15336 on 1 procs for 100 steps with 128 atoms
 
-Performance: 0.245 ns/day, 98.019 hours/ns, 5.668 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 2.006 ns/day, 11.963 hours/ns, 46.439 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 17.641     | 17.641     | 17.641     |   0.0 | 99.99
-Neigh   | 0.00054359 | 0.00054359 | 0.00054359 |   0.0 |  0.00
-Comm    | 0.00080729 | 0.00080729 | 0.00080729 |   0.0 |  0.00
-Output  | 0.00026512 | 0.00026512 | 0.00026512 |   0.0 |  0.00
-Modify  | 0.00033879 | 0.00033879 | 0.00033879 |   0.0 |  0.00
-Other   |            | 0.0005448  |            |       |  0.00
+Pair    | 2.1524     | 2.1524     | 2.1524     |   0.0 | 99.96
+Neigh   | 0.00030732 | 0.00030732 | 0.00030732 |   0.0 |  0.01
+Comm    | 0.00026202 | 0.00026202 | 0.00026202 |   0.0 |  0.01
+Output  | 0.00013041 | 0.00013041 | 0.00013041 |   0.0 |  0.01
+Modify  | 0.00010085 | 0.00010085 | 0.00010085 |   0.0 |  0.00
+Other   |            | 0.0001643  |            |       |  0.01
 
 Nlocal:    128 ave 128 max 128 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -179,4 +177,4 @@ Ave neighs/atom = 53.5156
 Neighbor list builds = 1
 Dangerous builds = 0
 
-Total wall time: 0:00:17
+Total wall time: 0:00:02