Merge branch 'master' into feature-cnt

.github/CODEOWNERS

@@ -117,6 +117,9 @@ tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
 
+# tests
+unittest/*            @akohlmey @rbberger
+
 # cmake
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin

cmake/CMakeLists.txt

@@ -3,6 +3,11 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
+# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
+if(POLICY CMP0074)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+########################################
 
 project(lammps CXX)
 set(SOVERSION 0)
@@ -27,6 +32,12 @@ endif()
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+# make sure LIBRARY_PATH is set if environment variable is set
+if (DEFINED ENV{LIBRARY_PATH})
+  list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
+  message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
+endif()
+
 include(LAMMPSUtils)
 
 get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@@ -60,11 +71,11 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
 endif()
 
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+  set(CMAKE_TUNE_DEFAULT "-march=native")
 endif()
 
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
-  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+  set(CMAKE_TUNE_DEFAULT "-march=native")
 endif()
 
 # we require C++11 without extensions
@@ -547,8 +558,6 @@ if(BUILD_SHARED_LIBS)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-  file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
-  install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
   include(CMakePackageConfigHelpers)
   configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
   write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)

cmake/LAMMPSConfig.cmake.in

@@ -1,11 +1,5 @@
-list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
 endif()
-if(@PKG_KSPACE@)
-  if(@FFT@ STREQUAL "FFTW3")
-    find_dependency(@FFTW@ REQUIRED MODULE)
-  endif()
-endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/CodeCoverage.cmake

@@ -15,14 +15,35 @@ if(ENABLE_COVERAGE)
             gen_coverage_xml
             COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating XML Coverage Report..."
+            COMMENT "Generating XML coverage report..."
         )
 
+        set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
+
+        add_custom_target(coverage_html_folder
+            COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
+
         add_custom_target(
             gen_coverage_html
-            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating HTML Coverage Report..."
+            COMMENT "Generating HTML coverage report..."
         )
+        add_dependencies(gen_coverage_html coverage_html_folder)
+
+        add_custom_target(clean_coverage_html
+            ${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
+            COMMENT "Deleting HTML coverage report..."
+        )
+
+        add_custom_target(reset_coverage
+            ${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
+                              */*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
+            WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Deleting coverage data files..."
+        )
+        add_dependencies(reset_coverage clean_coverage_html)
     endif()
 endif()

cmake/Modules/FindTBB_MALLOC.cmake

@@ -6,7 +6,6 @@
 #  TBB_MALLOC_FOUND        - True if tbb found.
 #
 
-
 ########################################################
 # TBB Malloc
 

cmake/Modules/FindYAML.cmake

@@ -0,0 +1,30 @@
+# - Find libyaml
+# Find the native Yaml headers and libraries.
+#
+#  YAML_INCLUDE_DIRS - where to find yaml.h
+#  YAML_LIBRARIES    - List of libraries when using libyaml
+#  YAML_FOUND        - True if libyaml is found.
+#
+
+find_path(YAML_INCLUDE_DIR yaml.h PATH_SUFFIXES yaml)
+find_library(YAML_LIBRARY NAMES yaml)
+
+# handle the QUIET and REQUIRED arguments and
+# set YAML_FOUND to TRUE if all variables are non-zero
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(YAML DEFAULT_MSG YAML_LIBRARY YAML_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(YAML_FOUND)
+  set(YAML_LIBRARIES ${YAML_LIBRARY})
+  set(YAML_INCLUDE_DIRS ${YAML_INCLUDE_DIR})
+
+  if(NOT TARGET Yaml::Yaml)
+    add_library(Yaml::Yaml UNKNOWN IMPORTED)
+    set_target_properties(Yaml::Yaml PROPERTIES
+      IMPORTED_LOCATION "${YAML_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${YAML_INCLUDE_DIR}")
+  endif()
+endif()
+
+mark_as_advanced(YAML_INCLUDE_DIR YAML_LIBRARY)

cmake/Modules/GTest.cmake

@@ -0,0 +1,77 @@
+message(STATUS "Downloading and building Google Test library")
+
+if(CMAKE_BUILD_TYPE STREQUAL Debug)
+  set(GTEST_LIB_POSTFIX d)
+else()
+  set(GTEST_LIB_POSTFIX)
+endif()
+
+include(ExternalProject)
+ExternalProject_Add(googletest
+                    GIT_REPOSITORY  https://github.com/google/googletest.git
+                    GIT_TAG         release-1.10.0
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(googletest SOURCE_DIR)
+set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
+set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
+
+ExternalProject_Get_Property(googletest BINARY_DIR)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+
+# Prevent GoogleTest from overriding our compiler/linker options
+# when building with Visual Studio
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+find_package(Threads QUIET)
+
+add_library(GTest::GTest UNKNOWN IMPORTED)
+set_target_properties(GTest::GTest PROPERTIES
+        IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GTest googletest)
+
+add_library(GTest::GMock UNKNOWN IMPORTED)
+set_target_properties(GTest::GMock PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GMock googletest)
+
+add_library(GTest::GTestMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GTestMain PROPERTIES
+        IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GTestMain googletest)
+
+add_library(GTest::GMockMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GMockMain PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GMockMain googletest)

cmake/Modules/Packages/GPU.cmake

@@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
+  # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  if (GPU_LIB_OLD_CUBIN_HEADERS)
+    message(FATAL_ERROR "########################################################################\n"
+      "Found file(s) generated by the make-based build system in lib/gpu\n"
+      "Please run\n"
+      "  make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
+      "to remove\n"
+      "########################################################################")
+  endif()
+
   file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
@@ -79,7 +90,7 @@ if(GPU_API STREQUAL "CUDA")
     string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
   endif()
 
-  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
           -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}

cmake/Modules/Packages/KSPACE.cmake

@@ -2,7 +2,7 @@ option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" O
 set(FFTW "FFTW3")
 if(FFT_SINGLE)
   set(FFTW "FFTW3F")
-  target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
+  target_compile_definitions(lammps PRIVATE -DFFT_SINGLE)
 endif()
 find_package(${FFTW} QUIET)
 if(${FFTW}_FOUND)
@@ -17,8 +17,8 @@ string(TOUPPER ${FFT} FFT)
 
 if(FFT STREQUAL "FFTW3")
   find_package(${FFTW} REQUIRED)
-  target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
+  target_compile_definitions(lammps PRIVATE -DFFT_FFTW3)
-  target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
+  target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW})
   if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
     option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
   else()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -1,8 +1,5 @@
 enable_language(C)
 
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
-  cmake_policy(SET CMP0074 NEW)
-endif()
 find_package(HDF5 REQUIRED)
 target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
 target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,8 +1,7 @@
 # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
+
-  cmake_policy(SET CMP0074 NEW)
+# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
-endif()
 if(NOT BUILD_MPI)
   find_package(NetCDF REQUIRED)
 else()

cmake/Modules/Testing.cmake

@@ -4,48 +4,7 @@
 option(ENABLE_TESTING "Enable testing" OFF)
 if(ENABLE_TESTING)
   enable_testing()
-  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
-  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
-  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+  add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
-
-  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
-    include(FetchContent)
-
-    FetchContent_Declare(lammps-testing
-      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
-      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
-    )
-
-    FetchContent_GetProperties(lammps-testing)
-    if(NOT lammps-testing_POPULATED)
-      message(STATUS "Downloading tests...")
-      FetchContent_Populate(lammps-testing)
-    endif()
-
-    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
-  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
-    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
-                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
-  endif()
-
-  add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
-
-  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
-    message(STATUS "Running test discovery...")
-
-    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
-    foreach(script_path ${TEST_SCRIPTS})
-      get_filename_component(TEST_NAME ${script_path} EXT)
-      get_filename_component(SCRIPT_NAME ${script_path} NAME)
-      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
-      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
-      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
-      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
-      set(TEST_NAME "test_core_${TEST_NAME}_serial")
-      add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
-    endforeach()
-    list(LENGTH TEST_SCRIPTS NUM_TESTS)
-
-    message(STATUS "Found ${NUM_TESTS} tests.")
-  endif()
 endif()

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "5 May 2020" "2020-05-5"
+.TH LAMMPS "2 June 2020" "2020-06-02"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_cmake.rst

@@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``cmake .`` and then compile again. The included dependency tracking
 should make certain that only the necessary subset of files are
 re-compiled.  You can also delete compiled objects, libraries and
-executables with ``cmake --build . clean`` (or ``make clean``).
+executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
 your system with:

doc/src/Build_development.rst

@@ -57,53 +57,252 @@ variable during configuration. Examples:
 
 .. _testing:
 
-Code Coverage and Testing
+Code Coverage and Unit Testing
----------------------------------------
+------------------------------
 
-We do extensive regression testing of the LAMMPS code base on a continuous
+The LAMMPS code is subject to multiple levels of automated testing
-basis. Some of the logic to do this has been added to the CMake build so
+during development: integration testing (i.e. whether the code compiles
-developers can run the tests directly on their workstation.
+on various platforms and with a variety of settings), unit testing
+(i.e. whether certain individual parts of the code produce the expected
+results for given inputs), run testing (whether selected complete input
+decks run without crashing for multiple configurations), and regression
+testing (i.e. whether selected input examples reproduce the same
+results over a given number of steps and operations within a given
+error margin).  The status of this automated testing can be viewed on
+`https://ci.lammps.org <https://ci.lammps.org>`_.
+
+The unit testing facility is integrated into the CMake build process
+of the LAMMPS source code distribution itself.  It can be enabled by
+setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
+It requires the `YAML <http://pyyaml.org/>`_ library and development
+headers to compile and will download and compile a recent version of the
+`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+for implementing the tests.
+
+After compilation is complete, the unit testing is started in the build
+folder using the ``ctest`` command, which is part of the CMake software.
+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
+         Start  2: MolPairStyle:hybrid
+    2/26 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
+   
+   100% tests passed, 0 tests failed out of 26
+   
+   Total Test time (real) =   0.27 sec
+
+
+The ``ctest`` command has many options, the most important ones are:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -V
+     - verbose output: display output of individual test runs
+   * - -j <num>
+     - parallel run: run <num> tests in parallel
+   * - -R <regex>
+     - run subset of tests matching the regular expression <regex>
+   * - -E <regex>
+     - exclude subset of tests matching the regular expression <regex>
+   * - -N
+     - dry-run: display list of tests without running them
+
+In its full implementation, the unit test framework will consist of multiple
+kinds of tests implemented in different programming languages (C++, C, Python,
+Fortran) and testing different aspects of the LAMMPS software and its features.
+At the moment only tests for "force styles" are implemented. More on those
+in the next section.
 
 .. note::
 
-   this is incomplete and only represents a small subset of tests that we run
+   This unit test framework is new and still under development.
+   The coverage is only minimal and will be expanded over time.
+   Tests styles of the same kind of style (e.g. pair styles or
+   bond styles) are performed with the same executable using
+   different input files in YAML format.  So to add a test for
+   another pair style can be done by copying the YAML file and
+   editing the style settings and then running the individual test
+   program with a flag to update the computed reference data.
+   Detailed documentation about how to add new test program and
+   the contents of the YAML files for existing test programs
+   will be provided in time as well.
+
+Unit tests for force styles
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A large part of LAMMPS are different "styles" for computing non-bonded
+and bonded interactions selected through the :doc:`pair_style`,
+:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
+:doc:`improper_style`, and :doc:`kspace_style`.  Since these all share
+common interfaces, it is possible to write generic test programs that
+will call those common interfaces for small test systems with less than
+100 atoms and compare the results with pre-recorded reference results.
+A test run is then a a collection multiple individual test runs each
+with many comparisons to reference results based on template input
+files, individual command settings, relative error margins, and
+reference data stored in a YAML format file with ``.yaml``
+suffix. Currently the programs ``pair_style``, ``bond_style``, and
+``angle_style`` are implemented.  They will compare forces, energies and
+(global) stress for all atoms after a ``run 0`` calculation and after a
+few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
+with different settings and also for multiple accelerated styles. If a
+prerequisite style or package is missing, the individual tests are
+skipped.  All tests will be executed on a single MPI process, so using
+the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
+since this will skip the MPI initialization for each test run.
+Below is an example command and output:
+
+.. parsed-literal::
+
+   [tests]$ pair_style mol-pair-lj_cut.yaml
+   [==========] Running 6 tests from 1 test suite.
+   [----------] Global test environment set-up.
+   [----------] 6 tests from PairStyle
+   [ RUN      ] PairStyle.plain
+   [       OK ] PairStyle.plain (24 ms)
+   [ RUN      ] PairStyle.omp
+   [       OK ] PairStyle.omp (18 ms)
+   [ RUN      ] PairStyle.intel
+   [       OK ] PairStyle.intel (6 ms)
+   [ RUN      ] PairStyle.opt
+   [  SKIPPED ] PairStyle.opt (0 ms)
+   [ RUN      ] PairStyle.single
+   [       OK ] PairStyle.single (7 ms)
+   [ RUN      ] PairStyle.extract
+   [       OK ] PairStyle.extract (6 ms)
+   [----------] 6 tests from PairStyle (62 ms total)
+
+   [----------] Global test environment tear-down
+   [==========] 6 tests from 1 test suite ran. (63 ms total)
+   [  PASSED  ] 5 tests.
+   [  SKIPPED ] 1 test, listed below:
+   [  SKIPPED ] PairStyle.opt
+
+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.
+
+The force style test programs have a common set of options:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -g <newfile>
+     - regenerate reference data in new YAML file
+   * - -u
+     - update reference data in the original YAML file
+   * - -s
+     - print error statistics for each group of comparisons
+   * - -v
+     - verbose output: also print the executed LAMMPS commands
+
+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
+run test command with either the *-g* and the replace the initial
+test file with the regenerated one or the *-u* option.  The *-u* option
+will destroy the original file, if the generation run does not complete,
+so using *-g* is recommended unless the YAML file is fully tested
+and working.
+
+.. admonition:: Recommendations and notes for YAML files
+   :class: note
+
+   - The reference results should be recorded without any code
+     optimization or related compiler flags enabled.
+   - The ``epsilon`` parameter defines the relative precision with which
+     the reference results must be met.  The test geometries often have
+     high and low energy parts and thus a significant impact from
+     floating-point math truncation errors is to be expected. Some
+     functional forms and potentials are more noisy than others, so this
+     parameter needs to be adjusted. Typically a value around 1.0e-13
+     can be used, but it may need to be as large as 1.0e-8 in some
+     cases.
+   - The tests for pair styles from OPT, USER-OMP and USER-INTEL are
+     performed with automatically rescaled epsilon to account for
+     additional loss of precision from code optimizations and different
+     summation orders.
+   - When compiling with aggressive compiler optimization, some tests
+     are likely to fail.  It is recommended to inspect the individual
+     tests in detail to decide whether the specific error for a specific
+     property is acceptable (it often is), or this may be an indication
+     of mis-compiled code (or undesired large of precision due to
+     reordering of operations).
+
+Collect and visualize code coverage metrics
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can also collect code coverage metrics while running LAMMPS or the
+tests by enabling code coverage support during the CMake configuration:
 
 .. code-block:: bash
 
-   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+   -D ENABLE_COVERAGE=on  # enable coverage measurements (off by default)
-   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
-   -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
 
-If you enable testing in the CMake build it will create an additional
+This will instrument all object files to write information about which
-target called "test". You can run them with:
+lines of code were accessed during execution in files next to the
+corresponding object files.  These can be post-processed to visually
+show the degree of coverage and which code paths are accessed and which
+are not taken.  When working on unit tests (see above), this can be
+extremely helpful to determine which parts of the code are not executed
+and thus what kind of tests are still missing. The coverage data is
+cumulative, i.e. new data is added with each new run.
+
+Enabling code coverage will also add the following build targets to
+generate coverage reports after running the LAMMPS executable or the
+unit tests:
 
 .. code-block:: bash
 
-   cmake --build . test
+   make gen_coverage_html   # generate coverage report in HTML format
+   make gen_coverage_xml    # generate coverage report in XML format
+   make clean_coverage_html # delete folder with HTML format coverage report
+   make reset_coverage      # delete all collected coverage data and HTML output
 
-The test cases used come from the lammps-testing repository. They are
+These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
-derivatives of the examples folder with some modifications to make the
+to do this to install it via pip:
-run faster.
-
-You can also collect code coverage metrics while running the tests by
-enabling coverage support during building.
-
-.. code-block:: bash
-
-   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
-
-This will also add the following targets to generate coverage reports
-after running the LAMMPS executable:
-
-.. code-block:: bash
-
-   make test               # run tests first!
-   make gen_coverage_html  # generate coverage report in HTML format
-   make gen_coverage_xml   # generate coverage report in XML format
-
-These reports require GCOVR to be installed. The easiest way to do this
-to install it via pip:
 
 .. code-block:: bash
 
    pip install git+https://github.com/gcovr/gcovr.git
+
+After post-processing with ``gen_coverage_html`` the results are in
+a folder ``coverage_html`` and can be viewed with a web browser.
+The images below illustrate how the data is presented.
+
+.. list-table::
+
+      * - .. figure:: JPG/coverage-overview-top.png
+             :target: JPG/coverage-overview-top.png
+
+          Top of the overview page
+
+        - .. figure:: JPG/coverage-overview-manybody.png
+             :target: JPG/coverage-overview-manybody.png
+
+          Styles with good coverage
+
+        - .. figure:: JPG/coverage-file-top.png
+             :target: JPG/coverage-file-top.png
+
+          Top of individual source page
+
+        - .. figure:: JPG/coverage-file-branches.png
+             :target: JPG/coverage-file-branches.png
+
+          Source page with branches

doc/src/Build_extras.rst

@@ -132,6 +132,10 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
 the preferred GPU architecture directly included rather than having to wait
 for the JIT compiler of the CUDA driver to translate it.
 
+When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
+using the traditional build procedure. CMake will detect files generated by that
+process and will terminate with an error and a suggestion for how to remove them.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`

doc/src/Commands_all.rst

@@ -94,6 +94,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`package <package>`
    * :doc:`pair_coeff <pair_coeff>`
    * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`

doc/src/Commands_fix.rst

@@ -147,6 +147,7 @@ OPT.
    * :doc:`oneway <fix_oneway>`
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
+   * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Commands_pair.rst

@@ -92,8 +92,8 @@ OPT.
    * :doc:`drip <pair_drip>`
    * :doc:`eam (gikot) <pair_eam>`
    * :doc:`eam/alloy (gikot) <pair_eam>`
-   * :doc:`eam/cd (o) <pair_eam>`
+   * :doc:`eam/cd <pair_eam>`
-   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`

doc/src/Howto_cmake.rst

@@ -415,8 +415,10 @@ This is particularly convenient, if you have set a custom build command
 via the ``CMAKE_MAKE_PROGRAM`` variable.
 
 When calling the build program, you can also select which "target" is to
-be build through appending the name of the target to the build command.
+be build through appending the ``--target`` flag and the name of the target
-Example: ``cmake --build . all``. The following abstract targets are available:
+to the build command.  When using ``make`` as build tool, you can just append
+the target name to the command. Example: ``cmake --build . --target all`` or
+``make all``.  The following abstract targets are available:
 
 .. list-table::
    :header-rows: 1
@@ -432,7 +434,7 @@ Example: ``cmake --build . all``. The following abstract targets are available:
    * - ``install``
      - install all target files into folders in ``CMAKE_INSTALL_PREFIX``
    * - ``test``
-     - run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
+     - run some tests (if configured with ``-D ENABLE_TESTING=on``)
    * - ``clean``
      - remove all generated files
 

doc/src/Modify_contribute.rst

@@ -1,37 +1,51 @@
 Submitting new features for inclusion in LAMMPS
 ===============================================
 
-We encourage users to submit new features or modifications for LAMMPS
+We encourage users to submit new features or modifications for LAMMPS to
-to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
+`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
-can be added to the LAMMPS distribution. The preferred way to manage
+can be added to the LAMMPS distribution. The preferred way to manage and
-and coordinate this is as of Fall 2016 via the LAMMPS project on
+coordinate this is via the LAMMPS project on `GitHub
-`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
+<https://github.com/lammps/lammps>`_.  Please see the :doc:`GitHub
-contact the LAMMPS developers or the indicated developer of a package
+Tutorial <Howto_github>` for a demonstration on how to do that.  An
-or feature directly and send in your contribution via e-mail.
+alternative is to contact the LAMMPS developers or the indicated
+developer of a package or feature directly and send in your contribution
+via e-mail, but that can add a significant delay on getting your
+contribution included, depending on how busy the developer is you
+contact, how complex a task it would be to integrate that code, and how
+many - if any - changes are required before the code can be included.
 
-For any larger modifications or programming project, you are
+For any larger modifications or programming project, you are encouraged
-encouraged to contact the LAMMPS developers ahead of time, in order to
+to contact the LAMMPS developers ahead of time, in order to discuss
-discuss implementation strategies and coding guidelines, that will
+implementation strategies and coding guidelines, that will make it
-make it easier to integrate your contribution and result in less work
+easier to integrate your contribution and result in less work for
-for everybody involved. You are also encouraged to search through the
+everybody involved. You are also encouraged to search through the list
-list of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_ and submit a new issue
+of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
-for a planned feature, so you would not duplicate the work of others
+and submit a new issue for a planned feature, so you would not duplicate
-(and possibly get scooped by them) or have your work duplicated by
+the work of others (and possibly get scooped by them) or have your work
-others.
+duplicated by others.
 
-How quickly your contribution will be integrated depends largely on
+For informal communication with (some of) the LAMMPS developers you may
-how much effort it will cause to integrate and test it, how much it
+ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
-requires changes to the core codebase, and of how much interest it is
+This slack work space is by invitation only. Thus for access, please
-to the larger LAMMPS community.  Please see below for a checklist of
+send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
-typical requirements. Once you have prepared everything, see the
+you are working on.  Only discussions related to LAMMPS development are
-:doc:`Using GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on how to
+tolerated, so this is **NOT** for people that look for help with compiling,
-submit your changes or new files through a GitHub pull request. If you
+installing, or using LAMMPS. Please contact the `lammps-users mailing
-prefer to submit patches or full files, you should first make certain,
+list <https://lammps.sandia.gov>`_ for those purposes instead.
-that your code works correctly with the latest patch-level version of
+
-LAMMPS and contains all bug fixes from it. Then create a gzipped tar
+How quickly your contribution will be integrated depends largely on how
-file of all changed or added files or a corresponding patch file using
+much effort it will cause to integrate and test it, how much it requires
-'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
+changes to the core codebase, and of how much interest it is to the
-compression, as this works well on all platforms.
+larger LAMMPS community.  Please see below for a checklist of typical
+requirements. Once you have prepared everything, see the :doc:`Using
+GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on
+how to submit your changes or new files through a GitHub pull
+request. If you prefer to submit patches or full files, you should first
+make certain, that your code works correctly with the latest patch-level
+version of LAMMPS and contains all bug fixes from it. Then create a
+gzipped tar file of all changed or added files or a corresponding patch
+file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
+use gzip compression, as this works well on all platforms.
 
 If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a

doc/src/Packages_details.rst

@@ -2098,7 +2098,7 @@ molecules, and chiral-sensitive reactions.
 * examples/USER/reaction
 * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
 * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
-* disarmmd.org
+* reacter.org
 
 ----------
 

doc/src/compute_gyration_shape_chunk.rst

@@ -37,7 +37,7 @@ and the relative shape anisotropy, k:
  b = & l_y - l_x \\
  k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
 
-where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description
+where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description
 of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems
 can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity  is always non-negative and zero
 only when the three principal moments are equal. This zero condition is met when the distribution

doc/src/dump_modify.rst

@@ -552,9 +552,9 @@ when writing to XTC files.  By default they are initialized for
 whatever :doc:`units <units>` style is being used, to write out
 coordinates in nanometers and time in picoseconds.  I.e. for *real*
 units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
-Angstroms and fmsec used by *real* units are 0.1 nm and 0.001 psec
+Angstroms and fs used by *real* units are 0.1 nm and 0.001 ps
 respectively.  If you are using a units system with distance and time
-units far from nm and psec, you may wish to write XTC files with
+units far from nm and ps, you may wish to write XTC files with
 different units, since the compression algorithm used in XTC files is
 most effective when the typical magnitude of position data is between
 10.0 and 0.1.

doc/src/fix.rst

@@ -290,6 +290,7 @@ accelerated styles exist.
 * :doc:`oneway <fix_oneway>` - constrain particles on move in one direction
 * :doc:`orient/bcc <fix_orient>` - add grain boundary migration force for BCC
 * :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
+* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane

doc/src/fix_bond_react.rst

@@ -300,7 +300,8 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword. The fifth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there are four types of constraints available, as discussed below.
+there are four types of constraints available, as discussed below:
+'distance', 'angle', 'dihedral', and 'arrhenius'.
 
 A sample map file is given below:
 
@@ -353,8 +354,9 @@ has syntax as follows:
    distance *ID1* *ID2* *rmin* *rmax*
 
 where 'distance' is the required keyword, *ID1* and *ID2* are
-pre-reaction atom IDs, and these two atoms must be separated by a
+pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
-distance between *rmin* and *rmax* for the reaction to occur.
+two atoms must be separated by a distance between *rmin* and *rmax*
+for the reaction to occur.
 
 The constraint of type 'angle' has the following syntax:
 
@@ -363,11 +365,11 @@ The constraint of type 'angle' has the following syntax:
    angle *ID1* *ID2* *ID3* *amin* *amax*
 
 where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are
-pre-reaction atom IDs, and these three atoms must form an angle
+pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
-between *amin* and *amax* for the reaction to occur (where *ID2* is
+three atoms must form an angle between *amin* and *amax* for the
-the central atom). Angles must be specified in degrees. This
+reaction to occur (where *ID2* is the central atom). Angles must be
-constraint can be used to enforce a certain orientation between
+specified in degrees. This constraint can be used to enforce a certain
-reacting molecules.
+orientation between reacting molecules.
 
 The constraint of type 'dihedral' has the following syntax:
 
@@ -376,15 +378,23 @@ The constraint of type 'dihedral' has the following syntax:
    dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
 
 where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*
-and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in
+and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see
-the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`
+below). Dihedral angles are calculated in the interval (-180,180].
-documentation for further details on convention. If *amin* is less
+Refer to the :doc:`dihedral style <dihedral_style>` documentation for
-than *amax*, these four atoms must form a dihedral angle greater than
+further details on convention. If *amin* is less than *amax*, these
-*amin* **and** less than *amax* for the reaction to occur. If *amin*
+four atoms must form a dihedral angle greater than *amin* **and** less
-is greater than *amax*, these four atoms must form a dihedral angle
+than *amax* for the reaction to occur. If *amin* is greater than
-greater than *amin* **or** less than *amax* for the reaction to occur.
+*amax*, these four atoms must form a dihedral angle greater than
-Angles must be specified in degrees. Optionally, a second range of
+*amin* **or** less than *amax* for the reaction to occur. Angles must
-permissible angles *amin2*-*amax2* can be specified.
+be specified in degrees. Optionally, a second range of permissible
+angles *amin2*-*amax2* can be specified.
+
+For the 'distance', 'angle', and 'dihedral' constraints (explained
+above), atom IDs can be replaced by pre-reaction molecule-fragment
+IDs. The molecule-fragment ID must begin with a letter. The location
+of the ID is the geometric center of all atom positions in the
+fragment. The molecule fragment must have been defined in the
+:doc:`molecule <molecule>` command for the pre-reaction template.
 
 The constraint of type 'arrhenius' imposes an additional reaction
 probability according to the temperature-dependent Arrhenius equation:

doc/src/fix_deform.rst

@@ -154,8 +154,8 @@ specified in units of distance/time.  This is effectively a "constant
 engineering strain rate", where rate = V/L0 and L0 is the initial box
 length.  The distance can be in lattice or box distance units.  See
 the discussion of the units keyword below.  For example, if the
-initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
+initial box length is 100 Angstroms, and V is 10 Angstroms/ps, then
-after 10 psec, the box length will have doubled.  After 20 psec, it
+after 10 ps, the box length will have doubled.  After 20 ps, it
 will have tripled.
 
 The *erate* style changes a dimension of the box at a "constant
@@ -174,7 +174,7 @@ function of time will change as
 where dt is the elapsed time (in time units).  Thus if *erate* R is
 specified as 0.1 and time units are picoseconds, this means the box
 length will increase by 10% of its original length every picosecond.
-I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.  R =
+I.e. strain after 1 ps = 0.1, strain after 2 ps = 0.2, etc.  R =
 -0.01 means the box length will shrink by 1% of its original length
 every picosecond.  Note that for an "engineering" rate the change is
 based on the original box length, so running with R = 1 for 10
@@ -201,7 +201,7 @@ The box length L as a function of time will change as
 where dt is the elapsed time (in time units).  Thus if *trate* R is
 specified as ln(1.1) and time units are picoseconds, this means the
 box length will increase by 10% of its current (not original) length
-every picosecond.  I.e. strain after 1 psec = 0.1, strain after 2 psec
+every picosecond.  I.e. strain after 1 ps = 0.1, strain after 2 ps
 = 0.21, etc.  R = ln(2) or ln(3) means the box length will double or
 triple every picosecond.  R = ln(0.99) means the box length will
 shrink by 1% of its current length every picosecond.  Note that for a
@@ -317,8 +317,8 @@ specified in units of distance/time.  This is effectively an
 initial box length perpendicular to the direction of shear.  The
 distance can be in lattice or box distance units.  See the discussion
 of the units keyword below.  For example, if the initial tilt factor
-is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
+is 5 Angstroms, and the V is 10 Angstroms/ps, then after 1 ps, the
-tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
+tilt factor will be 15 Angstroms.  After 2 ps, it will be 25
 Angstroms.
 
 The *erate* style changes a tilt factor at a "constant engineering
@@ -342,9 +342,9 @@ box perpendicular to the shear direction (e.g. y box length for xy
 deformation), and dt is the elapsed time (in time units).  Thus if
 *erate* R is specified as 0.1 and time units are picoseconds, this
 means the shear strain will increase by 0.1 every picosecond.  I.e. if
-the xy shear strain was initially 0.0, then strain after 1 psec = 0.1,
+the xy shear strain was initially 0.0, then strain after 1 ps = 0.1,
-strain after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at
+strain after 2 ps = 0.2, etc.  Thus the tilt factor would be 0.0 at
-time 0, 0.1\*ybox at 1 psec, 0.2\*ybox at 2 psec, etc, where ybox is the
+time 0, 0.1\*ybox at 1 ps, 0.2\*ybox at 2 ps, etc, where ybox is the
 original y box length.  R = 1 or 2 means the tilt factor will increase
 by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
 strain by 0.01 every picosecond.
@@ -373,7 +373,7 @@ where T0 is the initial tilt factor and dt is the elapsed time (in
 time units).  Thus if *trate* R is specified as ln(1.1) and time units
 are picoseconds, this means the shear strain or tilt factor will
 increase by 10% every picosecond.  I.e. if the xy shear strain was
-initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
+initially 0.1, then strain after 1 ps = 0.11, strain after 2 ps =
 0.121, etc.  R = ln(2) or ln(3) means the tilt factor will double or
 triple every picosecond.  R = ln(0.99) means the tilt factor will
 shrink by 1% every picosecond.  Note that the change is continuous, so

doc/src/fix_heat.rst

@@ -57,7 +57,7 @@ its current value(s) used to determine the flux.
 
 If *eflux* is a numeric constant or equal-style variable which evaluates
 to a scalar value, then *eflux* determines the change in aggregate energy
-of the entire group of atoms per unit time, e.g. in eV/psec for
+of the entire group of atoms per unit time, e.g. in eV/ps for
 :doc:`metal units <units>`.  In this case it is an "extensive" quantity,
 meaning its magnitude should be scaled with the number of atoms in the
 group.  Note that since *eflux* also has per-time units (i.e. it is a

doc/src/fix_langevin_drude.rst

@@ -188,7 +188,7 @@ particles.
 *damp_com* is the characteristic time for reaching thermal equilibrium
 of the centers of mass.  For example, a value of 100.0 means to relax
 the temperature of the centers of mass in a timespan of (roughly) 100
-time units (tau or fmsec or psec - see the :doc:`units <units>`
+time units (tau or fs or ps - see the :doc:`units <units>`
 command).  *damp_drude* is the characteristic time for reaching
 thermal equilibrium of the dipoles. It is typically a few timesteps.
 

doc/src/fix_meso_move.rst

@@ -196,7 +196,7 @@ The *units* keyword determines the meaning of the distance units used
 to define the *linear* velocity and *wiggle* amplitude and *rotate*
 origin.  This setting is ignored for the *variable* style.  A *box*
 value selects standard units as defined by the :doc:`units <units>`
-command, e.g. velocity in Angstroms/fmsec and amplitude and position
+command, e.g. velocity in Angstroms/fs and amplitude and position
 in Angstroms for units = real.  A *lattice* value means the velocity
 units are in lattice spacings per time and the amplitude and position
 are in lattice spacings.  The :doc:`lattice <lattice>` command must have

doc/src/fix_move.rst

@@ -193,7 +193,7 @@ The *units* keyword determines the meaning of the distance units used
 to define the *linear* velocity and *wiggle* amplitude and *rotate*
 origin.  This setting is ignored for the *variable* style.  A *box*
 value selects standard units as defined by the :doc:`units <units>`
-command, e.g. velocity in Angstroms/fmsec and amplitude and position
+command, e.g. velocity in Angstroms/fs and amplitude and position
 in Angstroms for units = real.  A *lattice* value means the velocity
 units are in lattice spacings per time and the amplitude and position
 are in lattice spacings.  The :doc:`lattice <lattice>` command must have

doc/src/fix_nh.rst

@@ -46,7 +46,7 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
+     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *ptemp* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
        *temp* values = Tstart Tstop Tdamp
          Tstart,Tstop = external temperature at start/end of run
          Tdamp = temperature damping parameter (time units)
@@ -69,6 +69,8 @@ Syntax
        *nreset* value = reset reference cell every this many timesteps
        *drag* value = Df
          Df = drag factor added to barostat/thermostat (0.0 = no drag)
+       *ptemp* value = Ttarget
+         Ttarget = target temperature for barostat
        *dilate* value = dilate-group-ID
          dilate-group-ID = only dilate atoms in this group due to barostat volume changes
        *scalexy* value = *yes* or *no* = scale xy with ly
@@ -137,8 +139,8 @@ description below.  The desired temperature at each timestep is a
 ramped value during the run from *Tstart* to *Tstop*\ .  The *Tdamp*
 parameter is specified in time units and determines how rapidly the
 temperature is relaxed.  For example, a value of 10.0 means to relax
-the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+the temperature in a timespan of (roughly) 10 time units (e.g. :math:`\tau`
-fmsec or psec - see the :doc:`units <units>` command).  The atoms in the
+or fs or ps - see the :doc:`units <units>` command).  The atoms in the
 fix group are the only ones whose velocities and positions are updated
 by the velocity/position update portion of the integration.
 
@@ -195,8 +197,8 @@ simulation box must be triclinic, even if its initial tilt factors are
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 .. note::
 
@@ -208,6 +210,28 @@ the :doc:`units <units>` command).
    time units, and that timesteps are NOT the same as time units for most
    :doc:`units <units>` settings.
 
+The relaxation rate of the barostat is set by its inertia :math:`W`:
+
+.. math::
+
+   W = (N + 1) k T_{\rm target} P_{\rm damp}^2
+
+where :math:`N` is the number of atoms, :math:`k` is the Boltzmann constant,
+and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
+If a thermostat is defined, :math:`T_{\rm target}` is the target temperature
+of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`
+is set to the current temperature of the system when the barostat is initialized.
+If this temperature is too low the simulation will quit with an error.
+Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to
+a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature
+of exactly zero.
+
+If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be
+manually specified using the *Ptemp* parameter. This may be useful if the
+barostat is initialized when the current temperature does not reflect the
+steady state temperature of the system. This keyword may also be useful in
+athermal simulations where the temperature is not well defined.
+
 Regardless of what atoms are in the fix group (the only atoms which
 are time integrated), a global pressure or stress tensor is computed
 for all atoms.  Similarly, when the size of the simulation box is

doc/src/fix_npt_cauchy.rst

@@ -103,8 +103,8 @@ description below.  The desired temperature at each timestep is a
 ramped value during the run from *Tstart* to *Tstop*\ .  The *Tdamp*
 parameter is specified in time units and determines how rapidly the
 temperature is relaxed.  For example, a value of 10.0 means to relax
-the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+the temperature in a timespan of (roughly) 10 time units (e.g. :math:`\tau`
-fmsec or psec - see the :doc:`units <units>` command).  The atoms in the
+or fs or ps - see the :doc:`units <units>` command).  The atoms in the
 fix group are the only ones whose velocities and positions are updated
 by the velocity/position update portion of the integration.
 
@@ -154,8 +154,8 @@ simulation box must be triclinic, even if its initial tilt factors are
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 .. note::
 

doc/src/fix_nve_dotc_langevin.rst

@@ -94,7 +94,7 @@ corresponds to T = 300 K.
 The *damp* parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
 means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the :doc:`units <units>` command).
+units :math:`\tau` (see the :doc:`units <units>` command).
 The damp factor can be thought of as inversely related to the
 viscosity of the solvent, i.e. a small relaxation time implies a
 high-viscosity solvent and vice versa.  See the discussion about gamma

doc/src/fix_orient.rst

@@ -6,6 +6,9 @@ fix orient/fcc command
 fix orient/bcc command
 ======================
 
+Syntax
+""""""
+
 .. parsed-literal::
 
    fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1

doc/src/fix_orient_eco.rst

@@ -0,0 +1,154 @@
+..  index:: fix orient/eco
+
+fix orient/eco command
+======================
+
+
+.. parsed-literal::
+
+   fix ID group-ID orient/eco u0 eta cutoff orientationsFile
+
+
+* ID, group-ID are documented in fix command
+* u0 = energy added to each atom (energy units)
+* eta = cutoff value (usually 0.25)
+* cutoff = cutoff radius for orientation parameter calculation
+* orientationsFile = file that specifies orientation of each grain
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix gb all orient/eco 0.08 0.25 3.524 sigma5.ori
+
+
+Description
+"""""""""""
+
+The fix applies a synthetic driving force to a grain boundary which can
+be used for the investigation of grain boundary motion. The affiliation
+of atoms to either of the two grains forming the grain boundary is
+determined from an orientation-dependent order parameter as described
+in :ref:`(Ulomek) <Ulomek>`. The potential energy of atoms is either increased by an amount
+of 0.5*\ *u0* or -0.5*\ *u0* according to the orientation of the surrounding
+crystal. This creates a potential energy gradient which pushes atoms near
+the grain boundary to orient according to the energetically favorable
+grain orientation. This fix is designed for applications in bicrystal system
+with one grain boundary and open ends, or two opposite grain boundaries in
+a periodic system. In either case, the entire system can experience a
+displacement during the simulation which needs to be accounted for in the
+evaluation of the grain boundary velocity. While the basic method is
+described in :ref:`(Ulomek) <Ulomek>`, the implementation follows the efficient
+implementation from :ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy added to an
+atom j is given by the following formulas
+
+.. math::
+
+   w(|\vec{r}_{jk}|) = w_{jk} & = \left\{\begin{array}{lc} \frac{|\vec{r}_{jk}|^{4}}{r_{\mathrm{cut}}^{4}}
+     -2\frac{|\vec{r}_{jk}|^{2}}{r_{\mathrm{cut}}^{2}}+1, & |\vec{r}_{jk}|<r_{\mathrm{cut}} \\
+      0, & |\vec{r}_{jk}|\ge r_{\mathrm{cut}}
+      \end{array}\right. \\
+   \chi_{j} & = \frac{1}{N}\sum_{l=1}^{3}\left\lbrack\left\vert\psi_{l}^{\mathrm{I}}(\vec{r}_{j})\right\vert^{2}-\left\vert\psi_{l}^{\mathrm{II}}(\vec{r}_{j})\right\vert^{2}\right\rbrack \\
+   \psi_{l}^{\mathrm{X}}(\vec{r}_{j}) & = \sum_{k\in\mathit{\Gamma}_{j}}w_{jk}\exp\left(\mathrm{i}\vec{r}_{jk}\cdot\vec{q}_{l}^{\mathrm{X}}\right) \\
+   u(\chi_{j}) & = \frac{u_{0}}{2}\left\{\begin{array}{lc}
+   1, & \chi_{j}\ge\eta\\
+   \sin\left(\frac{\pi\chi_{j}}{2\eta}\right), &  -\eta<\chi_{j}<\eta\\
+   -1, & \chi_{j}\le-\eta
+   \end{array}\right.
+
+which are fully explained in :ref:`(Ulomek) <Ulomek>`
+and :ref:`(Schratt & Mohles) <Schratt>`.
+
+The force on each atom is the negative gradient of the synthetic potential energy. It
+depends on the surrounding of this atom. An atom far from the grain boundary does not
+experience a synthetic force as its surrounding is that of an oriented single crystal
+and thermal fluctuations are masked by the parameter *eta*\ . Near the grain boundary
+however, the gradient is nonzero and synthetic force terms are computed.
+The orientationsFile specifies the perfect oriented crystal basis vectors for the
+two adjoining crystals. The first three lines (line=row vector) for the energetically penalized and the
+last three lines for the energetically favored grain assuming *u0* is positive. For
+negative *u0*, this is reversed. With the *cutoff* parameter, the size of the region around
+each atom which is used in the order parameter computation is defined. The cutoff must be
+smaller than the interaction range of the MD potential. It should at
+least include the nearest neighbor shell. For high temperatures or low angle
+grain boundaries, it might be beneficial to increase the cutoff in order to get a more
+precise identification of the atoms surrounding. However, computation time will
+increase as more atoms are considered in the order parameter and force computation.
+It is also worth noting that the cutoff radius must not exceed the communication
+distance for ghost atoms in LAMMPS. With orientationsFile, the
+6 oriented crystal basis vectors is specified. Each line of the input file
+contains the three components of a primitive lattice vector oriented according to
+the grain orientation in the simulation box. The first (last) three lines correspond
+to the primitive lattice vectors of the first (second) grain. An example for
+a :math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
+
+If no synthetic energy difference between the grains is created, :math:`u0=0`, the
+force computation is omitted. In this case, still, the order parameter of the
+driving force is computed and can be used to track the grain boundary motion throughout the
+simulation.
+
+
+
+**Restart, fix_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc: `binary restart files <restart>`.
+
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to
+add the potential energy of atom interactions with the grain boundary
+driving force to the system's potential energy as part of thermodynamic output.
+The total sum of added synthetic potential energy is computed and can be accessed
+by various output options. The order parameter as well as the thermally masked
+output parameter are stored in per-atom arrays and can also be accessed by various
+:doc:`output commands <Howto_output>`.
+
+No parameter of this fix can be used with the start/stop keywords of the run command. This fix is
+not invoked during energy minimization.
+
+
+
+Restrictions
+""""""""""""
+
+This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
+built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix_modify <fix_modify>`
+
+:doc:`fix_orient <fix_orient>`
+
+**Default:** none
+
+----------
+
+.. _Ulomek:
+
+**(Ulomek)** Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
+
+.. _Schratt:
+
+**(Schratt & Mohles)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774
+
+----------
+
+
+For illustration purposes, here is an example file that specifies a
+:math:`\Sigma=5 \langle 001 \rangle` tilt grain boundary. This is for a lattice constant of 3.52 Angstrom:
+
+.. parsed-literal::
+
+    sigma5.ori:
+
+    1.671685  0.557228  1.76212
+    0.557228 -1.671685  1.76212
+    2.228913 -1.114456  0.00000
+    0.557228  1.671685  1.76212
+    1.671685 -0.557228  1.76212
+    2.228913  1.114456  0.00000
+
+

doc/src/fix_poems.rst

@@ -3,7 +3,8 @@
 fix poems command
 =================
 
-Syntax:
+Syntax
+""""""
 
 .. parsed-literal::
 

doc/src/fix_press_berendsen.rst

@@ -90,7 +90,7 @@ although you have the option to change that dimension via the :doc:`fix deform <
 For all barostat keywords, the *Pdamp* parameter determines the time
 scale on which pressure is relaxed.  For example, a value of 10.0
 means to relax the pressure in a timespan of (roughly) 10 time units
-(tau or fmsec or psec - see the :doc:`units <units>` command).
+(tau or fs or ps - see the :doc:`units <units>` command).
 
 .. note::
 

doc/src/fix_rhok.rst

@@ -3,6 +3,9 @@
 fix rhok command
 ================
 
+Syntax
+""""""
+
 .. parsed-literal::
 
    fix ID group-ID rhok nx ny nz K a

doc/src/fix_rigid.rst

@@ -429,8 +429,8 @@ that dimension via the :doc:`fix deform <fix_deform>` command.
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 Regardless of what atoms are in the fix group (the only atoms which
 are time integrated), a global pressure or stress tensor is computed
@@ -514,7 +514,7 @@ desired temperature at each timestep is a ramped value during the run
 from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in time
 units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (:math:`\tau` or fs or ps - see the
 :doc:`units <units>` command).  The random # *seed* must be a positive
 integer.
 
@@ -539,7 +539,7 @@ timestep is a ramped value during the run from *Tstart* to *Tstop*\ .
 The *Tdamp* parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
 means to relax the temperature in a timespan of (roughly) 100 time
-units (tau or fmsec or psec - see the :doc:`units <units>` command).
+units (tau or fs or ps - see the :doc:`units <units>` command).
 
 Nose/Hoover chains are used in conjunction with this thermostat.  The
 *tparam* keyword can optionally be used to change the chain settings

doc/src/fix_temp_berendsen.rst

@@ -45,7 +45,7 @@ The desired temperature at each timestep is a ramped value during the
 run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (tau or fs or ps - see the
 :doc:`units <units>` command).
 
 *Tstart* can be specified as an equal-style :doc:`variable <variable>`.

doc/src/fix_temp_csvr.rst

@@ -59,7 +59,7 @@ The desired temperature at each timestep is a ramped value during the
 run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (tau or fs or ps - see the
 :doc:`units <units>` command).
 
 *Tstart* can be specified as an equal-style :doc:`variable <variable>`.

doc/src/fix_ti_spring.rst

@@ -88,7 +88,7 @@ time:
 
   \lambda(\tau) = \tau
 
-where tau is the scaled time variable *t/t_s*. The option *2* performs
+where :math:`\tau` is the scaled time variable *t/t_s*. The option *2* performs
 the lambda switching at a rate defined by the following switching
 function
 

doc/src/fix_wall_gran.rst

@@ -45,7 +45,7 @@ Syntax
          radius = cylinder radius (distance units)
 
 * zero or more keyword/value pairs may be appended to args
-* keyword = *wiggle* or *shear*
+* keyword = *wiggle* or *shear* or *contacts*
 
   .. parsed-literal::
 
@@ -56,6 +56,9 @@ Syntax
        *shear* values = dim vshear
          dim = *x* or *y* or *z*
          vshear = magnitude of shear velocity (velocity units)
+      *contacts* value = none
+         generate contact information for each particle
+
 
 Examples
 """"""""
@@ -68,6 +71,7 @@ Examples
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
    fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix 6 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
 
 Description
 """""""""""
@@ -171,6 +175,7 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
 *vshear* < 0.  In this case, *vshear* is the tangential velocity of
 the wall at whatever *radius* has been defined.
 
+
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
 This fix writes the shear friction state of atoms interacting with the
@@ -181,11 +186,37 @@ info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+If the :code:`contacts` option is used, this fix generates a per-atom array
-fix.  No global or per-atom quantities are stored by this fix for
+with 8 columns as output, containing the contact information for owned
-access by various :doc:`output commands <Howto_output>`.  No parameter
+particles (nlocal on each processor). All columns in this per-atom array will
-of this fix can be used with the *start/stop* keywords of the
+be zero if no contact has occurred.  The values of these columns are listed in
-:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the following table:
+
++-------+----------------------------------------------------+----------------+
+| Index | Value                                              | Units          |
++=======+====================================================+================+
+|     1 | 1.0 if particle is in contact with wall,           |                |
+|       | 0.0 otherwise                                      |                |
++-------+----------------------------------------------------+----------------+
+|     2 | Force :math:`f_x` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     3 | Force :math:`f_y` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     4 | Force :math:`f_z` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     5 | :math:`\Delta x` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     6 | :math:`\Delta y` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     7 | :math:`\Delta z` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     8 | Radius :math:`r` of atom                           | distance units |
++-------+----------------------------------------------------+----------------+
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+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>`.
 
 Restrictions
 """"""""""""

doc/src/fix_wall_gran_region.rst

@@ -8,7 +8,7 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID
+   fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID keyword values ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * wall/region = style name of this fix command
@@ -36,6 +36,12 @@ Syntax
 
 * wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
 * region-ID = region whose boundary will act as wall
+* keyword = *contacts*
+
+  .. parsed-literal::
+
+      *contacts* value = none
+         generate contact information for each particle
 
 Examples
 """"""""
@@ -46,6 +52,7 @@ Examples
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
    fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone contacts
 
 Description
 """""""""""
@@ -215,11 +222,37 @@ uninterrupted fashion.
    use the same fix ID for fix wall/gran/region, but assign it a region
    with a different region ID.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+If the :code:`contacts` option is used, this fix generates a per-atom array
-fix.  No global or per-atom quantities are stored by this fix for
+with 8 columns as output, containing the contact information for owned
-access by various :doc:`output commands <Howto_output>`.  No parameter
+particles (nlocal on each processor). All columns in this per-atom array will
-of this fix can be used with the *start/stop* keywords of the
+be zero if no contact has occurred. The values of these columns are listed in
-:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the following table:
+
++-------+----------------------------------------------------+----------------+
+| Index | Value                                              | Units          |
++=======+====================================================+================+
+|     1 | 1.0 if particle is in contact with wall,           |                |
+|       | 0.0 otherwise                                      |                |
++-------+----------------------------------------------------+----------------+
+|     2 | Force :math:`f_x` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     3 | Force :math:`f_y` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     4 | Force :math:`f_z` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     5 | :math:`\Delta x` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     6 | :math:`\Delta y` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     7 | :math:`\Delta z` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     8 | Radius :math:`r` of atom                           | distance units |
++-------+----------------------------------------------------+----------------+
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+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>`.
 
 Restrictions
 """"""""""""

doc/src/kspace_modify.rst

@@ -145,16 +145,16 @@ parameters, see the :doc:`How-To <Howto_dispersion>` discussion.
 
 The *fftbench* keyword applies only to PPPM. It is off by default. If
 this option is turned on, LAMMPS will perform a short FFT benchmark
-computation and report its timings, and will thus finish a some seconds
+computation and report its timings, and will thus finish some seconds
 later than it would if this option were off.
 
 ----------
 
 The *force/disp/real* and *force/disp/kspace* keywords set the force
-accuracy for the real and space computations for the dispersion part
+accuracy for the real and reciprocal space computations for the dispersion
-of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+part of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`,
-performance and accuracy in the results is obtained when these values
+optimal performance and accuracy in the results is obtained when these
-are different.
+values are different.
 
 ----------
 
@@ -413,10 +413,10 @@ slab correction has also been extended to point dipole interactions
 ----------
 
 The *force/disp/real* and *force/disp/kspace* keywords set the force
-accuracy for the real and space computations for the dispersion part
+accuracy for the real and reciprocal space computations for the dispersion
-of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+part of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`,
-performance and accuracy in the results is obtained when these values
+optimal performance and accuracy in the results is obtained when these
-are different.
+values are different.
 
 The *disp/auto* option controls whether the pppm/disp is allowed to
 generate PPPM parameters automatically. If set to *no*\ , parameters

doc/src/pair_eam.rst

@@ -39,15 +39,9 @@ pair_style eam/alloy/opt command
 pair_style eam/cd command
 =========================
 
-pair_style eam/cd/omp command
-=============================
-
 pair_style eam/cd/old command
 =============================
 
-pair_style eam/cd/old/omp command
-=================================
-
 pair_style eam/fs command
 =========================
 

doc/src/pair_lubricate.rst

@@ -28,7 +28,9 @@ Syntax
 * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
 * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
 
-**Examples:** (all assume radius = 1)
+Examples
+""""""""
+(all assume radius = 1)
 
 .. code-block:: LAMMPS
 

doc/src/pair_lubricateU.rst

@@ -22,7 +22,9 @@ Syntax
 * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
 * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
 
-**Examples:** (all assume radius = 1)
+Examples
+""""""""
+(all assume radius = 1)
 
 .. code-block:: LAMMPS
 

doc/src/reset_ids.rst

@@ -8,7 +8,14 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   reset_ids
+   reset_ids keyword values ...
+
+   * zero or more keyword/value pairs may be appended
+   * keyword = *sort*
+
+.. parsed-literal::
+
+   *sort* value = *yes* or *no*
 
 Examples
 """"""""
@@ -16,6 +23,7 @@ Examples
 .. code-block:: LAMMPS
 
    reset_ids
+   reset_ids sort yes
 
 Description
 """""""""""
@@ -33,11 +41,32 @@ e.g. due to atoms moving outside a simulation box with fixed
 boundaries (see the "boundary command"), or due to evaporation (see
 the "fix evaporate" command).
 
-Note that the resetting of IDs is not really a compression, where gaps
+If the *sort* keyword is used with a setting of *yes*, then the
-in atom IDs are removed by decrementing atom IDs that are larger.
+assignment of new atom IDs will be the same no matter how many
-Instead the IDs for all atoms are erased, and new IDs are assigned so
+processors LAMMPS is running on.  This is done by first doing a
-that the atoms owned by an individual processor have consecutive IDs,
+spatial sort of all the atoms into bins and sorting them within each
-as the :doc:`create_atoms <create_atoms>` command explains.
+bin.  Because the set of bins is independent of the number of
+processors, this enables a consistent assignment of new IDs to each
+atom.
+
+This can be useful to do after using the "create_atoms" command and/or
+"replicate" command.  In general those commands do not guarantee
+assignment of the same atom ID to the same physical atom when LAMMPS
+is run on different numbers of processors.  Enforcing consistent IDs
+can be useful for debugging or comparing output from two different
+runs.
+
+Note that the spatial sort requires communication of atom IDs and
+coordinates between processors in an all-to-all manner.  This is done
+efficiently in LAMMPS, but it is more expensive than how atom IDs are
+reset without sorting.
+
+Note that whether sorting or not, the resetting of IDs is not a
+compression, where gaps in atom IDs are removed by decrementing atom
+IDs that are larger.  Instead the IDs for all atoms are erased, and
+new IDs are assigned so that the atoms owned by an individual
+processor have consecutive IDs, as the :doc:`create_atoms
+<create_atoms>` command explains.
 
 .. note::
 
@@ -59,4 +88,7 @@ Related commands
 
 :doc:`delete_atoms <delete_atoms>`
 
-**Default:** none
+Default
+"""""""
+
+By default, *sort* is no.

doc/src/run_style.rst

@@ -150,8 +150,8 @@ timestep, angle interactions computed 4x, pair interactions computed
 
 The :doc:`timestep <timestep>` command sets the large timestep for the
 outermost rRESPA level.  Thus if the 3 loop factors are "2 2 2" for
-4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
+4-level rRESPA, and the outer timestep is set to 4.0 fs, then the
-inner timestep would be 8x smaller or 0.5 fmsec.  All other LAMMPS
+inner timestep would be 8x smaller or 0.5 fs.  All other LAMMPS
 commands that specify number of timesteps (e.g. :doc:`thermo <thermo>`
 for thermo output every N steps, :doc:`neigh_modify delay/every <neigh_modify>` parameters, :doc:`dump <dump>` every N
 steps, etc) refer to the outermost timesteps.
@@ -213,10 +213,10 @@ With that caveat, a few rules-of-thumb may be useful in selecting
 simulations using the CHARMM or a similar all-atom force field, but
 the concepts are adaptable to other problems.  Without SHAKE, bonds
 involving hydrogen atoms exhibit high-frequency vibrations and require
-a timestep on the order of 0.5 fmsec in order to conserve energy.  The
+a timestep on the order of 0.5 fs in order to conserve energy.  The
 relatively inexpensive force computations for the bonds, angles,
-impropers, and dihedrals can be computed on this innermost 0.5 fmsec
+impropers, and dihedrals can be computed on this innermost 0.5 fs
-step.  The outermost timestep cannot be greater than 4.0 fmsec without
+step.  The outermost timestep cannot be greater than 4.0 fs without
 risking energy drift.  Smooth switching of forces between the levels
 of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
 angstrom "healing distance" (the distance between the outer and inner
@@ -230,14 +230,14 @@ simulations:
    run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
 
 With these settings, users can expect good energy conservation and
-roughly a 2.5 fold speedup over the *verlet* style with a 0.5 fmsec
+roughly a 2.5 fold speedup over the *verlet* style with a 0.5 fs
 timestep.
 
 If SHAKE is used with the *respa* style, time reversibility is lost,
 but substantially longer time steps can be achieved.  For biomolecular
 simulations using the CHARMM or similar all-atom force field, bonds
 involving hydrogen atoms exhibit high frequency vibrations and require
-a time step on the order of 0.5 fmsec in order to conserve energy.
+a time step on the order of 0.5 fs in order to conserve energy.
 These high frequency modes also limit the outer time step sizes since
 the modes are coupled.  It is therefore desirable to use SHAKE with
 respa in order to freeze out these high frequency motions and increase
@@ -253,7 +253,7 @@ rRESPA:
 
 With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the *verlet* style with SHAKE and a
-2.0 fmsec timestep.
+2.0 fs timestep.
 
 For non-biomolecular simulations, the *respa* style can be
 advantageous if there is a clear separation of time scales - fast and

doc/src/special_bonds.rst

@@ -28,7 +28,8 @@ Syntax
        *angle* value = *yes* or *no*
        *dihedral* value = *yes* or *no*
 
-Examples:
+Examples
+""""""""
 
 .. code-block:: LAMMPS
 

doc/src/timestep.rst

@@ -46,22 +46,22 @@ Related commands
 Default
 """""""
 
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| choice of :doc:`units <units>` | time units | default timestep size |
+| choice of :doc:`units <units>` | time units    | default timestep size |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| lj                             | tau        | 0.005 tau             |
+| lj                             | :math:`\tau`  | 0.005 :math:`\tau`    |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| real                           | fmsec      | 1.0 fmsec             |
+| real                           | fs            | 1.0 fs                |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| metal                          | psec       | 0.001 psec            |
+| metal                          | ps            | 0.001 ps              |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| si                             | sec        | 1.0e-8 sec (10 nsec)  |
+| si                             | s             | 1.0e-8 s (10 ns)      |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| cgs                            | sec        | 1.0e-8 sec (10 nsec)  |
+| cgs                            | s             | 1.0e-8 s (10 ns)      |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| electron                       | fmsec      | 0.001 fmsec           |
+| electron                       | fs            | 0.001 fs              |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| micro                          | usec       | 2.0 usec              |
+| micro                          | :math:`\mu`\ s| 2.0 :math:`\mu`\ s    |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| nano                           | nsec       | 0.00045 nsec          |
+| nano                           | ns            | 0.00045 ns            |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+

doc/src/units.rst

@@ -203,7 +203,7 @@ For style *nano*\ , these are the units:
 The units command also sets the timestep size and neighbor skin
 distance to default values for each style:
 
-* For style *lj* these are dt = 0.005 tau and skin = 0.3 sigma.
+* For style *lj* these are dt = 0.005 :math:`\tau` and skin = 0.3 :math:`\sigma`.
 * For style *real* these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms.
 * For style *metal* these are dt = 0.001 picoseconds and skin = 2.0 Angstroms.
 * For style *si* these are dt = 1.0e-8 seconds and skin = 0.001 meters.

doc/src/velocity.rst

@@ -225,8 +225,8 @@ body defined by the fix, as described above.
 The *units* keyword is used by *set* and *ramp*\ .  If units = box,
 the velocities and coordinates specified in the velocity command are
 in the standard units described by the :doc:`units <units>` command
-(e.g. Angstroms/fmsec for real units).  If units = lattice, velocities
+(e.g. Angstroms/fs for real units).  If units = lattice, velocities
-are in units of lattice spacings per time (e.g. spacings/fmsec) and
+are in units of lattice spacings per time (e.g. spacings/fs) and
 coordinates are in lattice spacings.  The :doc:`lattice <lattice>`
 command must have been previously used to define the lattice spacing.
 

doc/utils/sphinx-config/false_positives.txt

@@ -136,6 +136,7 @@ atan
 atc
 AtC
 ATC
+athermal
 athomps
 atm
 atomeye
@@ -226,6 +227,7 @@ Bfrac
 bgq
 Bh
 Bialke
+bicrystal
 Biersack
 bigbig
 bigint
@@ -287,6 +289,7 @@ br
 Branduardi
 Branicio
 brennan
+Brien
 Brilliantov
 Broadwell
 Broglie
@@ -633,7 +636,6 @@ dipolar
 dir
 Direc
 dirname
-disarmmd
 discoverable
 discretization
 discretized
@@ -726,6 +728,7 @@ ebook
 ebt
 ec
 Ec
+eco
 ecoul
 ecp
 Ecut
@@ -950,7 +953,6 @@ fmackay
 fmag
 fmass
 fmm
-fmsec
 fmx
 fmy
 fmz
@@ -1834,6 +1836,7 @@ Modine
 mofff
 MOFFF
 Mohd
+Mohles
 mol
 Mol
 molfile
@@ -1999,6 +2002,7 @@ Neumann
 Nevent
 nevery
 Nevery
+newfile
 Newns
 newtype
 Neyts
@@ -2091,9 +2095,9 @@ Nroff
 nrun
 Ns
 Nsample
-nsec
 Nskip
 Nspecies
+ns
 nsq
 Nstart
 nstats
@@ -2177,6 +2181,7 @@ optimizations
 orangered
 organometallic
 orientational
+orientationsFile
 orientorder
 Orlikowski
 ornl
@@ -2366,7 +2371,6 @@ ps
 Ps
 pscreen
 pscrozi
-psec
 pseudodynamics
 pseudopotential
 Pstart
@@ -2471,6 +2475,7 @@ rdc
 rdf
 RDideal
 rdx
+reacter
 README
 realtime
 reamin
@@ -2642,6 +2647,7 @@ Schimansky
 Schiotz
 Schlitter
 Schmid
+Schratt
 Schoen
 Schotte
 Schulten
@@ -3060,6 +3066,7 @@ ul
 ulb
 Uleft
 uloop
+Ulomek
 ulsph
 uMech
 umin

examples/USER/misc/orient_eco/Ni_u3.eam

@@ -0,0 +1 @@
+../../../../potentials/Ni_u3.eam

examples/USER/misc/orient_eco/in.orient_eco

@@ -0,0 +1,20 @@
+
+units           metal
+atom_style      atomic
+read_data       data.sigma5
+
+pair_style      eam
+pair_coeff      * * Ni_u3.eam
+timestep        0.001
+
+fix integrator  all npt temp 750 750 0.1 iso 0 0 0.1
+fix eco         all orient/eco 0.08 0.25 3.6 sigma5.ori
+
+thermo          100
+thermo_style    custom step temp etotal press vol f_eco
+velocity        all create 750 18527782
+
+#dump            save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
+#dump_modify     save sort id
+
+run             1000

examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1

@@ -0,0 +1,91 @@
+LAMMPS (2 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+atom_style      atomic
+read_data       data.sigma5
+  orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  25600 atoms
+  read_data CPU = 0.020 secs
+
+pair_style      eam
+pair_coeff      * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+timestep        0.001
+
+fix integrator  all npt temp 750 750 0.1 iso 0 0 0.1
+fix eco         all orient/eco 0.08 0.25 3.6 sigma5.ori
+
+thermo          100
+thermo_style    custom step temp etotal press vol f_eco
+velocity        all create 750 18527782
+
+#dump            save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
+#dump_modify     save sort id
+
+run             1000
+  fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 54 27 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) fix orient/eco, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.15 | 42.15 | 42.15 Mbytes
+Step Temp TotEng Press Volume f_eco 
+       0          750   -111027.95    15148.458    279755.85 8.7507522e-10 
+     100     422.2475   -110928.85    214.27204    285332.91   -1.0089186 
+     200    388.79514   -110721.02    -481.9574    286443.13  -0.78446905 
+     300    441.87285   -110478.56   -174.88288    286640.75   -1.1348357 
+     400    486.71094    -110211.6    65.075638    287023.56    -1.495318 
+     500    531.12815   -109923.33    97.309245    287552.73   -2.9498072 
+     600    569.82126   -109622.61    -85.73157    288229.35   -4.2855812 
+     700    615.84724   -109317.16   -52.508824    288799.86   -6.5214427 
+     800    666.09015   -109018.62    38.120383    289305.37   -8.4745641 
+     900    705.03939   -108738.66    263.39673    289867.87     -12.4514 
+    1000    735.59866   -108500.52    242.46405    290353.65   -15.427653 
+Loop time of 109.966 on 1 procs for 1000 steps with 25600 atoms
+
+Performance: 0.786 ns/day, 30.546 hours/ns, 9.094 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    | 27.002     | 27.002     | 27.002     |   0.0 | 24.55
+Neigh   | 0.83228    | 0.83228    | 0.83228    |   0.0 |  0.76
+Comm    | 0.12623    | 0.12623    | 0.12623    |   0.0 |  0.11
+Output  | 0.00080323 | 0.00080323 | 0.00080323 |   0.0 |  0.00
+Modify  | 81.917     | 81.917     | 81.917     |   0.0 | 74.49
+Other   |            | 0.08839    |            |       |  0.08
+
+Nlocal:    25600 ave 25600 max 25600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    28259 ave 28259 max 28259 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.59326e+06 ave 1.59326e+06 max 1.59326e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  3.18651e+06 ave 3.18651e+06 max 3.18651e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3186510
+Ave neighs/atom = 124.473
+Neighbor list builds = 10
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:50

examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4

@@ -0,0 +1,91 @@
+LAMMPS (2 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+atom_style      atomic
+read_data       data.sigma5
+  orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
+  4 by 1 by 1 MPI processor grid
+  reading atoms ...
+  25600 atoms
+  read_data CPU = 0.025 secs
+
+pair_style      eam
+pair_coeff      * * Ni_u3.eam
+Reading potential file Ni_u3.eam with DATE: 2007-06-11
+timestep        0.001
+
+fix integrator  all npt temp 750 750 0.1 iso 0 0 0.1
+fix eco         all orient/eco 0.08 0.25 3.6 sigma5.ori
+
+thermo          100
+thermo_style    custom step temp etotal press vol f_eco
+velocity        all create 750 18527782
+
+#dump            save all custom 100 orient_eco.dump xs ys zs f_eco[1] f_eco[2]
+#dump_modify     save sort id
+
+run             1000
+  fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.8
+  ghost atom cutoff = 6.8
+  binsize = 3.4, bins = 54 27 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) fix orient/eco, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.69 | 11.7 | 11.72 Mbytes
+Step Temp TotEng Press Volume f_eco 
+       0          750   -111027.95    15148.458    279755.85 8.749339e-10 
+     100     422.2475   -110928.85    214.27204    285332.91   -1.0089186 
+     200    388.79514   -110721.02    -481.9574    286443.13  -0.78446905 
+     300    441.87285   -110478.56   -174.88288    286640.75   -1.1348357 
+     400    486.71094    -110211.6    65.075638    287023.56    -1.495318 
+     500    531.12815   -109923.33    97.309245    287552.73   -2.9498072 
+     600    569.82126   -109622.61    -85.73157    288229.35   -4.2855812 
+     700    615.84724   -109317.16   -52.508824    288799.86   -6.5214427 
+     800    666.09015   -109018.62    38.120383    289305.37   -8.4745641 
+     900    705.03939   -108738.66    263.39673    289867.87     -12.4514 
+    1000    735.59866   -108500.52    242.46405    290353.65   -15.427653 
+Loop time of 29.6634 on 4 procs for 1000 steps with 25600 atoms
+
+Performance: 2.913 ns/day, 8.240 hours/ns, 33.712 timesteps/s
+98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.0794     | 7.1053     | 7.1325     |   0.7 | 23.95
+Neigh   | 0.20947    | 0.21088    | 0.21231    |   0.2 |  0.71
+Comm    | 0.15708    | 0.18471    | 0.22338    |   6.7 |  0.62
+Output  | 0.00032616 | 0.00064683 | 0.0015936  |   0.0 |  0.00
+Modify  | 22.105     | 22.118     | 22.139     |   0.3 | 74.56
+Other   |            | 0.0437     |            |       |  0.15
+
+Nlocal:    6400 ave 6421 max 6384 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    9872.5 ave 9892 max 9855 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    398314 ave 400737 max 395743 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+FullNghs:  796628 ave 801194 max 792566 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 3186510
+Ave neighs/atom = 124.473
+Neighbor list builds = 10
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:29

examples/USER/misc/orient_eco/sigma5.ori

@@ -0,0 +1,6 @@
+1.671685 0.557228 1.76212
+0.557228 -1.671685 1.76212
+2.228913 -1.114456 0.000000
+0.557228 1.671685 1.76212
+1.671685 -0.557228 1.76212
+2.228913 1.114456 0.000000

examples/hyper/log.2Jun2020.hyper.local.g++.4

@@ -0,0 +1,647 @@
+LAMMPS (2 Jun 2020)
+  using 1 OpenMP thread(s) per MPI task
+# 3d EAM surface for local HD
+
+# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
+# hop event on (100) surface is same distance
+# exchange event is 2 atoms moving same distance
+
+variable        Tequil index 400.0
+variable        Vmax index 0.4
+variable        qfactor index 0.3
+variable        cutbond index 3.2
+variable        Dcut index 10.0
+variable        cutevent index 1.1
+variable        alpha index 200.0
+variable        boost index 4000.0
+variable        ghostcut index 12.0
+variable        steps index 2000
+variable        nevent index 100
+variable        nx index 2
+variable        ny index 2
+variable        zoom index 1.8
+variable        seed index 3875984
+variable        tol index 1.0e-15
+variable        add index 50
+
+units           metal
+atom_style	atomic
+atom_modify     map array
+boundary        p p p
+comm_modify     cutoff ${ghostcut}
+comm_modify     cutoff 12.0
+
+lattice		fcc 3.92
+Lattice spacing in x,y,z = 3.92 3.92 3.92
+region		box block 0 6 0 6 0 4
+create_box	2 box
+Created orthogonal box = (0.0 0.0 0.0) to (23.52 23.52 15.68)
+  2 by 2 by 1 MPI processor grid
+create_atoms	1 box
+Created 576 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass            * 1.0
+
+change_box      all z final -0.1 5.0 boundary p p f
+  orthogonal box = (0.0 0.0 -0.392) to (23.52 23.52 19.6)
+WARNING: Reset image flags for non-periodic boundary (src/domain.cpp:1909)
+
+# replicate in xy
+
+replicate       ${nx} ${ny} 1
+replicate       2 ${ny} 1
+replicate       2 2 1
+  orthogonal box = (0.0 0.0 -0.392) to (47.04 47.04 19.6)
+  2 by 2 by 1 MPI processor grid
+  2304 atoms
+  replicate CPU = 0.000324488 secs
+
+# add adatoms
+
+include         adatoms.list.${add}
+include         adatoms.list.50
+create_atoms 1 single 5 9 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4.5 7.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6 6 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 5 6 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4.5 1.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6.5 7.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 10.5 5.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 2.5 1.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3.5 4.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 0 10 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 11 10 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6.5 10.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3.5 5.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 7.5 10.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1.5 1.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1.5 6.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 7 2 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4 0 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 9 0 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4 9 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 10 7 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4 4 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 9.5 2.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1 5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 7 10 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 0 4 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1 10 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 7.5 6.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4 10 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6.5 3.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3 6 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 8.5 4.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6.5 0.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1 4 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 8.5 11.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3 9 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 2 3 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 6.5 8.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1 0 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 0.5 10.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 4 11 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3 5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 0 1 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 2 11 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 2 0 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 7.5 11.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 1 7 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 3.5 10.5 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 0 2 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+create_atoms 1 single 8 4 4
+Created 1 atoms
+  create_atoms CPU = 0.000 seconds
+
+# define frozen substrate and mobile atoms
+
+region          base block INF INF INF INF 0 1.8
+set             region base type 2
+  1152 settings made for typegroup           base type 2
+1152 atoms in group base
+group           mobile type 1
+1202 atoms in group mobile
+
+# pair style
+
+pair_style	eam/alloy
+pair_coeff	* * ptvoterlammps.eam Pt Pt
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 mobile nve
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 400.0 1.0 3875984 zero yes
+
+timestep	0.005
+
+compute         tmobile mobile temp
+
+thermo		100
+thermo_modify   temp tmobile
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:486)
+
+# thermal equilibration
+
+run             1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.07583
+  ghost atom cutoff = 12
+  binsize = 3.03792, bins = 16 16 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eam/alloy, 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) = 3.443 | 3.443 | 3.443 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -13067.188            0   -13067.188   -53763.139 
+     100    216.49187   -13065.694            0   -13032.085   -24077.115 
+     200    285.11905   -13057.047            0   -13012.785   -38815.844 
+     300    321.67264   -13048.005            0   -12998.068   -29296.124 
+     400    352.90893   -13045.707            0    -12990.92   -34630.884 
+     500     371.9393   -13041.234            0   -12983.494   -28913.827 
+     600    379.08135    -13040.06            0   -12981.211     -33399.8 
+     700    388.73836   -13039.691            0   -12979.343   -29446.954 
+     800    402.13628   -13040.606            0   -12978.178   -33026.861 
+     900    389.43806   -13036.884            0   -12976.427   -30328.658 
+    1000    388.66198   -13037.479            0   -12977.142   -30859.145 
+Loop time of 0.572404 on 4 procs for 1000 steps with 2354 atoms
+
+Performance: 754.712 ns/day, 0.032 hours/ns, 1747.018 timesteps/s
+96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.45189    | 0.4594     | 0.46833    |   0.9 | 80.26
+Neigh   | 0.039092   | 0.039772   | 0.040386   |   0.3 |  6.95
+Comm    | 0.040249   | 0.051709   | 0.060548   |   3.4 |  9.03
+Output  | 0.00014281 | 0.0002625  | 0.00061965 |   0.0 |  0.05
+Modify  | 0.017148   | 0.017244   | 0.017364   |   0.1 |  3.01
+Other   |            | 0.004017   |            |       |  0.70
+
+Nlocal:    588.5 ave 592 max 581 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Nghost:    1964 ave 1973 max 1959 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Neighs:    14148.8 ave 14283 max 13931 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 56595
+Ave neighs/atom = 24.0421
+Neighbor list builds = 91
+Dangerous builds = 0
+reset_timestep  0
+
+# pin base so will not move during quenches
+
+fix             freeze base setforce 0.0 0.0 0.0
+
+# event detection
+
+compute         event all event/displace ${cutevent}
+compute         event all event/displace 1.1
+
+# hyper/local
+
+fix             HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 4000.0
+
+# thermo output
+
+thermo_style    custom step temp pe f_HL f_HL[*]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:709)
+
+thermo_modify   lost ignore
+thermo_modify   temp tmobile
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:486)
+
+thermo          ${nevent}
+thermo          100
+
+# dump
+
+region          substrate block INF INF INF INF 1.8 3.8
+region          adatoms block INF INF INF INF 3.8 INF
+variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
+
+dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
+
+# run
+
+hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           2000 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           2000 100 HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           2000 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
+hyper           2000 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
+WARNING: Resetting reneighboring criteria during hyper (src/REPLICA/hyper.cpp:131)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.07583
+  ghost atom cutoff = 12
+  binsize = 3.03792, bins = 16 16 7
+  3 neighbor lists, perpetual/occasional/extra = 1 2 0
+  (1) pair eam/alloy, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix hyper/local, occasional
+      attributes: full, newton on, cut 10
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) fix hyper/local, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 6.786 | 6.786 | 6.786 Mbytes
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+       0    388.66198   -13037.479            0            1            0            0          0.4            1            0            0            0            0            0            0            0            0            0            0        1e+20            0            0            0            0            0            0            0            0            0            0            1            0 
+      68    388.66198   -13101.057            0            1            0            0          0.4            1            0            0            0            0            0            0            0            0            0            0        1e+20            0            0            0            0            0            0         1360            0            0            0            1            0 
+Loop time of 0.078882 on 4 procs for 68 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+       0    388.66198   -13037.479    2.1560986            0            7   0.19075505          0.4            0            0            0    5.9276206    1380.4406            0            0            0            0    3.2725891            0        1e+20            0            0            0            0            0            0            0            0            0            0    10345.213            0 
+     100    388.08547   -13035.803    1.9458797      5579.52            7   0.22444002          0.4   0.99435481   0.98307948    1.0037683    5.9276206    1380.4406     7612.921         5.23            0            0    3.4801431   0.99683836   0.98307948    1.0037683            0            0            0            0            0         2000            0            0            0    4811.1645            0 
+Loop time of 0.0768972 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     100    388.08547   -13035.803    1.9458797      5579.52            7   0.22444002          0.4   0.99435481   0.98307948    1.0037683    5.9276206    1380.4406     7612.921         5.23            0            0    3.4801431   0.99683836   0.98307948    1.0037683            0            0            0            0            0         2000            0            0            0    4811.1645            0 
+     171    388.08547   -13101.057    1.9458797      5579.52            7   0.22444002          0.4   0.99435481   0.98307948    1.0037683    5.9276206    1380.4406     7612.921    3.0584795            0            0    3.4801431   0.99683836   0.98307948    1.0037683            0            0            0            0            0         3420            0            0            0    4811.1645            0 
+Loop time of 0.0822812 on 4 procs for 71 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     100    388.08547   -13035.803    1.9458309      5579.52            7   0.22444002          0.4   0.99435481   0.98307948    1.0037683    5.9276206    1380.4406     7612.921         5.23            0            0    3.4801431   0.99683836   0.98307948    1.0037683            0            0            0            0            0         2000            0            0            0     4806.677            0 
+     200    401.00579   -13036.475    1.7413518    5055.0046            7   0.31164106          0.4   0.99292126   0.97454567    1.0099107    5.9276206    1380.4406    6265.1974          5.8  0.026724138            0    3.7115994   0.99518634   0.97454567    1.0099107            0            0            0            0            0         4000            0            0            0    5975.1486            1 
+Loop time of 0.0801389 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     200    401.00579   -13036.475    1.7413518    5055.0046            7   0.31164106          0.4   0.99292126   0.97454567    1.0099107    5.9276206    1380.4406    6265.1974          5.8  0.026724138            0    3.7115994   0.99518634   0.97454567    1.0099107            0            0            0            0            0         4000            0            0            0    5975.1486            1 
+     270    401.00579   -13101.057    1.7413518    5055.0046            7   0.31164106          0.4   0.99292126   0.97454567    1.0099107    5.9276206    1380.4406    6265.1974    4.2962963  0.026724138            0    3.7115994   0.99518634   0.97454567    1.0099107            0            0            0            0            0         5400            0            0            0    5975.1486            1 
+Loop time of 0.0823423 on 4 procs for 70 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     200    401.00579   -13036.475    1.7412451    5055.0046            7   0.31164106          0.4   0.99292126   0.97454567    1.0099107    5.9276206    1380.4406    6265.1974          5.8  0.026724138            0    3.7115994   0.99518634   0.97454567    1.0099107            0            0            0            0            0         4000            0            0            0    5960.9703            1 
+     300    393.06665   -13036.447    1.2104123    4309.6701            6   0.25677049          0.4   0.99077715   0.96163085    1.0121227    5.9276206    1380.4406    5967.5417         5.82   0.03722795 0.0011454754    3.7958861   0.99407566   0.96163085    1.0121227            0            0            0            0            0         6000            0            0            0    2438.7867            0 
+Loop time of 0.07828 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     300    393.06665   -13036.447    1.2104123    4309.6701            6   0.25677049          0.4   0.99077715   0.96163085    1.0121227    5.9276206    1380.4406    5967.5417         5.82   0.03722795 0.0011454754    3.7958861   0.99407566   0.96163085    1.0121227            0            0            0            0            0         6000            0            0            0    2438.7867            0 
+     371    393.06665   -13101.057    1.2104123    4309.6701            6   0.25677049          0.4   0.99077715   0.96163085    1.0121227    5.9276206    1380.4406    5967.5417    4.7061995   0.03722795 0.0011454754    3.7958861   0.99407566   0.96163085    1.0121227            0            0            0            0            0         7420            0            0            0    2438.7867            0 
+Loop time of 0.0849175 on 4 procs for 71 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     300    393.06665   -13036.447     1.210401    4309.6701            6   0.25677049          0.4   0.99077715   0.96163085    1.0121227    5.9276206    1380.4406    5967.5417         5.82   0.03722795 0.0011454754    3.7958861   0.99407566   0.96163085    1.0121227            0            0            0            0            0         6000            0            0            0    2432.9129            0 
+     400    395.31214   -13036.548   0.97543536      3697.18            5   0.29627573          0.4   0.99121527   0.95719757    1.0171656    5.9276206    1380.4406    5405.5572       5.8525  0.064502349 0.00085433575    3.8763827   0.99330778   0.95719757    1.0171656            0            0            0            0            0         8000            0            0            0     1494.721            0 
+Loop time of 0.0789399 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     400    395.31214   -13036.548   0.97543536      3697.18            5   0.29627573          0.4   0.99121527   0.95719757    1.0171656    5.9276206    1380.4406    5405.5572       5.8525  0.064502349 0.00085433575    3.8763827   0.99330778   0.95719757    1.0171656            0            0            0            0            0         8000            0            0            0     1494.721            0 
+     472    395.31214   -13101.057   0.97543536      3697.18            5   0.29627573          0.4   0.99121527   0.95719757    1.0171656    5.9276206    1380.4406    5405.5572    4.9597458  0.064502349 0.00085433575    3.8763827   0.99330778   0.95719757    1.0171656            0            0            0            0            0         9440            0            0            0     1494.721            0 
+Loop time of 0.0826263 on 4 procs for 72 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     400    395.31214   -13036.548   0.97546459      3697.18            5   0.29627573          0.4   0.99121527   0.95719757    1.0171656    5.9276206    1380.4406    5405.5572       5.8525  0.064502349 0.00085433575    3.8763827   0.99330778   0.95719757    1.0171656            0            0            0            0            0         8000            0            0            0    1495.2683            0 
+     500    407.51943   -13034.684    1.5129292    3762.6056            7   0.32103986          0.4   0.99260954   0.95025478     1.023175    5.9276206    1380.4406    4945.9788        5.798  0.092100724 0.00068989307    3.8763827   0.99301979   0.95024238     1.023175            0            0            0            0            0        10000            0            0            0    2846.6451            1 
+Loop time of 0.0785343 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     500    407.51943   -13034.684    1.5129292    3762.6056            7   0.32103986          0.4   0.99260954   0.95025478     1.023175    5.9276206    1380.4406    4945.9788        5.798  0.092100724 0.00068989307    3.8763827   0.99301979   0.95024238     1.023175            0            0            0            0            0        10000            0            0            0    2846.6451            1 
+     570    407.51943   -13101.057    1.5129292    3762.6056            7   0.32103986          0.4   0.99260954   0.95025478     1.023175    5.9276206    1380.4406    4945.9788    5.0859649  0.092100724 0.00068989307    3.8763827   0.99301979   0.95024238     1.023175            0            0            0            0            0        11400            0            0            0    2846.6451            1 
+Loop time of 0.0831875 on 4 procs for 70 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     500    407.51943   -13034.684    1.5129263    3762.6056            7   0.32103986          0.4   0.99260954   0.95025478     1.023175    5.9276206    1380.4406    4945.9788        5.798  0.092100724 0.00068989307    3.8763827   0.99301979   0.95024238     1.023175            0            0            0            0            0        10000            0            0            0    2845.3486            1 
+     600    403.68879   -13034.437    1.6119602    3538.1789            8   0.37263827          0.4   0.99175914   0.94814388    1.0294169    5.9276206    1380.4406    4879.0252        5.805  0.091587712 0.0054550675    3.8763827   0.99287249   0.94770585    1.0294169            0            0            0            0            0        12000            0            0            0    4550.0103            1 
+Loop time of 0.0778956 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     600    403.68879   -13034.437    1.6119602    3538.1789            8   0.37263827          0.4   0.99175914   0.94814388    1.0294169    5.9276206    1380.4406    4879.0252        5.805  0.091587712 0.0054550675    3.8763827   0.99287249   0.94770585    1.0294169            0            0            0            0            0        12000            0            0            0    4550.0103            1 
+     673    403.68879   -13101.057    1.6119602    3538.1789            8   0.37263827          0.4   0.99175914   0.94814388    1.0294169    5.9276206    1380.4406    4879.0252    5.1753343  0.091587712 0.0054550675    3.8763827   0.99287249   0.94770585    1.0294169            0            0            0            0            0        13460            0            0            0    4550.0103            1 
+Loop time of 0.0866084 on 4 procs for 73 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     600    403.68879   -13034.437    1.6118577    3538.1789            8   0.37263827          0.4   0.99175914   0.94814388    1.0294169    5.9276206    1380.4406    4879.0252        5.805  0.091587712 0.0054550675    3.8763827   0.99287249   0.94770585    1.0294169            0            0            0            0            0        12000            0            0            0     4540.524            1 
+     700    402.40951   -13034.611   0.81457022    3996.0376            5   0.31795282          0.4   0.99307568    0.9469785    1.0356629    5.9276206    1380.4406    4633.0803    5.7657143   0.10332012 0.0047076313    3.8763827    0.9927955   0.94558506    1.0356629            0            0            0            0            0        14000            0            0            0    2433.3681            2 
+Loop time of 0.0783963 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     700    402.40951   -13034.611   0.81457022    3996.0376            5   0.31795282          0.4   0.99307568    0.9469785    1.0356629    5.9276206    1380.4406    4633.0803    5.7657143   0.10332012 0.0047076313    3.8763827    0.9927955   0.94558506    1.0356629            0            0            0            0            0        14000            0            0            0    2433.3681            2 
+     773    402.40951   -13101.057   0.81457022    3996.0376            5   0.31795282          0.4   0.99307568    0.9469785    1.0356629    5.9276206    1380.4406    4633.0803     5.221216   0.10332012 0.0047076313    3.8763827    0.9927955   0.94558506    1.0356629            0            0            0            0            0        15460            0            0            0    2433.3681            2 
+Loop time of 0.0879632 on 4 procs for 73 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     700    402.40951   -13034.611    0.8145522    3996.0376            5   0.31795282          0.4   0.99307568    0.9469785    1.0356629    5.9276206    1380.4406    4633.0803    5.7657143   0.10332012 0.0047076313    3.8763827    0.9927955   0.94558506    1.0356629            0            0            0            0            0        14000            0            0            0    2429.4864            2 
+     800     404.0219    -13035.35    2.0280594     2522.768            9   0.29614163          0.4   0.99235515   0.94241897     1.041911    5.9276206    1380.4406    4611.5881         5.75    0.1123913 0.0041304348    3.8763827   0.99277876   0.94229366     1.041911            0            0            0            0            0        16000            0            0            0    3341.5414            0 
+Loop time of 0.0830372 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     800     404.0219    -13035.35    2.0280594     2522.768            9   0.29614163          0.4   0.99235515   0.94241897     1.041911    5.9276206    1380.4406    4611.5881         5.75    0.1123913 0.0041304348    3.8763827   0.99277876   0.94229366     1.041911            0            0            0            0            0        16000            0            0            0    3341.5414            0 
+     875     404.0219   -13101.057    2.0280594     2522.768            9   0.29614163          0.4   0.99235515   0.94241897     1.041911    5.9276206    1380.4406    4611.5881    5.2571429    0.1123913 0.0041304348    3.8763827   0.99277876   0.94229366     1.041911            0            0            0            0            0        17500            0            0            0    3341.5414            0 
+Loop time of 0.106053 on 4 procs for 75 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     800     404.0219    -13035.35    2.0280349     2522.768            9   0.29614163          0.4   0.99235515   0.94241897     1.041911    5.9276206    1380.4406    4611.5881         5.75    0.1123913 0.0041304348    3.8763827   0.99277876   0.94229366     1.041911            0            0            0            0            0        16000            0            0            0     3339.579            0 
+     900    399.91074   -13034.973   0.95275442    3161.8387            5   0.36638548          0.4   0.99295506   0.93909912    1.0481595    5.9276206    1380.4406    4500.9735    5.7177778   0.12436844 0.0038865138    3.8763827   0.99275079   0.93842885    1.0481595            0            0            0            0            0        18000            0            0            0    1628.7316            2 
+Loop time of 0.0954949 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     900    399.91074   -13034.973   0.95275442    3161.8387            5   0.36638548          0.4   0.99295506   0.93909912    1.0481595    5.9276206    1380.4406    4500.9735    5.7177778   0.12436844 0.0038865138    3.8763827   0.99275079   0.93842885    1.0481595            0            0            0            0            0        18000            0            0            0    1628.7316            2 
+     976    399.91074   -13102.244   0.95275442    3161.8387            5   0.36638548          0.4   0.99295506   0.93909912    1.0481595    5.9276206    1380.4406    4500.9735     5.272541   0.12436844 0.0038865138    3.8763827   0.99275079   0.93842885    1.0481595            0            0            0            0            0        19520            0            0            0    1628.7316            2 
+Loop time of 0.0902783 on 4 procs for 76 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+     900    399.91074   -13034.973   0.95307991    3160.9514            5   0.42271366          0.4   0.99267641   0.93909912    1.0481595    5.9292845    1379.4982    4500.9735    5.7177778   0.12436844 0.0038865138    3.8763827   0.99275079   0.93842885    1.0481595    2.7471779            0            0            0            0        18000            1            1            4    1627.8857            2 
+    1000    417.82316   -13039.554    1.4089391    6086.7002            6    0.2668611          0.4   0.99526586   0.94236305    1.0494983    5.9292845    1379.4982    4302.6407        5.774   0.12573606 0.0034638033    3.8763827   0.99291291   0.93842885    1.0529963    2.7471779            0            0            0            0        20000            1            1            4    10750.027            0 
+Loop time of 0.0780252 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1000    417.82316   -13039.554    1.4089391    6086.7002            6    0.2668611          0.4   0.99526586   0.94236305    1.0494983    5.9292845    1379.4982    4302.6407        5.774   0.12573606 0.0034638033    3.8763827   0.99291291   0.93842885    1.0529963    2.7471779            0            0            0            0        20000            1            1            4    10750.027            0 
+    1069    417.82316   -13102.244    1.4089391    6086.7002            6    0.2668611          0.4   0.99526586   0.94236305    1.0494983    5.9292845    1379.4982    4302.6407    5.4013096   0.12573606 0.0034638033    3.8763827   0.99291291   0.93842885    1.0529963    2.7471779            0            0            0            0        21380            1            1            4    10750.027            0 
+Loop time of 0.0806106 on 4 procs for 69 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1000    417.82316   -13039.554    1.4087876    6086.7002            6    0.2668611          0.4   0.99526586   0.94236305    1.0494983    5.9292845    1379.4982    4302.6407        5.774   0.12573606 0.0034638033    3.8763827   0.99291291   0.93842885    1.0529963    2.7471779            0            0            0            0        20000            1            1            4    10700.259            0 
+    1100    388.96194   -13034.299    1.2536756     3347.844            7   0.31351452          0.4   0.99338469   0.94091364    1.0522698    5.9292845    1379.4982    4384.5779    5.7981818   0.11774851 0.0039197241    3.8763827   0.99302197   0.93842885    1.0529963    2.7471779            0            0            0            0        22000            1            1            4    3842.8412            1 
+Loop time of 0.078698 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1100    388.96194   -13034.299    1.2536756     3347.844            7   0.31351452          0.4   0.99338469   0.94091364    1.0522698    5.9292845    1379.4982    4384.5779    5.7981818   0.11774851 0.0039197241    3.8763827   0.99302197   0.93842885    1.0529963    2.7471779            0            0            0            0        22000            1            1            4    3842.8412            1 
+    1169    388.96194   -13102.244    1.2536756     3347.844            7   0.31351452          0.4   0.99338469   0.94091364    1.0522698    5.9292845    1379.4982    4384.5779    5.4559453   0.11774851 0.0039197241    3.8763827   0.99302197   0.93842885    1.0529963    2.7471779            0            0            0            0        23380            1            1            4    3842.8412            1 
+Loop time of 0.0793428 on 4 procs for 69 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1100    388.96194   -13034.299    1.2536216     3347.844            7   0.31351452          0.4   0.99338469   0.94091364    1.0522698    5.9292845    1379.4982    4384.5779    5.7981818   0.11774851 0.0039197241    3.8763827   0.99302197   0.93842885    1.0529963    2.7471779            0            0            0            0        22000            1            1            4     3837.378            1 
+    1200    416.13133   -13039.115     1.136132    3568.4524            6   0.35533996          0.4   0.99425562    0.9364246    1.0585182    5.9292845    1379.4982    4306.0803    5.8033333   0.12464101 0.0035898909    4.0254085   0.99310701    0.9364246    1.0585182    2.7471779            0            0            0            0        24000            1            1            4     2979.741            3 
+Loop time of 0.0783656 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1200    416.13133   -13039.115     1.136132    3568.4524            6   0.35533996          0.4   0.99425562    0.9364246    1.0585182    5.9292845    1379.4982    4306.0803    5.8033333   0.12464101 0.0035898909    4.0254085   0.99310701    0.9364246    1.0585182    2.7471779            0            0            0            0        24000            1            1            4     2979.741            3 
+    1273    416.13133   -13102.244     1.136132    3568.4524            6   0.35533996          0.4   0.99425562    0.9364246    1.0585182    5.9292845    1379.4982    4306.0803     5.470542   0.12464101 0.0035898909    4.0254085   0.99310701    0.9364246    1.0585182    2.7471779            0            0            0            0        25460            1            1            4     2979.741            3 
+Loop time of 0.0876518 on 4 procs for 73 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1200    416.13133   -13039.115    1.1361057    3568.4524            6   0.35533996          0.4   0.99425562    0.9364246    1.0585182    5.9292845    1379.4982    4306.0803    5.8033333   0.12464101 0.0035898909    4.0254085   0.99310701    0.9364246    1.0585182    2.7471779            0            0            0            0        24000            1            1            4    2976.9031            3 
+    1300    410.00168   -13035.264   0.69108116    2815.6646            5   0.33760803          0.4   0.99554496   0.93639346     1.064754    5.9292845    1379.4982    4219.0606    5.7769231   0.12822903 0.0045272969    4.0475228   0.99322786   0.93631673     1.064754    2.7471779            0            0            0            0        26000            1            1            4    3571.3217            2 
+Loop time of 0.0806069 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1300    410.00168   -13035.264   0.69108116    2815.6646            5   0.33760803          0.4   0.99554496   0.93639346     1.064754    5.9292845    1379.4982    4219.0606    5.7769231   0.12822903 0.0045272969    4.0475228   0.99322786   0.93631673     1.064754    2.7471779            0            0            0            0        26000            1            1            4    3571.3217            2 
+    1372    410.00168   -13102.244   0.69108116    2815.6646            5   0.33760803          0.4   0.99554496   0.93639346     1.064754    5.9292845    1379.4982    4219.0606    5.4737609   0.12822903 0.0045272969    4.0475228   0.99322786   0.93631673     1.064754    2.7471779            0            0            0            0        27440            1            1            4    3571.3217            2 
+Loop time of 0.101343 on 4 procs for 72 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1300    410.00168   -13035.264   0.69104928    2815.6646            5   0.33760803          0.4   0.99554496   0.93639346     1.064754    5.9292845    1379.4982    4219.0606    5.7769231   0.12822903 0.0045272969    4.0475228   0.99322786   0.93631673     1.064754    2.7471779            0            0            0            0        26000            1            1            4    3567.5136            2 
+    1400     423.4606   -13036.225     1.703102    2579.4314            7   0.24557477          0.4   0.99782055   0.93345496    1.0682561    5.9292845    1379.4982    4099.3865    5.7721429   0.12609826 0.0042074001    4.0475228   0.99346354   0.93345496    1.0682561    2.7471779            0            0            0            0        28000            1            1            4    2627.7529            0 
+Loop time of 0.0779268 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1400     423.4606   -13036.225     1.703102    2579.4314            7   0.24557477          0.4   0.99782055   0.93345496    1.0682561    5.9292845    1379.4982    4099.3865    5.7721429   0.12609826 0.0042074001    4.0475228   0.99346354   0.93345496    1.0682561    2.7471779            0            0            0            0        28000            1            1            4    2627.7529            0 
+    1472     423.4606   -13102.244     1.703102    2579.4314            7   0.24557477          0.4   0.99782055   0.93345496    1.0682561    5.9292845    1379.4982    4099.3865    5.4898098   0.12609826 0.0042074001    4.0475228   0.99346354   0.93345496    1.0682561    2.7471779            0            0            0            0        29440            1            1            4    2627.7529            0 
+Loop time of 0.0863118 on 4 procs for 72 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1400     423.4606   -13036.225    1.7031193    2579.4314            7   0.24557477          0.4   0.99782055   0.93345496    1.0682561    5.9292845    1379.4982    4099.3865    5.7721429   0.12609826 0.0042074001    4.0475228   0.99346354   0.93345496    1.0682561    2.7471779            0            0            0            0        28000            1            1            4    2626.4636            0 
+    1500    417.42191   -13035.425   0.63879915    3265.9276            5   0.29228757          0.4    1.0007582   0.93528148    1.0742773    5.9292845    1379.4982    3967.4215        5.808   0.12396694  0.003902663    4.0475228   0.99383929    0.9320167    1.0742773    2.7471779            0            0            0            0        30000            1            1            4     1469.864            0 
+Loop time of 0.078608 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1500    417.42191   -13035.425   0.63879915    3265.9276            5   0.29228757          0.4    1.0007582   0.93528148    1.0742773    5.9292845    1379.4982    3967.4215        5.808   0.12396694  0.003902663    4.0475228   0.99383929    0.9320167    1.0742773    2.7471779            0            0            0            0        30000            1            1            4     1469.864            0 
+    1575    417.42191   -13102.244   0.63879915    3265.9276            5   0.29228757          0.4    1.0007582   0.93528148    1.0742773    5.9292845    1379.4982    3967.4215    5.5314286   0.12396694  0.003902663    4.0475228   0.99383929    0.9320167    1.0742773    2.7471779            0            0            0            0        31500            1            1            4     1469.864            0 
+Loop time of 0.0875254 on 4 procs for 75 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1500    417.42191   -13035.425   0.63881053    3265.9276            5   0.29228757          0.4    1.0007582   0.93528148    1.0742773    5.9292845    1379.4982    3967.4215        5.808   0.12396694  0.003902663    4.0475228   0.99383929    0.9320167    1.0742773    2.7471779            0            0            0            0        30000            1            1            4    1469.1489            0 
+    1600    401.08407   -13036.858    2.3070534     2462.029            9   0.26709092          0.4    1.0019205   0.93145421    1.0802698    5.9292845    1379.4982    3922.9667      5.83625   0.12368816 0.0036410366    4.0475228    0.9942857   0.93077554    1.0802698    2.7471779            0            0            0            0        32000            1            1            4    5228.0098            0 
+Loop time of 0.0780517 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1600    401.08407   -13036.858    2.3070534     2462.029            9   0.26709092          0.4    1.0019205   0.93145421    1.0802698    5.9292845    1379.4982    3922.9667      5.83625   0.12368816 0.0036410366    4.0475228    0.9942857   0.93077554    1.0802698    2.7471779            0            0            0            0        32000            1            1            4    5228.0098            0 
+    1667    401.08407   -13102.244    2.3070534     2462.029            9   0.26709092          0.4    1.0019205   0.93145421    1.0802698    5.9292845    1379.4982    3922.9667    5.6016797   0.12368816 0.0036410366    4.0475228    0.9942857   0.93077554    1.0802698    2.7471779            0            0            0            0        33340            1            1            4    5228.0098            0 
+Loop time of 0.0795826 on 4 procs for 67 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1600    401.08407   -13036.858    2.3069745     2462.029            9   0.26709092          0.4    1.0019205   0.93145421    1.0802698    5.9292845    1379.4982    3922.9667      5.83625   0.12368816 0.0036410366    4.0475228    0.9942857   0.93077554    1.0802698    2.7471779            0            0            0            0        32000            1            1            4    5216.9826            0 
+    1700    390.57304   -13035.592   0.75779993    1179.4046            6   0.28725951          0.4    1.0026134    0.9311732    1.0858013    5.9292845    1379.4982    3901.4109    5.8264706   0.12155477  0.003634528    4.0475228   0.99473366   0.93050239    1.0858013    2.7471779            0            0            0            0        34000            1            1            4    400.12853            0 
+Loop time of 0.0782826 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1700    390.57304   -13035.592   0.75779993    1179.4046            6   0.28725951          0.4    1.0026134    0.9311732    1.0858013    5.9292845    1379.4982    3901.4109    5.8264706   0.12155477  0.003634528    4.0475228   0.99473366   0.93050239    1.0858013    2.7471779            0            0            0            0        34000            1            1            4    400.12853            0 
+    1769    390.57304   -13102.244   0.75779993    1179.4046            6   0.28725951          0.4    1.0026134    0.9311732    1.0858013    5.9292845    1379.4982    3901.4109    5.5992086   0.12155477  0.003634528    4.0475228   0.99473366   0.93050239    1.0858013    2.7471779            0            0            0            0        35380            1            1            4    400.12853            0 
+Loop time of 0.0823042 on 4 procs for 69 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1700    390.57304   -13035.592   0.75783515    1179.4046            6   0.28725951          0.4    1.0026134    0.9311732    1.0858013    5.9292845    1379.4982    3901.4109    5.8264706   0.12155477  0.003634528    4.0475228   0.99473366   0.93050239    1.0858013    2.7471779            0            0            0            0        34000            1            1            4    400.32271            0 
+    1800    398.05229   -13039.968    1.4993394    4237.7772            6   0.25966095          0.4    1.0035311     0.929455    1.0894688    5.9292845    1379.4982     3874.257    5.8227778   0.11487453 0.0034347868    4.0475228   0.99520141     0.929455    1.0894875    2.7471779            0            0            0            0        36000            1            1            4    5377.4056            0 
+Loop time of 0.07784 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1800    398.05229   -13039.968    1.4993394    4237.7772            6   0.25966095          0.4    1.0035311     0.929455    1.0894688    5.9292845    1379.4982     3874.257    5.8227778   0.11487453 0.0034347868    4.0475228   0.99520141     0.929455    1.0894875    2.7471779            0            0            0            0        36000            1            1            4    5377.4056            0 
+    1870    398.05229   -13102.244    1.4993394    4237.7772            6   0.25966095          0.4    1.0035311     0.929455    1.0894688    5.9292845    1379.4982     3874.257    5.6048128   0.11487453 0.0034347868    4.0475228   0.99520141     0.929455    1.0894875    2.7471779            0            0            0            0        37400            1            1            4    5377.4056            0 
+Loop time of 0.0836493 on 4 procs for 70 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1800    398.05229   -13039.968    1.4993215    4237.7772            6   0.25966095          0.4    1.0035311     0.929455    1.0894688    5.9292845    1379.4982     3874.257    5.8227778   0.11487453 0.0034347868    4.0475228   0.99520141     0.929455    1.0894875    2.7471779            0            0            0            0        36000            1            1            4    5369.6279            0 
+    1900    413.06274   -13039.873    1.3826465    7339.1562            5   0.22717549          0.4     0.999658   0.92261066    1.0792934    5.9292845    1379.4982    4011.3391    5.8310526   0.11065981 0.0032493907    4.0475228   0.99552368   0.92261066    1.0894875    2.7471779            0            0            0            0        38000            1            1            4     10818.73            0 
+Loop time of 0.0805019 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1900    413.06274   -13039.873    1.3826465    7339.1562            5   0.22717549          0.4     0.999658   0.92261066    1.0792934    5.9292845    1379.4982    4011.3391    5.8310526   0.11065981 0.0032493907    4.0475228   0.99552368   0.92261066    1.0894875    2.7471779            0            0            0            0        38000            1            1            4     10818.73            0 
+    1969    413.06274   -13102.244    1.3826465    7339.1562            5   0.22717549          0.4     0.999658   0.92261066    1.0792934    5.9292845    1379.4982    4011.3391    5.6267141   0.11065981 0.0032493907    4.0475228   0.99552368   0.92261066    1.0894875    2.7471779            0            0            0            0        39380            1            1            4     10818.73            0 
+Loop time of 0.0814294 on 4 procs for 69 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    1900    413.06274   -13039.873    1.3825572    7339.1562            5   0.22717549          0.4     0.999658   0.92261066    1.0792934    5.9292845    1379.4982    4011.3391    5.8310526   0.11065981 0.0032493907    4.0475228   0.99552368   0.92261066    1.0894875    2.7471779            0            0            0            0        38000            1            1            4    10781.258            0 
+    2000    399.72382   -13038.217    1.1754671    2735.2303            6   0.31028081          0.4   0.99858834   0.92453074    1.0748234    5.9292845    1379.4982    4045.0012        5.811   0.10841507 0.0030975736    4.0475228   0.99572029     0.922532    1.0894875    2.7471779            0            0            0            0        40000            1            1            4    2622.0819            1 
+Loop time of 0.0794099 on 4 procs for 100 steps with 2354 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
+    2000    399.72382   -13038.217    1.1754671    2735.2303            6   0.31028081          0.4   0.99858834   0.92453074    1.0748234    5.9292845    1379.4982    4045.0012        5.811   0.10841507 0.0030975736    4.0475228   0.99572029     0.922532    1.0894875    2.7471779            0            0            0            0        40000            1            1            4    2622.0819            1 
+    2071    399.72382   -13102.244    1.1754671    2735.2303            6   0.31028081          0.4   0.99858834   0.92453074    1.0748234    5.9292845    1379.4982    4045.0012    5.6117817   0.10841507 0.0030975736    4.0475228   0.99572029     0.922532    1.0894875    2.7471779            0            0            0            0        41420            1            1            4    2622.0819            1 
+Loop time of 0.0837786 on 4 procs for 71 steps with 2354 atoms
+
+Final hyper stats ...
+
+Cummulative quantities for fix hyper:
+  hyper time = 40000
+  time boost factor = 4000
+  event timesteps = 1
+  # of atoms in events = 1
+Quantities for this hyper run:
+  event timesteps = 1
+  # of atoms in events = 1
+  max length of any bond = 4.04752
+  max drift distance of any atom = 2.74718
+  fraction of biased bonds with zero bias = 0.108415
+  fraction of biased bonds with negative strain = 0.00309757
+Current quantities:
+  ave bonds/atom = 5.92928
+Cummulative quantities specific to fix hyper/local:
+  # of new bonds formed = 4
+  max bonds/atom = 12
+Quantities for this hyper run specific to fix hyper/local:
+  ave boost for all bonds/step = 4045
+  ave biased bonds/step = 5.811
+  ave bias coeff of all bonds = 0.99572
+  min bias coeff of any bond = 0.922532
+  max bias coeff of any bond = 1.08949
+  max dist from my subbox of any non-maxstrain bond ghost atom = 0
+  max dist from my box of any bond ghost atom = 0
+  count of bond ghost neighbors not found on reneighbor steps = 0
+  bias overlaps = 0
+  CPU time for bond builds = 0.00247526
+Current quantities specific to fix hyper/local:
+  neighbor bonds/bond = 1379.5
+  ave boost coeff for all bonds = 0.998588
+
+Loop time of 3.52992 on 4 procs for 2000 steps with 2354 atoms
+
+Performance: 244.765 ns/day, 0.098 hours/ns, 566.585 timesteps/s
+114.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Hyper stats:
+  Dynamics time (%) = 1.59393 (45.1549)
+  Quench   time (%) = 1.71979 (48.7203)
+  Other    time (%) = 0.219256 (6.21136)
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4735     | 2.4914     | 2.5135     |   1.0 | 70.58
+Neigh   | 0.11535    | 0.11805    | 0.12056    |   0.7 |  3.34
+Comm    | 0.20734    | 0.21636    | 0.22119    |   1.1 |  6.13
+Output  | 0.00089145 | 0.0014108  | 0.0029645  |   2.4 |  0.04
+Modify  | 0.47314    | 0.48343    | 0.49869    |   1.4 | 13.70
+Other   |            | 0.2193     |            |       |  6.21
+
+Nlocal:    588.5 ave 607 max 577 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:    1965.75 ave 1977 max 1947 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs:    13775.8 ave 14221 max 13511 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+FullNghs:  136920 ave 139934 max 133922 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 547678
+Ave neighs/atom = 232.658
+Neighbor list builds = 193
+Dangerous builds = 0
+Total wall time: 0:00:04

examples/hyper/log.9Jan20.hyper.local.g++.4

@@ -1,646 +0,0 @@
-LAMMPS (09 Jan 2020)
-# 3d EAM surface for local HD
-
-# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
-# hop event on (100) surface is same distance
-# exchange event is 2 atoms moving same distance
-
-variable        Tequil index 400.0
-variable        Vmax index 0.4
-variable        qfactor index 0.3
-variable        cutbond index 3.2
-variable        Dcut index 10.0
-variable        cutevent index 1.1
-variable        alpha index 200.0
-variable        boost index 4000.0
-variable        ghostcut index 12.0
-variable        steps index 2000
-variable        nevent index 100
-variable        nx index 2
-variable        ny index 2
-variable        zoom index 1.8
-variable        seed index 3875984
-variable        tol index 1.0e-15
-variable        add index 50
-
-units           metal
-atom_style	atomic
-atom_modify     map array
-boundary        p p p
-comm_modify     cutoff ${ghostcut}
-comm_modify     cutoff 12.0
-
-lattice		fcc 3.92
-Lattice spacing in x,y,z = 3.92 3.92 3.92
-region		box block 0 6 0 6 0 4
-create_box	2 box
-Created orthogonal box = (0 0 0) to (23.52 23.52 15.68)
-  2 by 2 by 1 MPI processor grid
-create_atoms	1 box
-Created 576 atoms
-  create_atoms CPU = 0 secs
-
-mass            * 1.0
-
-change_box      all z final -0.1 5.0 boundary p p f
-  orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6)
-
-# replicate in xy
-
-replicate       ${nx} ${ny} 1
-replicate       2 ${ny} 1
-replicate       2 2 1
-  orthogonal box = (0 0 -0.392) to (47.04 47.04 19.6)
-  2 by 2 by 1 MPI processor grid
-  2304 atoms
-  replicate CPU = 0.00200009 secs
-
-# add adatoms
-
-include         adatoms.list.${add}
-include         adatoms.list.50
-create_atoms 1 single 5 9 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4.5 7.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6 6 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 5 6 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4.5 1.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6.5 7.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 10.5 5.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 2.5 1.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3.5 4.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 0 10 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 11 10 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6.5 10.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3.5 5.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 7.5 10.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1.5 1.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1.5 6.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 7 2 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4 0 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 9 0 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4 9 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 10 7 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4 4 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 9.5 2.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1 5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 7 10 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 0 4 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1 10 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 7.5 6.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4 10 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6.5 3.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3 6 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 8.5 4.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6.5 0.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1 4 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 8.5 11.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3 9 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 2 3 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 6.5 8.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1 0 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 0.5 10.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 4 11 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3 5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 0 1 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 2 11 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 2 0 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 7.5 11.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 1 7 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 3.5 10.5 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 0 2 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-create_atoms 1 single 8 4 4
-Created 1 atoms
-  create_atoms CPU = 0 secs
-
-# define frozen substrate and mobile atoms
-
-region          base block INF INF INF INF 0 1.8
-set             region base type 2
-  1152 settings made for type
-group           base type 2
-1152 atoms in group base
-group           mobile type 1
-1202 atoms in group mobile
-
-# pair style
-
-pair_style	eam/alloy
-pair_coeff	* * ptvoterlammps.eam Pt Pt
-
-neighbor	0.5 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 mobile nve
-fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 400.0 1.0 3875984 zero yes
-
-timestep	0.005
-
-compute         tmobile mobile temp
-
-thermo		100
-thermo_modify   temp tmobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:485)
-
-# thermal equilibration
-
-run             1000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.07583
-  ghost atom cutoff = 12
-  binsize = 3.03792, bins = 16 16 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, 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) = 3.082 | 3.082 | 3.082 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -13067.188            0   -13067.188   -53763.139 
-     100    216.49187   -13065.694            0   -13032.085   -24077.115 
-     200    285.11905   -13057.047            0   -13012.785   -38815.844 
-     300    321.67264   -13048.005            0   -12998.068   -29296.124 
-     400    352.90893   -13045.707            0    -12990.92   -34630.884 
-     500     371.9393   -13041.234            0   -12983.494   -28913.827 
-     600    379.08135    -13040.06            0   -12981.211     -33399.8 
-     700    388.73836   -13039.691            0   -12979.343   -29446.954 
-     800    402.13628   -13040.606            0   -12978.178   -33026.861 
-     900    389.43806   -13036.884            0   -12976.427   -30328.658 
-    1000    388.66198   -13037.479            0   -12977.142   -30859.145 
-Loop time of 1.28003 on 4 procs for 1000 steps with 2354 atoms
-
-Performance: 337.492 ns/day, 0.071 hours/ns, 781.232 timesteps/s
-100.0% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.054      | 1.077      | 1.094      |   1.6 | 84.14
-Neigh   | 0.054002   | 0.056502   | 0.060002   |   1.0 |  4.41
-Comm    | 0.087002   | 0.11025    | 0.133      |   5.6 |  8.61
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0.031003   | 0.031502   | 0.032002   |   0.3 |  2.46
-Other   |            | 0.00475    |            |       |  0.37
-
-Nlocal:    588.5 ave 592 max 581 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-Nghost:    1964 ave 1973 max 1959 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
-Neighs:    14148.8 ave 14283 max 13931 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 56595
-Ave neighs/atom = 24.0421
-Neighbor list builds = 91
-Dangerous builds = 0
-reset_timestep  0
-
-# pin base so will not move during quenches
-
-fix             freeze base setforce 0.0 0.0 0.0
-
-# event detection
-
-compute         event all event/displace ${cutevent}
-compute         event all event/displace 1.1
-
-# hyper/local
-
-fix             HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 4000.0
-
-# thermo output
-
-thermo_style    custom step temp pe f_HL f_HL[*]
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708)
-
-thermo_modify   lost ignore
-thermo_modify   temp tmobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:485)
-
-thermo          ${nevent}
-thermo          100
-
-# dump
-
-region          substrate block INF INF INF INF 1.8 3.8
-region          adatoms block INF INF INF INF 3.8 INF
-variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
-
-dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
-dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
-dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
-
-# run
-
-hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           2000 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           2000 100 HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           2000 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
-hyper           2000 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
-WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:131)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.07583
-  ghost atom cutoff = 12
-  binsize = 3.03792, bins = 16 16 7
-  3 neighbor lists, perpetual/occasional/extra = 1 2 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix hyper/local, occasional
-      attributes: full, newton on, cut 10
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (3) fix hyper/local, occasional, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 6.666 | 6.666 | 6.666 Mbytes
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-       0    388.66198   -13037.479            0            1            0            0          0.4            1            0            0            0            0            0            0            0            0            0            0        1e+20            0            0            0            0            0            0            0            0            0            0            1            0 
-      77    388.66198   -13101.057            0            1            0            0          0.4            1            0            0            0            0            0            0            0            0            0            0        1e+20            0            0            0            0            0            0         1540            0            0            0            1            0 
-Loop time of 0.179004 on 4 procs for 77 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-       0    388.66198   -13037.479    2.1560984            0            7   0.19075508          0.4            0            0            0    5.9276206    1380.4406            0            0            0            0    3.2725891            0        1e+20            0            0            0            0            0            0            0            0            0            0    10345.205            0 
-     100    398.83324   -13036.879    2.1057282    8397.3244            7   0.17605069          0.4   0.99370412   0.98222607    1.0036767    5.9276206    1380.4406    8029.3662         4.83            0            0    3.3896963    0.9967648   0.98222607    1.0036767            0            0            0            0            0         2000            0            0            0    8152.8259            0 
-Loop time of 0.127003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     100    398.83324   -13036.879    2.1057282    8397.3244            7   0.17605069          0.4   0.99370412   0.98222607    1.0036767    5.9276206    1380.4406    8029.3662         4.83            0            0    3.3896963    0.9967648   0.98222607    1.0036767            0            0            0            0            0         2000            0            0            0    8152.8259            0 
-     167    398.83324   -13101.057    2.1057282    8397.3244            7   0.17605069          0.4   0.99370412   0.98222607    1.0036767    5.9276206    1380.4406    8029.3662    2.8922156            0            0    3.3896963    0.9967648   0.98222607    1.0036767            0            0            0            0            0         3340            0            0            0    8152.8259            0 
-Loop time of 0.127003 on 4 procs for 67 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     100    398.83324   -13036.879    2.1055533    8397.3244            7   0.17605069          0.4   0.99370412   0.98222607    1.0036767    5.9276206    1380.4406    8029.3662         4.83            0            0    3.3896963    0.9967648   0.98222607    1.0036767            0            0            0            0            0         2000            0            0            0    8129.9856            0 
-     200    389.68041     -13036.5    1.3143359    4136.9005            6   0.31228203          0.4   0.99085481   0.96933773    1.0092702    5.9276206    1380.4406    6926.4597         5.43  0.035911602 0.00092081031    3.7338089   0.99450416   0.96933773    1.0092702            0            0            0            0            0         4000            0            0            0    3361.4715            1 
-Loop time of 0.127003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     200    389.68041     -13036.5    1.3143359    4136.9005            6   0.31228203          0.4   0.99085481   0.96933773    1.0092702    5.9276206    1380.4406    6926.4597         5.43  0.035911602 0.00092081031    3.7338089   0.99450416   0.96933773    1.0092702            0            0            0            0            0         4000            0            0            0    3361.4715            1 
-     270    389.68041   -13101.057    1.3143359    4136.9005            6   0.31228203          0.4   0.99085481   0.96933773    1.0092702    5.9276206    1380.4406    6926.4597    4.0222222  0.035911602 0.00092081031    3.7338089   0.99450416   0.96933773    1.0092702            0            0            0            0            0         5400            0            0            0    3361.4715            1 
-Loop time of 0.134003 on 4 procs for 70 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     200    389.68041     -13036.5    1.3143057    4136.9005            6   0.31228203          0.4   0.99085481   0.96933773    1.0092702    5.9276206    1380.4406    6926.4597         5.43  0.035911602 0.00092081031    3.7338089   0.99450416   0.96933773    1.0092702            0            0            0            0            0         4000            0            0            0    3356.2384            1 
-     300    410.34512   -13036.301    1.3677603    4656.4226            6   0.33838934          0.4   0.99110308   0.96057751    1.0154382    5.9276206    1380.4406    5898.0094         5.44  0.036764706 0.0006127451    3.7338089    0.9934181   0.96057751    1.0154382            0            0            0            0            0         6000            0            0            0    4213.1218            1 
-Loop time of 0.129003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     300    410.34512   -13036.301    1.3677603    4656.4226            6   0.33838934          0.4   0.99110308   0.96057751    1.0154382    5.9276206    1380.4406    5898.0094         5.44  0.036764706 0.0006127451    3.7338089    0.9934181   0.96057751    1.0154382            0            0            0            0            0         6000            0            0            0    4213.1218            1 
-     375    410.34512   -13101.057    1.3677603    4656.4226            6   0.33838934          0.4   0.99110308   0.96057751    1.0154382    5.9276206    1380.4406    5898.0094        4.352  0.036764706 0.0006127451    3.7338089    0.9934181   0.96057751    1.0154382            0            0            0            0            0         7500            0            0            0    4213.1218            1 
-Loop time of 0.143004 on 4 procs for 75 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     300    410.34512   -13036.301    1.3677058    4656.4226            6   0.33838934          0.4   0.99110308   0.96057751    1.0154382    5.9276206    1380.4406    5898.0094         5.44  0.036764706 0.0006127451    3.7338089    0.9934181   0.96057751    1.0154382            0            0            0            0            0         6000            0            0            0    4207.0688            1 
-     400    408.54896   -13036.835     1.090295    4172.0981            6   0.46750515          0.4   0.99130905   0.95644819    1.0207114    5.9276206    1380.4406    5390.5516        5.365  0.095060578 0.00046598322    3.9885296    0.9928942   0.95644819    1.0207114            0            0            0            0            0         8000            0            0            0    3865.6547            3 
-Loop time of 0.126003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     400    408.54896   -13036.835     1.090295    4172.0981            6   0.46750515          0.4   0.99130905   0.95644819    1.0207114    5.9276206    1380.4406    5390.5516        5.365  0.095060578 0.00046598322    3.9885296    0.9928942   0.95644819    1.0207114            0            0            0            0            0         8000            0            0            0    3865.6547            3 
-     471    408.54896   -13101.694     1.090295    4172.0981            6   0.46750515          0.4   0.99130905   0.95644819    1.0207114    5.9276206    1380.4406    5390.5516    4.5562633  0.095060578 0.00046598322    3.9885296    0.9928942   0.95644819    1.0207114            0            0            0            0            0         9420            0            0            0    3865.6547            3 
-Loop time of 0.131003 on 4 procs for 71 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     400    408.54896   -13036.835     1.090341    4171.5126            6   0.33910027          0.4   0.99116994   0.95644819    1.0207114    5.9284526    1380.3372    5390.5516        5.365  0.095060578 0.00046598322    3.9885296    0.9928942   0.95644819    1.0207114    2.7381277            0            0            0            0         8000            1            1            3    3863.7908            2 
-     500    408.04798   -13035.819     1.887274    2622.1876            8   0.25727119          0.4   0.99128739   0.95020853    1.0240862    5.9284526    1380.3372    5115.3824         5.63  0.077087034 0.00071047957    3.9885296   0.99251152   0.95020853    1.0240862    2.7381277            0            0            0            0        10000            1            1            3    4184.3452            0 
-Loop time of 0.128003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     500    408.04798   -13035.819     1.887274    2622.1876            8   0.25727119          0.4   0.99128739   0.95020853    1.0240862    5.9284526    1380.3372    5115.3824         5.63  0.077087034 0.00071047957    3.9885296   0.99251152   0.95020853    1.0240862    2.7381277            0            0            0            0        10000            1            1            3    4184.3452            0 
-     569    408.04798   -13101.694     1.887274    2622.1876            8   0.25727119          0.4   0.99128739   0.95020853    1.0240862    5.9284526    1380.3372    5115.3824    4.9472759  0.077087034 0.00071047957    3.9885296   0.99251152   0.95020853    1.0240862    2.7381277            0            0            0            0        11380            1            1            3    4184.3452            0 
-Loop time of 0.135003 on 4 procs for 69 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     500    408.04798   -13035.819    1.8872278    2622.1876            8   0.25727119          0.4   0.99128739   0.95020853    1.0240862    5.9284526    1380.3372    5115.3824         5.63  0.077087034 0.00071047957    3.9885296   0.99251152   0.95020853    1.0240862    2.7381277            0            0            0            0        10000            1            1            3    4177.8105            0 
-     600     419.0918    -13035.34    1.0950129    5050.5345            5   0.30933918          0.4   0.99315523   0.94243697       1.0303    5.9284526    1380.3372    4730.2494    5.7483333  0.082052769 0.00057987823    4.0620002   0.99251861   0.94243697       1.0303    2.7381277            0            0            0            0        12000            1            1            3    4375.7612            1 
-Loop time of 0.128003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     600     419.0918    -13035.34    1.0950129    5050.5345            5   0.30933918          0.4   0.99315523   0.94243697       1.0303    5.9284526    1380.3372    4730.2494    5.7483333  0.082052769 0.00057987823    4.0620002   0.99251861   0.94243697       1.0303    2.7381277            0            0            0            0        12000            1            1            3    4375.7612            1 
-     669     419.0918   -13101.694    1.0950129    5050.5345            5   0.30933918          0.4   0.99315523   0.94243697       1.0303    5.9284526    1380.3372    4730.2494    5.1554559  0.082052769 0.00057987823    4.0620002   0.99251861   0.94243697       1.0303    2.7381277            0            0            0            0        13380            1            1            3    4375.7612            1 
-Loop time of 0.131003 on 4 procs for 69 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     600     419.0918    -13035.34    1.0949592    5050.5345            5   0.30933918          0.4   0.99315523   0.94243697       1.0303    5.9284526    1380.3372    4730.2494    5.7483333  0.082052769 0.00057987823    4.0620002   0.99251861   0.94243697       1.0303    2.7381277            0            0            0            0        12000            1            1            3    4366.2434            1 
-     700    404.99792   -13038.375    1.7496634    5457.7386            6   0.20603012          0.4   0.99311471   0.93767338    1.0364661    5.9284526    1380.3372    4629.6326    5.7757143  0.077170418 0.00049468217    4.0620002   0.99261201   0.93732488    1.0364661    2.7381277            0            0            0            0        14000            1            1            3    5897.4776            0 
-Loop time of 0.128003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     700    404.99792   -13038.375    1.7496634    5457.7386            6   0.20603012          0.4   0.99311471   0.93767338    1.0364661    5.9284526    1380.3372    4629.6326    5.7757143  0.077170418 0.00049468217    4.0620002   0.99261201   0.93732488    1.0364661    2.7381277            0            0            0            0        14000            1            1            3    5897.4776            0 
-     775    404.99792   -13101.694    1.7496634    5457.7386            6   0.20603012          0.4   0.99311471   0.93767338    1.0364661    5.9284526    1380.3372    4629.6326    5.2167742  0.077170418 0.00049468217    4.0620002   0.99261201   0.93732488    1.0364661    2.7381277            0            0            0            0        15500            1            1            3    5897.4776            0 
-Loop time of 0.166004 on 4 procs for 75 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     700    404.99792   -13038.375    1.7495648    5457.7386            6   0.20603012          0.4   0.99311471   0.93767338    1.0364661    5.9284526    1380.3372    4629.6326    5.7757143  0.077170418 0.00049468217    4.0620002   0.99261201   0.93732488    1.0364661    2.7381277            0            0            0            0        14000            1            1            3    5888.5728            0 
-     800    421.10795   -13037.462    1.8512835    3051.7064            8   0.31933951          0.4    0.9902351   0.93814672    1.0426311    5.9284526    1380.3372    4781.2974       5.8125  0.070322581 0.00043010753    4.0620002   0.99242754   0.93732488    1.0426311    2.7381277            0            0            0            0        16000            1            1            3    3122.0342            1 
-Loop time of 0.245005 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     800    421.10795   -13037.462    1.8512835    3051.7064            8   0.31933951          0.4    0.9902351   0.93814672    1.0426311    5.9284526    1380.3372    4781.2974       5.8125  0.070322581 0.00043010753    4.0620002   0.99242754   0.93732488    1.0426311    2.7381277            0            0            0            0        16000            1            1            3    3122.0342            1 
-     869    421.10795   -13101.694    1.8512835    3051.7064            8   0.31933951          0.4    0.9902351   0.93814672    1.0426311    5.9284526    1380.3372    4781.2974    5.3509781  0.070322581 0.00043010753    4.0620002   0.99242754   0.93732488    1.0426311    2.7381277            0            0            0            0        17380            1            1            3    3122.0342            1 
-Loop time of 0.180005 on 4 procs for 69 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     800    421.10795   -13037.462    1.8512626    3051.7064            8   0.31933951          0.4    0.9902351   0.93814672    1.0426311    5.9284526    1380.3372    4781.2974       5.8125  0.070322581 0.00043010753    4.0620002   0.99242754   0.93732488    1.0426311    2.7381277            0            0            0            0        16000            1            1            3    3118.9745            1 
-     900    424.48211   -13036.231    1.5461807    1757.5544            7   0.25079261          0.4   0.99160613   0.94071212    1.0485957    5.9284526    1380.3372     4596.991    5.8511111  0.073300418 0.00037979491    4.0620002   0.99224254   0.93732488    1.0485957    2.7381277            0            0            0            0        18000            1            1            3     1803.828            0 
-Loop time of 0.158003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     900    424.48211   -13036.231    1.5461807    1757.5544            7   0.25079261          0.4   0.99160613   0.94071212    1.0485957    5.9284526    1380.3372     4596.991    5.8511111  0.073300418 0.00037979491    4.0620002   0.99224254   0.93732488    1.0485957    2.7381277            0            0            0            0        18000            1            1            3     1803.828            0 
-     969    424.48211   -13101.694    1.5461807    1757.5544            7   0.25079261          0.4   0.99160613   0.94071212    1.0485957    5.9284526    1380.3372     4596.991    5.4344685  0.073300418 0.00037979491    4.0620002   0.99224254   0.93732488    1.0485957    2.7381277            0            0            0            0        19380            1            1            3     1803.828            0 
-Loop time of 0.165004 on 4 procs for 69 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-     900    424.48211   -13036.231    1.5462201    1757.5544            7   0.25079261          0.4   0.99160613   0.94071212    1.0485957    5.9284526    1380.3372     4596.991    5.8511111  0.073300418 0.00037979491    4.0620002   0.99224254   0.93732488    1.0485957    2.7381277            0            0            0            0        18000            1            1            3    1803.5841            0 
-    1000    392.14281   -13033.226    1.3114425    4884.4012            6   0.28781471          0.4   0.99342697   0.93855058    1.0449678    5.9284526    1380.3372    4420.7581        5.862  0.076765609 0.00034118048    4.0620002   0.99230204   0.93732488    1.0514799    2.7381277            0            0            0            0        20000            1            1            3    6648.5089            0 
-Loop time of 0.159004 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1000    392.14281   -13033.226    1.3114425    4884.4012            6   0.28781471          0.4   0.99342697   0.93855058    1.0449678    5.9284526    1380.3372    4420.7581        5.862  0.076765609 0.00034118048    4.0620002   0.99230204   0.93732488    1.0514799    2.7381277            0            0            0            0        20000            1            1            3    6648.5089            0 
-    1070    392.14281   -13101.694    1.3114425    4884.4012            6   0.28781471          0.4   0.99342697   0.93855058    1.0449678    5.9284526    1380.3372    4420.7581    5.4785047  0.076765609 0.00034118048    4.0620002   0.99230204   0.93732488    1.0514799    2.7381277            0            0            0            0        21400            1            1            3    6648.5089            0 
-Loop time of 0.167004 on 4 procs for 70 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1000    392.14281   -13033.226    1.3113308    4884.4012            6   0.28781471          0.4   0.99342697   0.93855058    1.0449678    5.9284526    1380.3372    4420.7581        5.862  0.076765609 0.00034118048    4.0620002   0.99230204   0.93732488    1.0514799    2.7381277            0            0            0            0        20000            1            1            3    6627.3707            0 
-    1100    403.51397    -13035.66   0.54686506    3968.0952            5   0.36081738          0.4   0.99442104   0.93685489    1.0457452    5.9284526    1380.3372    4324.6709         5.89  0.077944127 0.00030868961    4.0620002   0.99241625   0.93604385    1.0514799    2.7381277            0            0            0            0        22000            1            1            3    1724.5221            2 
-Loop time of 0.143003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1100    403.51397    -13035.66   0.54686506    3968.0952            5   0.36081738          0.4   0.99442104   0.93685489    1.0457452    5.9284526    1380.3372    4324.6709         5.89  0.077944127 0.00030868961    4.0620002   0.99241625   0.93604385    1.0514799    2.7381277            0            0            0            0        22000            1            1            3    1724.5221            2 
-    1170    403.51397   -13101.694   0.54686506    3968.0952            5   0.36081738          0.4   0.99442104   0.93685489    1.0457452    5.9284526    1380.3372    4324.6709    5.5376068  0.077944127 0.00030868961    4.0620002   0.99241625   0.93604385    1.0514799    2.7381277            0            0            0            0        23400            1            1            3    1724.5221            2 
-Loop time of 0.134003 on 4 procs for 70 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1100    403.51397    -13035.66   0.54686188    3968.0952            5   0.36081738          0.4   0.99442104   0.93685489    1.0457452    5.9284526    1380.3372    4324.6709         5.89  0.077944127 0.00030868961    4.0620002   0.99241625   0.93604385    1.0514799    2.7381277            0            0            0            0        22000            1            1            3    1722.7748            2 
-    1200    407.58933   -13037.757   0.83605065    5192.3954            5    0.3055123          0.4   0.99647568   0.93650885    1.0519936    5.9284526    1380.3372     4188.034    5.8883333  0.092838947 0.0022643646    4.0620002   0.99266277    0.9344152    1.0519936    2.7381277            0            0            0            0        24000            1            1            3    3708.6014            1 
-Loop time of 0.127003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1200    407.58933   -13037.757   0.83605065    5192.3954            5    0.3055123          0.4   0.99647568   0.93650885    1.0519936    5.9284526    1380.3372     4188.034    5.8883333  0.092838947 0.0022643646    4.0620002   0.99266277    0.9344152    1.0519936    2.7381277            0            0            0            0        24000            1            1            3    3708.6014            1 
-    1275    407.58933   -13101.694   0.83605065    5192.3954            5    0.3055123          0.4   0.99647568   0.93650885    1.0519936    5.9284526    1380.3372     4188.034    5.5419608  0.092838947 0.0022643646    4.0620002   0.99266277    0.9344152    1.0519936    2.7381277            0            0            0            0        25500            1            1            3    3708.6014            1 
-Loop time of 0.147004 on 4 procs for 75 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1200    407.58933   -13037.757   0.83600436    5192.3954            5    0.3055123          0.4   0.99647568   0.93650885    1.0519936    5.9284526    1380.3372     4188.034    5.8883333  0.092838947 0.0022643646    4.0620002   0.99266277    0.9344152    1.0519936    2.7381277            0            0            0            0        24000            1            1            3    3695.4259            1 
-    1300    397.34752    -13035.27     1.143529    3889.5642            6   0.59455796          0.4   0.99734951   0.93577374    1.0582257    5.9284526    1380.3372    4130.5503    5.9123077  0.094977882  0.002081707    4.1048198   0.99297572    0.9344152    1.0582257    2.7381277            0            0            0            0        26000            1            1            3    2236.4525            2 
-Loop time of 0.129003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1300    397.34752    -13035.27     1.143529    3889.5642            6   0.59455796          0.4   0.99734951   0.93577374    1.0582257    5.9284526    1380.3372    4130.5503    5.9123077  0.094977882  0.002081707    4.1048198   0.99297572    0.9344152    1.0582257    2.7381277            0            0            0            0        26000            1            1            3    2236.4525            2 
-    1379    397.34752   -13102.882     1.143529    3889.5642            6   0.59455796          0.4   0.99734951   0.93577374    1.0582257    5.9284526    1380.3372    4130.5503    5.5736041  0.094977882  0.002081707    4.1048198   0.99297572    0.9344152    1.0582257    2.7381277            0            0            0            0        27580            1            1            3    2236.4525            2 
-Loop time of 0.130003 on 4 procs for 79 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1300    397.34752    -13035.27    0.8513344    3888.4728            5   0.43479061          0.4   0.99706967   0.93577374    1.0582257    5.9301165    1379.4348    4130.5503    5.9123077  0.094977882  0.002081707    4.1048198   0.99297572    0.9344152    1.0582257    2.7473869            0            0            0            0        26000            2            2            7    1674.6282            2 
-    1400    406.75788   -13035.822   0.98339012    2583.5703            5   0.26687439          0.4   0.99725016   0.93341809    1.0565516    5.9301165    1379.4348    4125.2065          5.9   0.09503632  0.001937046    4.1048198   0.99327179   0.93335055    1.0582257    2.7473869            0            0            0            0        28000            2            2            7    1900.8002            0 
-Loop time of 0.145003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1400    406.75788   -13035.822   0.98339012    2583.5703            5   0.26687439          0.4   0.99725016   0.93341809    1.0565516    5.9301165    1379.4348    4125.2065          5.9   0.09503632  0.001937046    4.1048198   0.99327179   0.93335055    1.0582257    2.7473869            0            0            0            0        28000            2            2            7    1900.8002            0 
-    1471    406.75788   -13102.882   0.98339012    2583.5703            5   0.26687439          0.4   0.99725016   0.93341809    1.0565516    5.9301165    1379.4348    4125.2065    5.6152277   0.09503632  0.001937046    4.1048198   0.99327179   0.93335055    1.0582257    2.7473869            0            0            0            0        29420            2            2            7    1900.8002            0 
-Loop time of 0.134003 on 4 procs for 71 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1400    406.75788   -13035.822   0.98339747    2583.5703            5   0.26687439          0.4   0.99725016   0.93341809    1.0565516    5.9301165    1379.4348    4125.2065          5.9   0.09503632  0.001937046    4.1048198   0.99327179   0.93335055    1.0582257    2.7473869            0            0            0            0        28000            2            2            7    1898.7054            0 
-    1500    403.04712   -13038.033    1.7734093    2587.2539            8   0.26021596          0.4   0.99949004   0.93136824    1.0627109    5.9301165    1379.4348    4021.2913        5.914  0.094465111 0.0018036298    4.1048198   0.99360825   0.93115568    1.0627109    2.7473869            0            0            0            0        30000            2            2            7    4239.5287            0 
-Loop time of 0.124003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1500    403.04712   -13038.033    1.7734093    2587.2539            8   0.26021596          0.4   0.99949004   0.93136824    1.0627109    5.9301165    1379.4348    4021.2913        5.914  0.094465111 0.0018036298    4.1048198   0.99360825   0.93115568    1.0627109    2.7473869            0            0            0            0        30000            2            2            7    4239.5287            0 
-    1568    403.04712   -13102.882    1.7734093    2587.2539            8   0.26021596          0.4   0.99949004   0.93136824    1.0627109    5.9301165    1379.4348    4021.2913    5.6575255  0.094465111 0.0018036298    4.1048198   0.99360825   0.93115568    1.0627109    2.7473869            0            0            0            0        31360            2            2            7    4239.5287            0 
-Loop time of 0.135003 on 4 procs for 68 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1500    403.04712   -13038.033    1.7733495    2587.2539            8   0.26021596          0.4   0.99949004   0.93136824    1.0627109    5.9301165    1379.4348    4021.2913        5.914  0.094465111 0.0018036298    4.1048198   0.99360825   0.93115568    1.0627109    2.7473869            0            0            0            0        30000            2            2            7    4227.4184            0 
-    1600    413.63587   -13039.863   0.67705876    2150.6698            5   0.32653141          0.4    1.0004587    0.9309105      1.06525    5.9301165    1379.4348    3981.2133      5.93375  0.090478197 0.0016852749    4.1048198   0.99397193   0.92879897      1.06525    2.7473869            0            0            0            0        32000            2            2            7    822.48747            1 
-Loop time of 0.132003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1600    413.63587   -13039.863   0.67705876    2150.6698            5   0.32653141          0.4    1.0004587    0.9309105      1.06525    5.9301165    1379.4348    3981.2133      5.93375  0.090478197 0.0016852749    4.1048198   0.99397193   0.92879897      1.06525    2.7473869            0            0            0            0        32000            2            2            7    822.48747            1 
-    1669    413.63587   -13102.882   0.67705876    2150.6698            5   0.32653141          0.4    1.0004587    0.9309105      1.06525    5.9301165    1379.4348    3981.2133    5.6884362  0.090478197 0.0016852749    4.1048198   0.99397193   0.92879897      1.06525    2.7473869            0            0            0            0        33380            2            2            7    822.48747            1 
-Loop time of 0.135003 on 4 procs for 69 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1600    413.63587   -13039.863   0.67707996    2150.6698            5   0.32653141          0.4    1.0004587    0.9309105      1.06525    5.9301165    1379.4348    3981.2133      5.93375  0.090478197 0.0016852749    4.1048198   0.99397193   0.92879897      1.06525    2.7473869            0            0            0            0        32000            2            2            7    822.44597            1 
-    1700    410.04422   -13040.035    1.0190943    1598.6072            7   0.29206253          0.4    1.0030056   0.92869822    1.0714971    5.9301165    1379.4348    3886.4362    5.9435294  0.093527316 0.0015835313    4.1048198   0.99441728   0.92869822    1.0714971    2.7473869            0            0            0            0        34000            2            2            7    1041.7855            0 
-Loop time of 0.129003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1700    410.04422   -13040.035    1.0190943    1598.6072            7   0.29206253          0.4    1.0030056   0.92869822    1.0714971    5.9301165    1379.4348    3886.4362    5.9435294  0.093527316 0.0015835313    4.1048198   0.99441728   0.92869822    1.0714971    2.7473869            0            0            0            0        34000            2            2            7    1041.7855            0 
-    1770    410.04422   -13102.882    1.0190943    1598.6072            7   0.29206253          0.4    1.0030056   0.92869822    1.0714971    5.9301165    1379.4348    3886.4362    5.7084746  0.093527316 0.0015835313    4.1048198   0.99441728   0.92869822    1.0714971    2.7473869            0            0            0            0        35400            2            2            7    1041.7855            0 
-Loop time of 0.145004 on 4 procs for 70 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1700    410.04422   -13040.035    1.0191295    1598.6072            7   0.29206253          0.4    1.0030056   0.92869822    1.0714971    5.9301165    1379.4348    3886.4362    5.9435294  0.093527316 0.0015835313    4.1048198   0.99441728   0.92869822    1.0714971    2.7473869            0            0            0            0        34000            2            2            7    1041.6898            0 
-    1800    413.56333   -13039.872    1.6705072     5357.337            7   0.28802305          0.4    1.0045556   0.92823157    1.0777313    5.9301165    1379.4348     3837.633    5.9366667  0.095545574 0.0014972862    4.1048198   0.99496874   0.92821036    1.0777313    2.7473869            0            0            0            0        36000            2            2            7     7008.708            0 
-Loop time of 0.157003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1800    413.56333   -13039.872    1.6705072     5357.337            7   0.28802305          0.4    1.0045556   0.92823157    1.0777313    5.9301165    1379.4348     3837.633    5.9366667  0.095545574 0.0014972862    4.1048198   0.99496874   0.92821036    1.0777313    2.7473869            0            0            0            0        36000            2            2            7     7008.708            0 
-    1868    413.56333   -13102.882    1.6705072     5357.337            7   0.28802305          0.4    1.0045556   0.92823157    1.0777313    5.9301165    1379.4348     3837.633    5.7205567  0.095545574 0.0014972862    4.1048198   0.99496874   0.92821036    1.0777313    2.7473869            0            0            0            0        37360            2            2            7     7008.708            0 
-Loop time of 0.143003 on 4 procs for 68 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1800    413.56333   -13039.872    1.6703547     5357.337            7   0.28802305          0.4    1.0045556   0.92823157    1.0777313    5.9301165    1379.4348     3837.633    5.9366667  0.095545574 0.0014972862    4.1048198   0.99496874   0.92821036    1.0777313    2.7473869            0            0            0            0        36000            2            2            7    6990.9088            0 
-    1900    389.96327   -13036.384   0.50418526    2970.8471            5    0.2897091          0.4    1.0069357   0.92635421     1.083738    5.9301165    1379.4348    3766.0095    5.9652632  0.092376919 0.0014116817    4.1048198    0.9955231   0.92635421     1.083738    2.7473869            0            0            0            0        38000            2            2            7    102.84786            0 
-Loop time of 0.161004 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1900    389.96327   -13036.384   0.50418526    2970.8471            5    0.2897091          0.4    1.0069357   0.92635421     1.083738    5.9301165    1379.4348    3766.0095    5.9652632  0.092376919 0.0014116817    4.1048198    0.9955231   0.92635421     1.083738    2.7473869            0            0            0            0        38000            2            2            7    102.84786            0 
-    1970    389.96327   -13102.882   0.50418526    2970.8471            5    0.2897091          0.4    1.0069357   0.92635421     1.083738    5.9301165    1379.4348    3766.0095    5.7532995  0.092376919 0.0014116817    4.1048198    0.9955231   0.92635421     1.083738    2.7473869            0            0            0            0        39400            2            2            7    102.84786            0 
-Loop time of 0.221005 on 4 procs for 70 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    1900    389.96327   -13036.384   0.50421483    2970.8471            5    0.2897091          0.4    1.0069357   0.92635421     1.083738    5.9301165    1379.4348    3766.0095    5.9652632  0.092376919 0.0014116817    4.1048198    0.9955231   0.92635421     1.083738    2.7473869            0            0            0            0        38000            2            2            7    102.91265            0 
-    2000    397.57054   -13037.793     1.296998    2702.0288            7    0.3344139          0.4    1.0080872    0.9254519     1.089981    5.9301165    1379.4348     3740.858       5.9815  0.094708685 0.0013374572    4.1048198   0.99612398    0.9252451     1.089981    2.7473869            0            0            0            0        40000            2            2            7    2970.9196            1 
-Loop time of 0.125003 on 4 procs for 100 steps with 2354 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] f_HL[24] f_HL[25] f_HL[26] f_HL[27] f_HL[28] 
-    2000    397.57054   -13037.793     1.296998    2702.0288            7    0.3344139          0.4    1.0080872    0.9254519     1.089981    5.9301165    1379.4348     3740.858       5.9815  0.094708685 0.0013374572    4.1048198   0.99612398    0.9252451     1.089981    2.7473869            0            0            0            0        40000            2            2            7    2970.9196            1 
-    2074    397.57054   -13102.882     1.296998    2702.0288            7    0.3344139          0.4    1.0080872    0.9254519     1.089981    5.9301165    1379.4348     3740.858     5.768081  0.094708685 0.0013374572    4.1048198   0.99612398    0.9252451     1.089981    2.7473869            0            0            0            0        41480            2            2            7    2970.9196            1 
-Loop time of 0.138003 on 4 procs for 74 steps with 2354 atoms
-
-Final hyper stats ...
-
-Cummulative quantities for fix hyper:
-  hyper time = 40000
-  time boost factor = 4000
-  event timesteps = 2
-  # of atoms in events = 2
-Quantities for this hyper run:
-  event timesteps = 2
-  # of atoms in events = 2
-  max length of any bond = 4.10482
-  max drift distance of any atom = 2.74739
-  fraction of biased bonds with zero bias = 0.0947087
-  fraction of biased bonds with negative strain = 0.00133746
-Current quantities:
-  ave bonds/atom = 5.93012
-Cummulative quantities specific to fix hyper/local:
-  # of new bonds formed = 7
-  max bonds/atom = 12
-Quantities for this hyper run specific to fix hyper/local:
-  ave boost for all bonds/step = 3740.86
-  ave biased bonds/step = 5.9815
-  ave bias coeff of all bonds = 0.996124
-  min bias coeff of any bond = 0.925245
-  max bias coeff of any bond = 1.08998
-  max dist from my subbox of any non-maxstrain bond ghost atom = 0
-  max dist from my box of any bond ghost atom = 0
-  count of bond ghost neighbors not found on reneighbor steps = 0
-  bias overlaps = 0
-  CPU time for bond builds = 0.00900006
-Current quantities specific to fix hyper/local:
-  neighbor bonds/bond = 1379.43
-  ave boost coeff for all bonds = 1.00809
-
-Loop time of 6.39915 on 4 procs for 2000 steps with 2354 atoms
-
-Performance: 135.018 ns/day, 0.178 hours/ns, 312.542 timesteps/s
-124.8% CPU use with 4 MPI tasks x no OpenMP threads
-
-Hyper stats:
-  Dynamics time (%) = 2.82706 (44.1788)
-  Quench   time (%) = 2.94107 (45.9603)
-  Other    time (%) = 0.559511 (8.74353)
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.2581     | 4.3754     | 4.4861     |   4.4 | 68.37
-Neigh   | 0.165      | 0.171      | 0.178      |   1.1 |  2.67
-Comm    | 0.40501    | 0.50426    | 0.58801    |   9.7 |  7.88
-Output  | 0          | 0.00049996 | 0.0019999  |   0.0 |  0.01
-Modify  | 0.74901    | 0.78851    | 0.82701    |   3.4 | 12.32
-Other   |            | 0.5595     |            |       |  8.74
-
-Nlocal:    588.5 ave 610 max 570 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-Nghost:    1965.75 ave 1984 max 1944 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Neighs:    13783.2 ave 14264 max 13396 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-FullNghs:  136894 ave 139463 max 134036 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-
-Total # of neighbors = 547576
-Ave neighs/atom = 232.615
-Neighbor list builds = 192
-Dangerous builds = 0
-Total wall time: 0:00:08

lib/kokkos/Makefile.kokkos

@@ -4,7 +4,11 @@
 ifndef KOKKOS_PATH
   KOKKOS_PATH=../../lib/kokkos
 endif
+
 CXXFLAGS=$(CCFLAGS)
+ifeq ($(mode),shared)
+CXXFLAGS += $(SHFLAGS)
+endif
 
 KOKKOS_VERSION_MAJOR = 3
 KOKKOS_VERSION_MINOR = 1
@@ -14,13 +18,13 @@ KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MIN
 # Options: Cuda,HIP,ROCm,OpenMP,Pthread,Serial
 KOKKOS_DEVICES ?= "OpenMP"
 #KOKKOS_DEVICES ?= "Pthread"
-# Options: 
+# Options:
 # Intel:    KNC,KNL,SNB,HSW,BDW,SKX
 # NVIDIA:   Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75
 # ARM:      ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2
 # IBM:      BGQ,Power7,Power8,Power9
 # AMD-GPUS: Vega900,Vega906
-# AMD-CPUS: AMDAVX,Ryzen,EPYC
+# AMD-CPUS: AMDAVX,EPYC
 KOKKOS_ARCH ?= ""
 # Options: yes,no
 KOKKOS_DEBUG ?= "no"
@@ -47,11 +51,15 @@ KOKKOS_HIP_OPTIONS ?= ""
 # Options: enable_async_dispatch
 KOKKOS_HPX_OPTIONS ?= ""
 
+# Helper functions for conversion to upper case
+uppercase_TABLE:=a,A b,B c,C d,D e,E f,F g,G h,H i,I j,J k,K l,L m,M n,N o,O p,P q,Q r,R s,S t,T u,U v,V w,W x,X y,Y z,Z
+uppercase_internal=$(if $1,$$(subst $(firstword $1),$(call uppercase_internal,$(wordlist 2,$(words $1),$1),$2)),$2)
+uppercase=$(eval uppercase_RESULT:=$(call uppercase_internal,$(uppercase_TABLE),$1))$(uppercase_RESULT)
 # Return a 1 if a string contains a substring and 0 if not
 # Note the search string should be without '"'
 # Example: $(call kokkos_has_string,"hwloc,librt",hwloc)
 #   Will return a 1
-kokkos_has_string=$(if $(findstring $2,$1),1,0)
+kokkos_has_string=$(if $(findstring $(call uppercase,$2),$(call uppercase,$1)),1,0)
 # Returns 1 if the path exists, 0 otherwise
 # Example: $(call kokkos_path_exists,/path/to/file)
 #   Will return a 1 if /path/to/file exists
@@ -336,9 +344,9 @@ KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLE
                                               + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
                                               + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
                                               + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
-											  + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70)   \
-											  + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72)   \
-											  + $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_TURING75)  \
                                               + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
                                               + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
                                               + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
@@ -353,9 +361,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
-												+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70)   \
-												+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72)   \
-												+ $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_TURING75)  \
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
                                                 + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
@@ -386,7 +394,6 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_
 
 # AMD based.
 KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX)
-KOKKOS_INTERNAL_USE_ARCH_RYZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Ryzen)
 KOKKOS_INTERNAL_USE_ARCH_EPYC := $(call kokkos_has_string,$(KOKKOS_ARCH),EPYC)
 KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
 KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
@@ -466,7 +473,7 @@ tmp := $(call kokkos_append_header,'\#endif')
 tmp := $(call kokkos_append_header,"")
 tmp := $(call kokkos_append_header,"\#define KOKKOS_VERSION $(KOKKOS_VERSION)")
 tmp := $(call kokkos_append_header,"")
-	
+
 tmp := $(call kokkos_append_header,"/* Execution Spaces */")
 
 ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
@@ -1015,8 +1022,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA_ARCH), 1)
   ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG=-arch
   else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
-		KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch
+    KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch
-		KOKKOS_CXXFLAGS += -x cuda
+    KOKKOS_CXXFLAGS += -x cuda
   else
     $(error Makefile.kokkos: CUDA is enabled but the compiler is neither NVCC nor Clang (got version string $(KOKKOS_CXX_VERSION)) )
   endif

potentials/ffield.comb

@@ -19,13 +19,13 @@
 # 27 entries for a system containing three elements A, B and C
 # These entries are in LAMMPS "metal" units
 #
-Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.85 0.20 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
+Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.85 0.20 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520 0 0.009410 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
 Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.43 0.05 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12  0
 O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12  0
 Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 3.0 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12  0
 Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12  0
-Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
+Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520 0 0.009410 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
-U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
+U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520 0 0.009410 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12  0
 #                                               
 Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
 O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0

src/.gitignore

@@ -645,6 +645,8 @@
 /fix_oneway.h
 /fix_orient_bcc.cpp
 /fix_orient_bcc.h
+/fix_orient_eco.cpp
+/fix_orient_eco.h
 /fix_orient_fcc.cpp
 /fix_orient_fcc.h
 /fix_peri_neigh.cpp

src/CLASS2/bond_class2.cpp

@@ -224,7 +224,7 @@ double BondClass2::single(int type, double rsq, int /*i*/, int /*j*/, double &ff
 
 /* ---------------------------------------------------------------------- */
 
-void *BondClass2::extract( char *str, int &dim )
+void *BondClass2::extract(const char *str, int &dim)
 {
   dim = 1;
   if (strcmp(str,"r0")==0) return (void*) r0;

src/CLASS2/bond_class2.h

@@ -35,7 +35,7 @@ class BondClass2 : public Bond {
   virtual void read_restart(FILE *);
   void write_data(FILE *);
   double single(int, double, int, int, double &);
-  virtual void *extract(char *, int &);
+  virtual void *extract(const char *, int &);
 
  protected:
   double *r0,*k2,*k3,*k4;

src/Depend.sh

@@ -69,6 +69,7 @@ if (test $1 = "DIPOLE") then
 fi
 
 if (test $1 = "GRANULAR") then
+  depend KOKKOS
   depend USER-OMP
 fi
 

src/GPU/pair_eam_alloy_gpu.cpp

@@ -31,11 +31,11 @@
 #include "domain.h"
 #include "utils.h"
 #include "suffix.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
-#define MAXLINE 1024
-
 // External functions from cuda library for atom decomposition
 
 int eam_alloy_gpu_init(const int ntypes, double host_cutforcesq,
@@ -369,94 +369,107 @@ void PairEAMAlloyGPU::read_file(char *filename)
 {
   Setfl *file = setfl;
 
-  // open potential file
+  // read potential file
+  if(comm->me == 0) {
+    PotentialFileReader reader(lmp, filename, "EAM");
 
-  int me = comm->me;
+    try {
-  FILE *fptr;
+      reader.skip_line();
-  char line[MAXLINE];
+      reader.skip_line();
+      reader.skip_line();
 
-  if (me == 0) {
+      // extract element names from nelements line
-    fptr = fopen(filename,"r");
+      ValueTokenizer values = reader.next_values(1);
-    if (fptr == NULL) {
+      file->nelements = values.next_int();
-      char str[128];
+
-      snprintf(str,128,"Cannot open EAM potential file %s",filename);
+      if (values.count() != file->nelements + 1)
-      error->one(FLERR,str);
+        error->one(FLERR,"Incorrect element names in EAM potential file");
+
+      file->elements = new char*[file->nelements];
+      for (int i = 0; i < file->nelements; i++) {
+        const std::string word = values.next_string();
+        const int n = word.length() + 1;
+        file->elements[i] = new char[n];
+        strcpy(file->elements[i], word.c_str());
+      }
+
+      //
+
+      values = reader.next_values(5);
+      file->nrho = values.next_int();
+      file->drho = values.next_double();
+      file->nr   = values.next_int();
+      file->dr   = values.next_double();
+      file->cut  = values.next_double();
+
+      if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
+        error->one(FLERR,"Invalid EAM potential file");
+
+      memory->create(file->mass, file->nelements, "pair:mass");
+      memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+      memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
+      memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+
+      for (int i = 0; i < file->nelements; i++) {
+        values = reader.next_values(2);
+        values.next_int(); // ignore
+        file->mass[i] = values.next_double();
+
+        reader.next_dvector(&file->frho[i][1], file->nrho);
+        reader.next_dvector(&file->rhor[i][1], file->nr);
+      }
+
+      for (int i = 0; i < file->nelements; i++) {
+        for (int j = 0; j <= i; j++) {
+          reader.next_dvector(&file->z2r[i][j][1], file->nr);
+        }
+      }
+    } catch (TokenizerException & e) {
+      error->one(FLERR, e.what());
     }
   }
 
-  // read and broadcast header
+  // broadcast potential information
-  // extract element names from nelements line
+  MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
 
-  int n;
+  MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
-  if (me == 0) {
+  MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
-    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+  MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
-    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+  MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
-    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+  MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
-    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
+
-    n = strlen(line) + 1;
+  // allocate memory on other procs
+  if (comm->me != 0) {
+    file->elements = new char*[file->nelements];
+    for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
+    memory->create(file->mass, file->nelements, "pair:mass");
+    memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+    memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
+    memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
   }
-  MPI_Bcast(&n,1,MPI_INT,0,world);
-  MPI_Bcast(line,n,MPI_CHAR,0,world);
 
-  sscanf(line,"%d",&file->nelements);
+  // broadcast file->elements string array
-  int nwords = atom->count_words(line);
-  if (nwords != file->nelements + 1)
-    error->all(FLERR,"Incorrect element names in EAM potential file");
-
-  char **words = new char*[file->nelements+1];
-  nwords = 0;
-  strtok(line," \t\n\r\f");
-  while ( (words[nwords++] = strtok(NULL," \t\n\r\f")) ) continue;
-
-  file->elements = new char*[file->nelements];
   for (int i = 0; i < file->nelements; i++) {
-    n = strlen(words[i]) + 1;
+    int n;
-    file->elements[i] = new char[n];
+    if (comm->me == 0) n = strlen(file->elements[i]) + 1;
-    strcpy(file->elements[i],words[i]);
+    MPI_Bcast(&n, 1, MPI_INT, 0, world);
-  }
+    if (comm->me != 0) file->elements[i] = new char[n];
-  delete [] words;
+    MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
-
-  if (me == 0) {
-    utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
-    sscanf(line,"%d %lg %d %lg %lg",
-           &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
 
-  MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
+  // broadcast file->mass, frho, rhor
-  MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
+  for (int i = 0; i < file->nelements; i++) {
-  MPI_Bcast(&file->nr,1,MPI_INT,0,world);
+    MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->rhor[i][1], file->nr, MPI_DOUBLE, 0, world);
+  }
 
-  file->mass = new double[file->nelements];
+  // broadcast file->z2r
-  memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
+  for (int i = 0; i < file->nelements; i++) {
-  memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
+    for (int j = 0; j <= i; j++) {
-  memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
+      MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
-                 "pair:z2r");
-
-  int i,j,tmp;
-  for (i = 0; i < file->nelements; i++) {
-    if (me == 0) {
-      utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error);
-      sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
-    MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
-    if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
-    MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
-    if (me == 0) grab(fptr,file->nr,&file->rhor[i][1]);
-    MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
   }
-
-  for (i = 0; i < file->nelements; i++)
-    for (j = 0; j <= i; j++) {
-      if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
-      MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
-    }
-
-  // close the potential file
-
-  if (me == 0) fclose(fptr);
 }
 
 /* ----------------------------------------------------------------------

src/GPU/pair_eam_fs_gpu.cpp

@@ -30,11 +30,12 @@
 #include "gpu_extra.h"
 #include "domain.h"
 #include "suffix.h"
+#include "utils.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
-#define MAXLINE 1024
-
 // External functions from cuda library for atom decomposition
 
 int eam_fs_gpu_init(const int ntypes, double host_cutforcesq,
@@ -368,99 +369,113 @@ void PairEAMFSGPU::read_file(char *filename)
 {
   Fs *file = fs;
 
-  // open potential file
+  // read potential file
+  if(comm->me == 0) {
+    PotentialFileReader reader(lmp, filename, "EAM");
 
-  int me = comm->me;
+    try {
-  FILE *fptr;
+      reader.skip_line();
-  char line[MAXLINE];
+      reader.skip_line();
+      reader.skip_line();
 
-  if (me == 0) {
+      // extract element names from nelements line
-    fptr = force->open_potential(filename);
+      ValueTokenizer values = reader.next_values(1);
-    if (fptr == NULL) {
+      file->nelements = values.next_int();
-      char str[128];
+
-      snprintf(str,128,"Cannot open EAM potential file %s",filename);
+      if (values.count() != file->nelements + 1)
-      error->one(FLERR,str);
+        error->one(FLERR,"Incorrect element names in EAM potential file");
+
+      file->elements = new char*[file->nelements];
+      for (int i = 0; i < file->nelements; i++) {
+        const std::string word = values.next_string();
+        const int n = word.length() + 1;
+        file->elements[i] = new char[n];
+        strcpy(file->elements[i], word.c_str());
+      }
+
+      //
+
+      values = reader.next_values(5);
+      file->nrho = values.next_int();
+      file->drho = values.next_double();
+      file->nr   = values.next_int();
+      file->dr   = values.next_double();
+      file->cut  = values.next_double();
+
+      if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
+        error->one(FLERR,"Invalid EAM potential file");
+
+      memory->create(file->mass, file->nelements, "pair:mass");
+      memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+      memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+      memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+
+      for (int i = 0; i < file->nelements; i++) {
+        values = reader.next_values(2);
+        values.next_int(); // ignore
+        file->mass[i] = values.next_double();
+
+        reader.next_dvector(&file->frho[i][1], file->nrho);
+
+        for (int j = 0; j < file->nelements; j++) {
+          reader.next_dvector(&file->rhor[i][j][1], file->nr);
+        }
+      }
+
+      for (int i = 0; i < file->nelements; i++) {
+        for (int j = 0; j <= i; j++) {
+          reader.next_dvector(&file->z2r[i][j][1], file->nr);
+        }
+      }
+    } catch (TokenizerException & e) {
+      error->one(FLERR, e.what());
     }
   }
 
-  // read and broadcast header
+  // broadcast potential information
-  // extract element names from nelements line
+  MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
 
-  int n;
+  MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
-  if (me == 0) {
+  MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+
-    n = strlen(line) + 1;
+  // allocate memory on other procs
+  if (comm->me != 0) {
+    file->elements = new char*[file->nelements];
+    for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
+    memory->create(file->mass, file->nelements, "pair:mass");
+    memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+    memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+    memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
   }
-  MPI_Bcast(&n,1,MPI_INT,0,world);
-  MPI_Bcast(line,n,MPI_CHAR,0,world);
 
-  sscanf(line,"%d",&file->nelements);
+  // broadcast file->elements string array
-  int nwords = atom->count_words(line);
-  if (nwords != file->nelements + 1)
-    error->all(FLERR,"Incorrect element names in EAM potential file");
-
-  char **words = new char*[file->nelements+1];
-  nwords = 0;
-  strtok(line," \t\n\r\f");
-  while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
-
-  file->elements = new char*[file->nelements];
   for (int i = 0; i < file->nelements; i++) {
-    n = strlen(words[i]) + 1;
+    int n;
-    file->elements[i] = new char[n];
+    if (comm->me == 0) n = strlen(file->elements[i]) + 1;
-    strcpy(file->elements[i],words[i]);
+    MPI_Bcast(&n, 1, MPI_INT, 0, world);
-  }
+    if (comm->me != 0) file->elements[i] = new char[n];
-  delete [] words;
+    MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
-
-  if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    sscanf(line,"%d %lg %d %lg %lg",
-           &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
 
-  MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
+  // broadcast file->mass, frho, rhor
-  MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
+  for (int i = 0; i < file->nelements; i++) {
-  MPI_Bcast(&file->nr,1,MPI_INT,0,world);
+    MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
 
-  file->mass = new double[file->nelements];
+    for (int j = 0; j < file->nelements; j++) {
-  memory->create(file->frho,file->nelements,file->nrho+1,
+      MPI_Bcast(&file->rhor[i][j][1], file->nr, MPI_DOUBLE, 0, world);
-                                              "pair:frho");
-  memory->create(file->rhor,file->nelements,file->nelements,
-                 file->nr+1,"pair:rhor");
-  memory->create(file->z2r,file->nelements,file->nelements,
-                 file->nr+1,"pair:z2r");
-
-  int i,j,tmp;
-  for (i = 0; i < file->nelements; i++) {
-    if (me == 0) {
-      fgets(line,MAXLINE,fptr);
-      sscanf(line,"%d %lg",&tmp,&file->mass[i]);
-    }
-    MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
-    if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
-    MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
-
-    for (j = 0; j < file->nelements; j++) {
-      if (me == 0) grab(fptr,file->nr,&file->rhor[i][j][1]);
-      MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
     }
   }
 
-  for (i = 0; i < file->nelements; i++)
+  // broadcast file->z2r
-    for (j = 0; j <= i; j++) {
+  for (int i = 0; i < file->nelements; i++) {
-      if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
+    for (int j = 0; j <= i; j++) {
-      MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
+      MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
     }
-
+  }
-  // close the potential file
-
-  if (me == 0) fclose(fptr);
 }
 
 /* ----------------------------------------------------------------------

src/GRANULAR/fix_wall_gran.cpp

@@ -370,7 +370,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
       vshear = force->numeric(FLERR,arg[iarg+2]);
       wshear = 1;
       iarg += 3;
-    } else if (strcmp(arg[iarg],"store_contacts") == 0) {
+    } else if (strcmp(arg[iarg],"contacts") == 0) {
       peratom_flag = 1;
       size_peratom_cols = 8;
       peratom_freq = 1;
@@ -426,10 +426,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
   }
 
   if (peratom_flag) {
-    int nlocal = atom->nlocal;
+    clear_stored_contacts();
-    for (int i = 0; i < nlocal; i++)
-      for (int m = 0; m < size_peratom_cols; m++)
-        array_atom[i][m] = 0.0;
   }
 
   time_origin = update->ntimestep;
@@ -596,6 +593,10 @@ void FixWallGran::post_force(int /*vflag*/)
 
   rwall = 0.0;
 
+  if (peratom_flag) {
+    clear_stored_contacts();
+  }
+
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
 
@@ -668,7 +669,7 @@ void FixWallGran::post_force(int /*vflag*/)
 
         // store contact info
         if (peratom_flag) {
-          array_atom[i][0] = (double)atom->tag[i];
+          array_atom[i][0] = 1.0;
           array_atom[i][4] = x[i][0] - dx;
           array_atom[i][5] = x[i][1] - dy;
           array_atom[i][6] = x[i][2] - dz;
@@ -702,6 +703,15 @@ void FixWallGran::post_force(int /*vflag*/)
   }
 }
 
+void FixWallGran::clear_stored_contacts() {
+  const int nlocal = atom->nlocal;
+  for (int i = 0; i < nlocal; i++) {
+    for (int m = 0; m < size_peratom_cols; m++) {
+      array_atom[i][m] = 0.0;
+    }
+  }
+}
+
 /* ---------------------------------------------------------------------- */
 
 void FixWallGran::post_force_respa(int vflag, int ilevel, int /*iloop*/)

src/GRANULAR/fix_wall_gran.h

@@ -110,6 +110,8 @@ class FixWallGran : public Fix {
   // store particle interactions
 
   int store;
+
+  void clear_stored_contacts();
 };
 
 }

src/GRANULAR/fix_wall_gran_region.cpp

@@ -178,6 +178,10 @@ void FixWallGranRegion::post_force(int /*vflag*/)
     region->set_velocity();
   }
 
+  if (peratom_flag) {
+    clear_stored_contacts();
+  }
+
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       if (!region->match(x[i][0],x[i][1],x[i][2])) continue;

src/KIM/kim_init.cpp

@@ -57,6 +57,8 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_init.h"
+#include "fix_store_kim.h"
+#include "kim_units.h"
 #include <cstring>
 #include <string>
 #include <sstream>
@@ -71,8 +73,8 @@
 #include "input.h"
 #include "variable.h"
 #include "citeme.h"
-#include "fix_store_kim.h"
+#include "utils.h"
-#include "kim_units.h"
+#include "fmt/format.h"
 
 extern "C" {
 #include "KIM_SimulatorHeaders.h"
@@ -275,7 +277,7 @@ void KimInit::determine_model_type_and_units(char * model_name,
       std::string mesg("Incompatible units for KIM Simulator Model, "
                        "required units = ");
       mesg += *model_units;
-      error->all(FLERR,mesg.c_str());
+      error->all(FLERR,mesg);
     }
   }
 }
@@ -302,7 +304,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
   fix_store->setptr("model_units", (void *) model_units);
 
   // Begin output to log file
-  kim_init_log_delimiter("begin");
+  input->write_echo("#=== BEGIN kim-init ==========================================\n");
 
   int kimerror;
   KIM_SimulatorModel * simulatorModel;
@@ -328,8 +330,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
       mesg += "\n";
       mesg += "#\n";
 
-      if (screen) fputs(mesg.c_str(),screen);
+      utils::logmesg(lmp,mesg);
-      if (logfile) fputs(mesg.c_str(),logfile);
     }
 
     fix_store->setptr("simulator_model", (void *) simulatorModel);
@@ -346,7 +347,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
 
   std::string cmd("units ");
   cmd += model_units;
-  input->one(cmd.c_str());
+  input->one(cmd);
 
   if (model_type == SM) {
     int sim_fields, sim_lines;
@@ -423,37 +424,14 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
         mesg += "\n";
       }
     }
-    else
+    else mesg += "No mutable parameters. \n";
-      mesg += "No mutable parameters. \n";
 
     KIM_Model_Destroy(&pkim);
-
+    input->write_echo(mesg);
-    if (comm->me == 0)
-    {
-      input->write_echo(mesg.c_str());
-    }
   }
 
   // End output to log file
-  kim_init_log_delimiter("end");
+  input->write_echo("#=== END kim-init ============================================\n\n");
-
-}
-
-/* ---------------------------------------------------------------------- */
-
-void KimInit::kim_init_log_delimiter(std::string const &begin_end) const
-{
-  if (comm->me == 0) {
-    std::string mesg;
-    if (begin_end == "begin")
-      mesg =
-          "#=== BEGIN kim-init ==========================================\n";
-    else if (begin_end == "end")
-      mesg =
-          "#=== END kim-init ============================================\n\n";
-
-    input->write_echo(mesg.c_str());
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -493,14 +471,8 @@ void KimInit::do_variables(char *user_units, char *model_units)
                          (char *)"efield",
                          (char *)"density"};
 
-  if (comm->me == 0) {
+  input->write_echo(fmt::format("# Conversion factors from {} to {}:\n",
-    std::string mesg("# Conversion factors from ");
+                                from,to));
-    mesg += from;
-    mesg += " to ";
-    mesg += to;
-    mesg += ":\n";
-    input->write_echo(mesg.c_str());
-  }
 
   for (int i = 0; i < nunits; i++) {
     var_str = std::string("_u_") + std::string(units[i]);
@@ -514,58 +486,43 @@ void KimInit::do_variables(char *user_units, char *model_units)
                                  from,
                                  to,
                                  conversion_factor);
-    if (ier != 0) {
+    if (ier != 0)
-      std::string err = std::string("Unable to obtain conversion factor: ") +
+      error->all(FLERR,fmt::format("Unable to obtain conversion factor: "
-                        "unit = " + units[i] + "; "
+                                   "unit = {}; from = {}; to = {}.",
-                        "from = " + from + "; "
+                                   units[i], from, to));
-                        "to = " + to + ".";
+
-      error->all(FLERR,err.c_str());
-    }
     variable->internal_set(v_unit,conversion_factor);
-    if (comm->me == 0) {
+    input->write_echo(fmt::format("variable {:<15s} internal {:<15.12e}\n",
-      std::stringstream mesg;
+                                  var_str, conversion_factor));
-      mesg << "variable " << std::setw(15) << std::left << var_str
-           << " internal "
-           << std::setprecision(12) << std::scientific << conversion_factor
-           << std::endl;
-      input->write_echo(mesg.str().c_str());
-    }
   }
-  if (comm->me == 0) input->write_echo("#\n");
+  input->write_echo("#\n");
 }
 
 /* ---------------------------------------------------------------------- */
 
-void KimInit::write_log_cite(char * model_name)
+void KimInit::write_log_cite(const std::string &model_name)
 {
   KIM_Collections * coll;
   int err = KIM_Collections_Create(&coll);
   if (err) return;
 
   int extent;
-  if (model_type == MO)
+  if (model_type == MO) {
-  {
     err = KIM_Collections_CacheListOfItemMetadataFiles(
-        coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name,&extent);
+      coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name.c_str(),&extent);
-  }
+  } else if (model_type == SM) {
-  else if (model_type == SM)
-  {
     err = KIM_Collections_CacheListOfItemMetadataFiles(
-        coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name,&extent);
+      coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name.c_str(),&extent);
-  }
+  } else {
-  else
-  {
     error->all(FLERR,"Unknown model type.");
   }
 
-  if (err)
+  if (err) {
-  {
     KIM_Collections_Destroy(&coll);
     return;
   }
 
-  for (int i = 0; i < extent;++i)
+  for (int i = 0; i < extent;++i) {
-  {
     char const * fileName;
     int availableAsString;
     char const * fileString;
@@ -573,8 +530,7 @@ void KimInit::write_log_cite(char * model_name)
         coll,i,&fileName,NULL,NULL,&availableAsString,&fileString);
     if (err) continue;
 
-    if (0 == strncmp("kimcite",fileName,7))
+    if (0 == strncmp("kimcite",fileName,7)) {
-    {
       if ((lmp->citeme) && (availableAsString)) lmp->citeme->add(fileString);
     }
   }

src/KIM/kim_init.h

@@ -83,10 +83,9 @@ class KimInit : protected Pointers {
   bool unit_conversion_mode;
 
   void determine_model_type_and_units(char *, char *, char **, KIM_Model *&);
-  void write_log_cite(char *);
+  void write_log_cite(const std::string &);
   void do_init(char *, char *, char *, KIM_Model *&);
   void do_variables(char*, char*);
-  void kim_init_log_delimiter(std::string const &begin_end) const;
 };
 
 }

src/KIM/kim_interactions.cpp

@@ -99,24 +99,6 @@ void KimInteractions::command(int narg, char **arg)
 
 /* ---------------------------------------------------------------------- */
 
-void KimInteractions::kim_interactions_log_delimiter(
-    std::string const begin_end) const
-{
-  if (comm->me == 0) {
-    std::string mesg;
-    if (begin_end == "begin")
-      mesg =
-          "#=== BEGIN kim_interactions ==================================\n";
-    else if (begin_end == "end")
-      mesg =
-          "#=== END kim_interactions ====================================\n\n";
-
-    input->write_echo(mesg.c_str());
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
 void KimInteractions::do_setup(int narg, char **arg)
 {
   bool fixed_types;
@@ -145,7 +127,7 @@ void KimInteractions::do_setup(int narg, char **arg)
   } else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'");
 
   // Begin output to log file
-  kim_interactions_log_delimiter("begin");
+  input->write_echo("#=== BEGIN kim_interactions ==================================\n");
 
   if (simulatorModel) {
 
@@ -167,7 +149,7 @@ void KimInteractions::do_setup(int narg, char **arg)
           simulatorModel,"atom-type-num-list",atom_type_num_list.c_str());
       KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
 
-      int len = strlen(atom_type_sym_list.c_str())+1;
+      int len = atom_type_sym_list.size()+1;
       char *strbuf = new char[len];
       char *strword;
 
@@ -192,7 +174,7 @@ void KimInteractions::do_setup(int narg, char **arg)
           std::string msg("Species '");
           msg += strword;
           msg += "' is not supported by this KIM Simulator Model";
-          error->all(FLERR,msg.c_str());
+          error->all(FLERR,msg);
         }
         strword = strtok(NULL," \t");
       }
@@ -276,13 +258,12 @@ void KimInteractions::do_setup(int narg, char **arg)
       cmd2 += " ";
     }
 
-    input->one(cmd1.c_str());
+    input->one(cmd1);
-    input->one(cmd2.c_str());
+    input->one(cmd2);
   }
 
   // End output to log file
-  kim_interactions_log_delimiter("end");
+  input->write_echo("#=== END kim_interactions ====================================\n\n");
-
 }
 
 /* ---------------------------------------------------------------------- */
@@ -377,7 +358,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(char const *const input_line) cons
 
 /* ---------------------------------------------------------------------- */
 
-int KimInteractions::species_to_atomic_no(std::string const species) const
+int KimInteractions::species_to_atomic_no(const std::string &species) const
 {
   if (species == "H") return 1;
   else if (species == "He") return 2;

src/KIM/kim_interactions.h

@@ -76,9 +76,8 @@ class KimInteractions : protected Pointers {
   void command(int, char **);
  private:
   void do_setup(int, char **);
-  int species_to_atomic_no(std::string const species) const;
+  int species_to_atomic_no(const std::string &species) const;
   void KIM_SET_TYPE_PARAMETERS(char const *const input_line) const;
-  void kim_interactions_log_delimiter(std::string const begin_end) const;
 };
 
 }

src/KIM/kim_param.cpp

@@ -56,6 +56,8 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_param.h"
+#include "fix_store_kim.h"
+#include "pair_kim.h"
 #include <mpi.h>
 #include <cstring>
 #include <string>
@@ -66,8 +68,7 @@
 #include "modify.h"
 #include "variable.h"
 #include "force.h"
-#include "fix_store_kim.h"
+#include "fmt/format.h"
-#include "pair_kim.h"
 
 extern "C"
 {
@@ -157,13 +158,12 @@ void KimParam::command(int narg, char **arg)
   if (narg < 4)
     error->all(FLERR, "Illegal kim_param command");
 
-  kim_param_get = (strcmp(arg[0], "get") == 0);
+  std::string kim_param_get_set = arg[0];
-  kim_param_set = (strcmp(arg[0], "set") == 0);
 
-  if (!kim_param_get && !kim_param_set) {
+  if ((kim_param_get_set != "get") && (kim_param_get_set != "set")) {
     std::string msg("Incorrect arguments in kim_param command.\n");
     msg += "'kim_param get/set' is mandatory.";
-    error->all(FLERR, msg.c_str());
+    error->all(FLERR, msg);
   }
 
   // Check if we called a kim_init command
@@ -193,7 +193,8 @@ void KimParam::command(int narg, char **arg)
   else
     error->all(FLERR, "Must use 'kim_init' before 'kim_param'");
 
-  kim_param_log_delimiter("begin");
+  input->write_echo(fmt::format("#=== BEGIN kim-param {} ==================="
+                                "==================\n",kim_param_get_set));
 
   KIM_Model *pkim = NULL;
 
@@ -211,7 +212,7 @@ void KimParam::command(int narg, char **arg)
       if (!pkim)
         error->all(FLERR, "Unable to get the KIM Portable Model.");
 
-      if (kim_param_set) {
+      if (kim_param_get_set == "set") {
         atom_type_list = pairKIM->get_atom_type_list();
         if (atom_type_list.empty())
           error->all(FLERR, "The requested atom type list is empty.");
@@ -220,12 +221,12 @@ void KimParam::command(int narg, char **arg)
       error->all(FLERR, "Pair style is defined,"
                         " but there is no match for kim style in lammps.");
   } else {
-    if (kim_param_set) {
+    if (kim_param_get_set == "set") {
       std::string msg("Wrong kim_param set command.\n");
       msg += "To set the new parameter values, pair style must be assigned.\n";
       msg += "Must use 'kim_interactions' or";
       msg += "'pair_style kim ' before 'kim_param set'";
-      error->all(FLERR, msg.c_str());
+      error->all(FLERR, msg);
     } else {
       KIM_LengthUnit lengthUnit;
       KIM_EnergyUnit energyUnit;
@@ -259,7 +260,7 @@ void KimParam::command(int narg, char **arg)
   KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters);
   if (numberOfParameters) {
     // Get the parameters
-    if (kim_param_get) {
+    if (kim_param_get_set == "get") {
       // Parameter name
       char *paramname = NULL;
       // Variable name
@@ -296,7 +297,7 @@ void KimParam::command(int narg, char **arg)
           msg += "This Model does not have the requested '";
           msg += paramname;
           msg += "' parameter.";
-          error->all(FLERR, msg.c_str());
+          error->all(FLERR, msg);
         }
 
         // Get the index_range for the requested parameter
@@ -313,7 +314,7 @@ void KimParam::command(int narg, char **arg)
             msg += "Expected integer parameter(s) instead of '";
             msg += argtostr;
             msg += "' in index_range.";
-            error->all(FLERR, msg.c_str());
+            error->all(FLERR, msg);
           }
 
           std::string::size_type npos = argtostr.find(':');
@@ -330,7 +331,7 @@ void KimParam::command(int narg, char **arg)
               msg += "' parameter with extent of '";
               msg += SNUM(extent);
               msg += "' .";
-              error->all(FLERR, msg.c_str());
+              error->all(FLERR, msg);
             }
           } else {
             std::stringstream str(argtostr);
@@ -342,7 +343,7 @@ void KimParam::command(int narg, char **arg)
               msg += "' with the extent of '";
               msg += SNUM(extent);
               msg += "' .";
-              error->all(FLERR, msg.c_str());
+              error->all(FLERR, msg);
             }
             nubound = nlbound;
           }
@@ -350,7 +351,7 @@ void KimParam::command(int narg, char **arg)
           std::string msg("Wrong number of arguments in ");
           msg += "kim_param get command.\n";
           msg += "Index range after parameter name is mandatory.";
-          error->all(FLERR, msg.c_str());
+          error->all(FLERR, msg);
         }
 
         int const nvars = nubound - nlbound + 1;
@@ -363,7 +364,7 @@ void KimParam::command(int narg, char **arg)
           std::string msg("Wrong number of arguments in ");
           msg += "kim_param get command.\n";
           msg += "The LAMMPS variable name is mandatory.";
-          error->all(FLERR, msg.c_str());
+          error->all(FLERR, msg);
         }
 
         // indicator flag for list request
@@ -400,7 +401,7 @@ void KimParam::command(int narg, char **arg)
               msg += "' variable names or '";
               msg += varname;
               msg += " split' is mandatory.";
-              error->all(FLERR, msg.c_str());
+              error->all(FLERR, msg);
             }
           } else {
             std::string msg("Wrong number of arguments in ");
@@ -410,7 +411,7 @@ void KimParam::command(int narg, char **arg)
             msg += "' variable names or '";
             msg += varname;
             msg += " split/list' is mandatory.";
-            error->all(FLERR, msg.c_str());
+            error->all(FLERR, msg);
           }
         } else {
           varsname = new char *[1];
@@ -524,7 +525,7 @@ void KimParam::command(int narg, char **arg)
         set_cmd += " ";
         set_cmd += arg[i];
       }
-      input->one(set_cmd.c_str());
+      input->one(set_cmd);
     }
   } else
     error->all(FLERR, "This model has No mutable parameters.");
@@ -532,38 +533,17 @@ void KimParam::command(int narg, char **arg)
   if (!isPairStyleAssigned)
     KIM_Model_Destroy(&pkim);
 
-  kim_param_log_delimiter("end");
+  input->write_echo(fmt::format("#=== END kim-param {} ====================="
+                                "==================\n",kim_param_get_set));
 }
 
 /* ---------------------------------------------------------------------- */
 
-void KimParam::kim_param_log_delimiter(std::string const &begin_end) const
+void KimParam::echo_var_assign(const std::string &name,
+                               const std::string &value) const
 {
-  if (comm->me == 0) {
+  input->write_echo(fmt::format("variable {} string {}\n",
-    std::string msg;
+                                name, value));
-    if (begin_end == "begin") {
-      msg = "#=== BEGIN kim-param ";
-      msg += kim_param_get ? "get " : "set ";
-      msg += "=====================================\n";
-    } else if (begin_end == "end") {
-      msg = "#=== END kim-param ";
-      msg += kim_param_get ? "get " : "set ";
-      msg += "=======================================\n\n";
-    }
-    input->write_echo(msg.c_str());
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void KimParam::echo_var_assign(std::string const &name,
-                               std::string const &value) const
-{
-  if (comm->me == 0) {
-    std::string msg;
-    msg += "variable " + name + " string " + value + "\n";
-    input->write_echo(msg.c_str());
-  }
 }
 
 #undef SNUM

src/KIM/kim_param.h

@@ -80,10 +80,7 @@ public:
   void command(int, char **);
 
 private:
-  void kim_param_log_delimiter(std::string const &begin_end) const;
+  void echo_var_assign(const std::string &name, const std::string &value) const;
-
-  void echo_var_assign(std::string const &name, std::string const &value)
-      const;
 
 private:
   bool kim_param_get;

src/KIM/kim_property.cpp

@@ -100,13 +100,13 @@ void kimProperty::command(int narg, char **arg)
     std::string msg("Error incorrect arguments in kim_property command.\n");
     msg += "`kim_property create/destroy/modify/remove/dump` ";
     msg += "is mandatory.";
-    error->all(FLERR, msg.c_str());
+    error->all(FLERR, msg);
   }
 
   if (comm->me == 0) {
     std::string msg;
     msg = "#=== kim-property ===========================================\n";
-    input->write_echo(msg.c_str());
+    input->write_echo(msg);
   }
 
   // Get the kim_str ptr to the data associated with a kim_property_str
@@ -464,7 +464,8 @@ void kimProperty::command(int narg, char **arg)
         error->one(FLERR, "Error Python `kim_property_dump` function "
                           "evaluation failed!");
       }
-    }
+    } else
+      pValue = NULL;
 
     // Destroy the variable
     kim_str_cmd[1] = const_cast<char *>("delete");

src/KIM/kim_query.cpp

@@ -56,6 +56,7 @@
 ------------------------------------------------------------------------- */
 
 #include "kim_query.h"
+#include "fix_store_kim.h"
 #include <mpi.h>
 #include <cstring>
 #include <string>
@@ -67,7 +68,7 @@
 #include "variable.h"
 #include "version.h"
 #include "info.h"
-#include "fix_store_kim.h"
+#include "fmt/format.h"
 
 #if defined(LMP_KIM_CURL)
 #include <sys/types.h>
@@ -153,7 +154,7 @@ void KimQuery::command(int narg, char **arg)
     error->all(FLERR,errmsg);
   }
 
-  kim_query_log_delimiter("begin");
+  input->write_echo("#=== BEGIN kim-query =========================================\n");
   char **varcmd = new char*[3];
   varcmd[1] = (char *) "string";
 
@@ -186,7 +187,7 @@ void KimQuery::command(int narg, char **arg)
     input->variable->set(3,varcmd);
     echo_var_assign(varname, value_string);
   }
-  kim_query_log_delimiter("end");
+  input->write_echo("#=== END kim-query ===========================================\n\n");
 
   delete[] varcmd;
   delete[] value;
@@ -342,29 +343,8 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
 
 /* ---------------------------------------------------------------------- */
 
-void KimQuery::kim_query_log_delimiter(std::string const begin_end) const
+void KimQuery::echo_var_assign(const std::string & name,
+                               const std::string & value) const
 {
-  if (comm->me == 0) {
+  input->write_echo(fmt::format("variable {} string {}\n",name,value));
-    std::string mesg;
-    if (begin_end == "begin")
-      mesg =
-          "#=== BEGIN kim-query =========================================\n";
-    else if (begin_end == "end")
-      mesg =
-          "#=== END kim-query ===========================================\n\n";
-
-    input->write_echo(mesg.c_str());
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void KimQuery::echo_var_assign(std::string const & name,
-                               std::string const & value) const
-{
-  if (comm->me == 0) {
-    std::string mesg;
-    mesg += "variable " + name + " string " + value + "\n";
-    input->write_echo(mesg.c_str());
-  }
 }

src/KIM/kim_query.h

@@ -73,8 +73,7 @@ class KimQuery : protected Pointers {
   KimQuery(class LAMMPS *lmp) : Pointers(lmp) {};
   void command(int, char **);
  private:
-  void kim_query_log_delimiter(std::string const begin_end) const;
+  void echo_var_assign(const std::string &name, const std::string &value)
-  void echo_var_assign(std::string const & name, std::string const & value)
   const;
 };
 

src/KIM/kim_units.cpp

@@ -1370,9 +1370,9 @@ double get_unit_conversion_factor(unit_type &unit_type_enum,
 
 //  Wrapper to the routine that gets the unit conversion. Translates strings
 //  to enumerations and then call get_unit_conversion_factor()
-int lammps_unit_conversion(string const &unit_type_str,
+int lammps_unit_conversion(const string &unit_type_str,
-                           string const &from_system_str,
+                           const string &from_system_str,
-                           string const &to_system_str,
+                           const string &to_system_str,
                            double &conversion_factor)
 {
     // initialize

src/KIM/kim_units.h

@@ -53,7 +53,7 @@
    Designed for use with the kim-api-2.0.2 (and newer) package
 ------------------------------------------------------------------------- */
 
-int lammps_unit_conversion(std::string const &unit_type_str,
+int lammps_unit_conversion(const std::string &unit_type_str,
-                           std::string const &from_system_str,
+                           const std::string &from_system_str,
-                           std::string const &to_system_str,
+                           const std::string &to_system_str,
                            double &conversion_factor);

src/KIM/pair_kim.cpp

@@ -429,7 +429,7 @@ void PairKIM::coeff(int narg, char **arg)
     } else {
       std::string msg("create_kim_particle_codes: symbol not found: ");
       msg += lmps_unique_elements[i];
-      error->all(FLERR, msg.c_str());
+      error->all(FLERR, msg);
     }
   }
   // Set the new values for PM parameters
@@ -441,7 +441,7 @@ void PairKIM::coeff(int narg, char **arg)
     if (!numberOfParameters) {
       std::string msg("Incorrect args for pair coefficients \n");
       msg += "This model has No mutable parameters.";
-      error->all(FLERR, msg.c_str());
+      error->all(FLERR, msg);
     }
 
     int kimerror;
@@ -477,7 +477,7 @@ void PairKIM::coeff(int narg, char **arg)
         msg += "This Model does not have the requested '";
         msg += paramname;
         msg += "' parameter.";
-        error->all(FLERR, msg.c_str());
+        error->all(FLERR, msg);
       }
 
       // Get the index_range for the requested parameter
@@ -493,7 +493,7 @@ void PairKIM::coeff(int narg, char **arg)
           msg += "Expected integer parameter(s) instead of '";
           msg += argtostr;
           msg += "' in index_range.";
-          error->all(FLERR, msg.c_str());
+          error->all(FLERR, msg);
         }
 
         std::string::size_type npos = argtostr.find(':');
@@ -510,7 +510,7 @@ void PairKIM::coeff(int narg, char **arg)
             msg += "' parameter with extent of '";
             msg += SNUM(extent);
             msg += "' .";
-            error->all(FLERR, msg.c_str());
+            error->all(FLERR, msg);
           }
         } else {
           std::stringstream str(argtostr);
@@ -522,7 +522,7 @@ void PairKIM::coeff(int narg, char **arg)
             msg += "' parameter with extent of '";
             msg += SNUM(extent);
             msg += "' .";
-            error->all(FLERR, msg.c_str());
+            error->all(FLERR, msg);
           }
           nubound = nlbound;
         }
@@ -530,7 +530,7 @@ void PairKIM::coeff(int narg, char **arg)
         std::string msg =
         "Wrong number of arguments for pair coefficients.\n";
         msg += "Index range after parameter name is mandatory.";
-        error->all(FLERR, msg.c_str());
+        error->all(FLERR, msg);
       }
 
       // Parameter values
@@ -561,7 +561,7 @@ void PairKIM::coeff(int narg, char **arg)
         msg += "' values are requested for '";
         msg += paramname;
         msg += "' parameter.";
-        error->all(FLERR, msg.c_str());
+        error->all(FLERR, msg);
       }
     }
 
@@ -1122,7 +1122,7 @@ void PairKIM::set_kim_model_has_flags()
                                      KIM_SUPPORT_STATUS_required)) {
       std::string msg("KIM Model requires unsupported compute argument: ");
       msg += KIM_ComputeArgumentName_ToString(computeArgumentName);
-      error->all(FLERR, msg.c_str());
+      error->all(FLERR, msg);
     }
   }
 

src/KOKKOS/atom_kokkos.cpp

@@ -340,7 +340,8 @@ void AtomKokkos::sync_modify(ExecutionSpace execution_space,
   modified(execution_space,datamask_modify);
 }
 
-AtomVec *AtomKokkos::new_avec(const char *style, int trysuffix, int &sflag)
+AtomVec *AtomKokkos::new_avec(const std::string &style,
+                              int trysuffix, int &sflag)
 {
   AtomVec* avec = Atom::new_avec(style,trysuffix,sflag);
   if (!avec->kokkosable)

src/KOKKOS/atom_kokkos.h

@@ -74,7 +74,7 @@ class AtomKokkos : public Atom {
   virtual void deallocate_topology();
   void sync_modify(ExecutionSpace, unsigned int, unsigned int);
  private:
-   class AtomVec *new_avec(const char *, int, int &);
+  class AtomVec *new_avec(const std::string &, int, int &);
 };
 
 template<class ViewType, class IndexView>

src/KOKKOS/pair_eam_alloy_kokkos.cpp

@@ -29,11 +29,12 @@
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
+#include "utils.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
-#define MAXLINE 1024
-
 // Cannot use virtual inheritance on the GPU, so must duplicate code
 
 /* ---------------------------------------------------------------------- */
@@ -982,94 +983,107 @@ void PairEAMAlloyKokkos<DeviceType>::read_file(char *filename)
 {
   Setfl *file = setfl;
 
-  // open potential file
+  // read potential file
+  if(comm->me == 0) {
+    PotentialFileReader reader(lmp, filename, "EAM");
 
-  int me = comm->me;
+    try {
-  FILE *fptr;
+      reader.skip_line();
-  char line[MAXLINE];
+      reader.skip_line();
+      reader.skip_line();
 
-  if (me == 0) {
+      // extract element names from nelements line
-    fptr = force->open_potential(filename);
+      ValueTokenizer values = reader.next_values(1);
-    if (fptr == NULL) {
+      file->nelements = values.next_int();
-      char str[128];
+
-      snprintf(str,128,"Cannot open EAM potential file %s",filename);
+      if (values.count() != file->nelements + 1)
-      error->one(FLERR,str);
+        error->one(FLERR,"Incorrect element names in EAM potential file");
+
+      file->elements = new char*[file->nelements];
+      for (int i = 0; i < file->nelements; i++) {
+        const std::string word = values.next_string();
+        const int n = word.length() + 1;
+        file->elements[i] = new char[n];
+        strcpy(file->elements[i], word.c_str());
+      }
+
+      //
+
+      values = reader.next_values(5);
+      file->nrho = values.next_int();
+      file->drho = values.next_double();
+      file->nr   = values.next_int();
+      file->dr   = values.next_double();
+      file->cut  = values.next_double();
+
+      if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
+        error->one(FLERR,"Invalid EAM potential file");
+
+      memory->create(file->mass, file->nelements, "pair:mass");
+      memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+      memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
+      memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+
+      for (int i = 0; i < file->nelements; i++) {
+        values = reader.next_values(2);
+        values.next_int(); // ignore
+        file->mass[i] = values.next_double();
+
+        reader.next_dvector(&file->frho[i][1], file->nrho);
+        reader.next_dvector(&file->rhor[i][1], file->nr);
+      }
+
+      for (int i = 0; i < file->nelements; i++) {
+        for (int j = 0; j <= i; j++) {
+          reader.next_dvector(&file->z2r[i][j][1], file->nr);
+        }
+      }
+    } catch (TokenizerException & e) {
+      error->one(FLERR, e.what());
     }
   }
 
-  // read and broadcast header
+  // broadcast potential information
-  // extract element names from nelements line
+  MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
 
-  int n;
+  MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
-  if (me == 0) {
+  MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+
-    n = strlen(line) + 1;
+  // allocate memory on other procs
+  if (comm->me != 0) {
+    file->elements = new char*[file->nelements];
+    for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
+    memory->create(file->mass, file->nelements, "pair:mass");
+    memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+    memory->create(file->rhor, file->nelements, file->nr + 1, "pair:rhor");
+    memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
   }
-  MPI_Bcast(&n,1,MPI_INT,0,world);
-  MPI_Bcast(line,n,MPI_CHAR,0,world);
 
-  sscanf(line,"%d",&file->nelements);
+  // broadcast file->elements string array
-  int nwords = atom->count_words(line);
-  if (nwords != file->nelements + 1)
-    error->all(FLERR,"Incorrect element names in EAM potential file");
-
-  char **words = new char*[file->nelements+1];
-  nwords = 0;
-  strtok(line," \t\n\r\f");
-  while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
-
-  file->elements = new char*[file->nelements];
   for (int i = 0; i < file->nelements; i++) {
-    n = strlen(words[i]) + 1;
+    int n;
-    file->elements[i] = new char[n];
+    if (comm->me == 0) n = strlen(file->elements[i]) + 1;
-    strcpy(file->elements[i],words[i]);
+    MPI_Bcast(&n, 1, MPI_INT, 0, world);
-  }
+    if (comm->me != 0) file->elements[i] = new char[n];
-  delete [] words;
+    MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
-
-  if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    sscanf(line,"%d %lg %d %lg %lg",
-           &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
 
-  MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
+  // broadcast file->mass, frho, rhor
-  MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
+  for (int i = 0; i < file->nelements; i++) {
-  MPI_Bcast(&file->nr,1,MPI_INT,0,world);
+    MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->rhor[i][1], file->nr, MPI_DOUBLE, 0, world);
+  }
 
-  file->mass = new double[file->nelements];
+  // broadcast file->z2r
-  memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
+  for (int i = 0; i < file->nelements; i++) {
-  memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
+    for (int j = 0; j <= i; j++) {
-  memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
+      MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
-                 "pair:z2r");
-
-  int i,j,tmp;
-  for (i = 0; i < file->nelements; i++) {
-    if (me == 0) {
-      fgets(line,MAXLINE,fptr);
-      sscanf(line,"%d %lg",&tmp,&file->mass[i]);
     }
-    MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
-    if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
-    MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
-    if (me == 0) grab(fptr,file->nr,&file->rhor[i][1]);
-    MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
   }
-
-  for (i = 0; i < file->nelements; i++)
-    for (j = 0; j <= i; j++) {
-      if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
-      MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
-    }
-
-  // close the potential file
-
-  if (me == 0) fclose(fptr);
 }
 
 /* ----------------------------------------------------------------------

src/KOKKOS/pair_eam_fs_kokkos.cpp

@@ -29,11 +29,12 @@
 #include "memory_kokkos.h"
 #include "error.h"
 #include "atom_masks.h"
+#include "utils.h"
+#include "tokenizer.h"
+#include "potential_file_reader.h"
 
 using namespace LAMMPS_NS;
 
-#define MAXLINE 1024
-
 // Cannot use virtual inheritance on the GPU, so must duplicate code
 
 /* ---------------------------------------------------------------------- */
@@ -982,99 +983,113 @@ void PairEAMFSKokkos<DeviceType>::read_file(char *filename)
 {
   Fs *file = fs;
 
-  // open potential file
+  // read potential file
+  if(comm->me == 0) {
+    PotentialFileReader reader(lmp, filename, "EAM");
 
-  int me = comm->me;
+    try {
-  FILE *fptr;
+      reader.skip_line();
-  char line[MAXLINE];
+      reader.skip_line();
+      reader.skip_line();
 
-  if (me == 0) {
+      // extract element names from nelements line
-    fptr = force->open_potential(filename);
+      ValueTokenizer values = reader.next_values(1);
-    if (fptr == NULL) {
+      file->nelements = values.next_int();
-      char str[128];
+
-      snprintf(str,128,"Cannot open EAM potential file %s",filename);
+      if (values.count() != file->nelements + 1)
-      error->one(FLERR,str);
+        error->one(FLERR,"Incorrect element names in EAM potential file");
+
+      file->elements = new char*[file->nelements];
+      for (int i = 0; i < file->nelements; i++) {
+        const std::string word = values.next_string();
+        const int n = word.length() + 1;
+        file->elements[i] = new char[n];
+        strcpy(file->elements[i], word.c_str());
+      }
+
+      //
+
+      values = reader.next_values(5);
+      file->nrho = values.next_int();
+      file->drho = values.next_double();
+      file->nr   = values.next_int();
+      file->dr   = values.next_double();
+      file->cut  = values.next_double();
+
+      if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
+        error->one(FLERR,"Invalid EAM potential file");
+
+      memory->create(file->mass, file->nelements, "pair:mass");
+      memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+      memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+      memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+
+      for (int i = 0; i < file->nelements; i++) {
+        values = reader.next_values(2);
+        values.next_int(); // ignore
+        file->mass[i] = values.next_double();
+
+        reader.next_dvector(&file->frho[i][1], file->nrho);
+
+        for (int j = 0; j < file->nelements; j++) {
+          reader.next_dvector(&file->rhor[i][j][1], file->nr);
+        }
+      }
+
+      for (int i = 0; i < file->nelements; i++) {
+        for (int j = 0; j <= i; j++) {
+          reader.next_dvector(&file->z2r[i][j][1], file->nr);
+        }
+      }
+    } catch (TokenizerException & e) {
+      error->one(FLERR, e.what());
     }
   }
 
-  // read and broadcast header
+  // broadcast potential information
-  // extract element names from nelements line
+  MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
 
-  int n;
+  MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
-  if (me == 0) {
+  MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+  MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
-    fgets(line,MAXLINE,fptr);
+
-    n = strlen(line) + 1;
+  // allocate memory on other procs
+  if (comm->me != 0) {
+    file->elements = new char*[file->nelements];
+    for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
+    memory->create(file->mass, file->nelements, "pair:mass");
+    memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+    memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+    memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
   }
-  MPI_Bcast(&n,1,MPI_INT,0,world);
-  MPI_Bcast(line,n,MPI_CHAR,0,world);
 
-  sscanf(line,"%d",&file->nelements);
+  // broadcast file->elements string array
-  int nwords = atom->count_words(line);
-  if (nwords != file->nelements + 1)
-    error->all(FLERR,"Incorrect element names in EAM potential file");
-
-  char **words = new char*[file->nelements+1];
-  nwords = 0;
-  strtok(line," \t\n\r\f");
-  while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
-
-  file->elements = new char*[file->nelements];
   for (int i = 0; i < file->nelements; i++) {
-    n = strlen(words[i]) + 1;
+    int n;
-    file->elements[i] = new char[n];
+    if (comm->me == 0) n = strlen(file->elements[i]) + 1;
-    strcpy(file->elements[i],words[i]);
+    MPI_Bcast(&n, 1, MPI_INT, 0, world);
-  }
+    if (comm->me != 0) file->elements[i] = new char[n];
-  delete [] words;
+    MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
-
-  if (me == 0) {
-    fgets(line,MAXLINE,fptr);
-    sscanf(line,"%d %lg %d %lg %lg",
-           &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
   }
 
-  MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
+  // broadcast file->mass, frho, rhor
-  MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
+  for (int i = 0; i < file->nelements; i++) {
-  MPI_Bcast(&file->nr,1,MPI_INT,0,world);
+    MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
+    MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
-  MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
 
-  file->mass = new double[file->nelements];
+    for (int j = 0; j < file->nelements; j++) {
-  memory->create(file->frho,file->nelements,file->nrho+1,
+      MPI_Bcast(&file->rhor[i][j][1], file->nr, MPI_DOUBLE, 0, world);
-                                              "pair:frho");
-  memory->create(file->rhor,file->nelements,file->nelements,
-                 file->nr+1,"pair:rhor");
-  memory->create(file->z2r,file->nelements,file->nelements,
-                 file->nr+1,"pair:z2r");
-
-  int i,j,tmp;
-  for (i = 0; i < file->nelements; i++) {
-    if (me == 0) {
-      fgets(line,MAXLINE,fptr);
-      sscanf(line,"%d %lg",&tmp,&file->mass[i]);
-    }
-    MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
-
-    if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
-    MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
-
-    for (j = 0; j < file->nelements; j++) {
-      if (me == 0) grab(fptr,file->nr,&file->rhor[i][j][1]);
-      MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
     }
   }
 
-  for (i = 0; i < file->nelements; i++)
+  // broadcast file->z2r
-    for (j = 0; j <= i; j++) {
+  for (int i = 0; i < file->nelements; i++) {
-      if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
+    for (int j = 0; j <= i; j++) {
-      MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
+      MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
     }
-
+  }
-  // close the potential file
-
-  if (me == 0) fclose(fptr);
 }
 
 /* ----------------------------------------------------------------------

src/KOKKOS/pair_exp6_rx_kokkos.cpp

@@ -32,6 +32,7 @@
 #include "neigh_request.h"
 #include "atom_kokkos.h"
 #include "kokkos.h"
+#include "utils.h"
 
 #ifdef _OPENMP
 #include <omp.h>
@@ -1752,7 +1753,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
     // strip comment, skip line if blank
 
     if ((ptr = strchr(line,'#'))) *ptr = '\0';
-    nwords = atom->count_words(line);
+    nwords = utils::count_words(line);
     if (nwords == 0) continue;
 
     // concatenate additional lines until have params_per_line words
@@ -1771,7 +1772,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
       MPI_Bcast(&n,1,MPI_INT,0,world);
       MPI_Bcast(line,n,MPI_CHAR,0,world);
       if ((ptr = strchr(line,'#'))) *ptr = '\0';
-      nwords = atom->count_words(line);
+      nwords = utils::count_words(line);
     }
 
     if (nwords != params_per_line)

src/KOKKOS/pair_kokkos.h

@@ -51,7 +51,8 @@ struct DoCoul<1> {
 
 //Specialisation for Neighborlist types Half, HalfThread, Full
 template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
-struct PairComputeFunctor  {
+class PairComputeFunctor  {
+ public:
   typedef typename PairStyle::device_type device_type ;
   typedef ArrayTypes<device_type> AT;
 

src/KOKKOS/pair_snap_kokkos.h

@@ -112,7 +112,7 @@ public:
   void operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU>::member_type& team) const;
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (TagPairSNAPBeta,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPBeta>::member_type& team) const;
+  void operator() (TagPairSNAPBeta,const int& ii) const;
 
   template<int NEIGHFLAG>
   KOKKOS_INLINE_FUNCTION