Merge pull request #2538 from akohlmey/next-patch-release

Step version strings for the next patch release

.github/CONTRIBUTING.md

@@ -108,7 +108,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 
 For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
 Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
-Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
 If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.

README

@@ -37,14 +37,14 @@ tools                      pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://lammps.sandia.gov/doc/Manual.html         LAMMPS user manual
+https://lammps.sandia.gov/doc/Manual.html         LAMMPS manual
 https://lammps.sandia.gov/doc/Intro.html          hi-level introduction
 https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
 https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
 https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/pg_library.html     LAMMPS programmer guide
+https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
 https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/pg_developer.html   LAMMPS developer guide
+https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
 
 You can also create these doc pages locally:
 

cmake/CMakeLists.txt

@@ -220,6 +220,7 @@ if(BUILD_OMP)
   endif()
 
   if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@@ -661,7 +662,7 @@ if(BUILD_SHARED_LIBS)
     add_custom_target(
       install-python
       ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-      -m ${LAMMPS_PYTHON_DIR}/lammps.py
+      -p ${LAMMPS_PYTHON_DIR}/lammps
       -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
       COMMENT "Installing LAMMPS Python module")
@@ -691,11 +692,8 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if (Python_EXECUTABLE)
-    execute_process(COMMAND ${Python_EXECUTABLE}
-      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
-    install(FILES ${LAMMPS_PYTHON_DIR}/lammps.py DESTINATION ${PYTHON_INSTDIR})
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
+    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
   endif()
 endif()
 

cmake/Modules/Packages/KIM.cmake

@@ -19,6 +19,8 @@ if(CURL_FOUND)
     target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
   endif()
 endif()
+set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
+mark_as_advanced(KIM_EXTRA_UNITTESTS)
 find_package(PkgConfig QUIET)
 set(DOWNLOAD_KIM_DEFAULT ON)
 if(PKG_CONFIG_FOUND)
@@ -34,8 +36,8 @@ if(DOWNLOAD_KIM)
   enable_language(C)
   enable_language(Fortran)
   ExternalProject_Add(kim_build
-    URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
-    URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
+    URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
+    URL_MD5 ae1ddda2ef7017ea07934e519d023dca
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@@ -53,11 +55,28 @@ if(DOWNLOAD_KIM)
   add_library(LAMMPS::KIM UNKNOWN IMPORTED)
   set_target_properties(LAMMPS::KIM PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}"
-    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
-  target_link_libraries(lammps PRIVATE LAMMPS::KIM)
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api"
+    )
   add_dependencies(LAMMPS::KIM kim_build)
+  target_link_libraries(lammps PRIVATE LAMMPS::KIM)
+  # Set rpath so lammps build directory is relocatable
+  if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(_rpath_prefix "@loader_path")
+  else()
+    set(_rpath_prefix "$ORIGIN")
+  endif()
+  set_target_properties(lmp PROPERTIES
+    BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
+    )
 else()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
-  target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
+  if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
+    # For kim-api >= 2.2.0
+    find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
+    target_link_libraries(lammps PRIVATE KIM-API::kim-api)
+  else()
+    # For kim-api 2.1.3 (consistent with previous version of this file)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
+    target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
+  endif()
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.2.00.tar.gz
-    URL_MD5 81569170fe232e5e64ab074f7cca5e50
+    URL https://github.com/kokkos/kokkos/archive/3.2.01.tar.gz
+    URL_MD5 ba72440e285ccde05b403694ea0c92e5
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -50,7 +50,7 @@ if(DOWNLOAD_KOKKOS)
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.2.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.2.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -55,8 +55,8 @@ if(DOWNLOAD_PLUMED)
   endif()
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.6.1/plumed-src-2.6.1.tgz
-    URL_MD5 89a9a450fc6025299fe16af235957163
+    URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz
+    URL_MD5 95f29dd0c067577f11972ff90dfc7d12
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

cmake/Modules/YAML.cmake

@@ -0,0 +1,32 @@
+message(STATUS "Downloading and building YAML library")
+
+include(ExternalProject)
+set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+mark_as_advanced(YAML_URL)
+ExternalProject_Add(libyaml
+                    URL               ${YAML_URL}
+                    URL_MD5           bb15429d8fb787e7d3f1c83ae129a999
+                    SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
+                    BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
+                    CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
+                                      CXX=${CMAKE_CXX_COMPILER}
+                                      CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared
+                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
+                    TEST_COMMAND      "")
+
+ExternalProject_Get_Property(libyaml INSTALL_DIR)
+set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
+set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
+
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
+
+add_library(Yaml::Yaml UNKNOWN IMPORTED)
+set_target_properties(Yaml::Yaml PROPERTIES
+        IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
+add_dependencies(Yaml::Yaml libyaml)

cmake/presets/pgi.cmake

@@ -0,0 +1,16 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "pgc++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "pgcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "pgfortran" CACHE STRING "" FORCE)
+set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

doc/Makefile

@@ -229,7 +229,7 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install --upgrade pip; \
-		pip install --use-feature=2020-resolver -r $(BUILDDIR)/utils/requirements.txt; \
+		pip install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 

doc/github-development-workflow.md

@@ -95,7 +95,7 @@ on the pull request discussion page on GitHub, so that other developers
 can later review the entire discussion after the fact and understand the
 rationale behind choices made.  Exceptions to this policy are technical
 discussions, that are centered on tools or policies themselves
-(git, github, c++) rather than on the content of the pull request.
+(git, GitHub, c++) rather than on the content of the pull request.
 
 ### Checklist for Pull Requests
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "29 October 2020" "2020-10-29"
+.TH LAMMPS "24 December 2020" "2020-12-24"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -236,12 +236,15 @@ LAMMPS.
          cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
          # Building with LLVM/Clang Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+         # Building with PGI/Nvidia Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
 
       For compiling with the Clang/LLVM compilers a CMake preset is
       provided that can be loaded with
       `-C ../cmake/presets/clang.cmake`.  Similarly,
       `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the Intel compilers.
+      toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
+      should switch the compiler to the PGI compilers.
 
       In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts. By

doc/src/Build_development.rst

@@ -108,11 +108,18 @@ 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 scripts and inputs for integration, run, and regression testing
+are maintained in a
+`separate repository <https://github.com/lammps/lammps-testing>`_
+of the LAMMPS project on GitHub.
+
 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 `PyYAML <http://pyyaml.org/>`_ library and development
-headers to compile and will download and compile a recent version of the
+It requires the `YAML <http://pyyaml.org/>`_ library and development
+headers (if those are not found locally a recent version will be
+downloaded and compiled along with LAMMPS and the test program) to
+compile and will download and compile a specific recent version of the
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
@@ -162,22 +169,21 @@ The ``ctest`` command has many options, the most important ones are:
 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.
+The tests will adapt to the compilation settings of LAMMPS, so that tests
+will be skipped if prerequisite features are not available in LAMMPS.
 
 .. note::
 
-   The 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.
+   The unit test framework was added in spring 2020 and is under active
+   development.  The coverage is not complete and will be expanded over
+   time.
+
+Tests for styles of the same kind of style (e.g. pair styles or bond
+styles) are performed with the same test executable using different
+input files in YAML format.  So to add a test for another style of the
+same kind it may be sufficient to add a suitable YAML file.
+:doc:`Detailed instructions for adding tests <Developer_unittest>` are
+provided in the Programmer Guide part of the manual.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Build_extras.rst

@@ -282,6 +282,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
          -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
          -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
          -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
+         -D KIM_EXTRA_UNITTESTS=value    # enables extra unit tests, value = no (default) or yes
 
       If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
       will be downloaded and built inside the CMake build directory.  If
@@ -290,6 +291,11 @@ minutes to hours) to build.  Of course you only need to do that once.)
       ``PKG_CONFIG_PATH`` environment variable so that libkim-api can be
       found, or run the command ``source kim-api-activate``.
 
+      Extra unit tests can only be available if they are explicitly requested
+      (``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
+      are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
+      more details on this.
+
    .. tab:: Traditional make
 
       You can download and build the KIM library manually if you prefer;
@@ -338,6 +344,38 @@ specify your own CA cert path by setting the environment variable
 ``CURL_CA_BUNDLE`` to the path of your choice.  A call to the KIM web
 query would get this value from the environment variable.
 
+.. _kim_extra_unittests:
+
+KIM Extra unit tests (CMake only)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+During development, testing, or debugging, if
+:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
+enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
+``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
+
+Enabling the extra unit tests have some requirements,
+
+* It requires to have internet access.
+* It requires to have libcurl installed with the matching development headers
+  and the curl-config tool.
+* It requires to build LAMMPS with the PYTHON package installed and linked to
+  Python 3.6 or later. See the :ref:`PYTHON package build info <python>` for
+  more details on this.
+* It requires to have ``kim-property`` Python package installed, which can be
+  easily done using *pip* as ``pip install kim-property``, or from the
+  *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
+  Conda. More detailed information is available at:
+  `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
+* It is also necessary to install
+  ``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
+  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
+  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+  to learn how to install a pre-build binary of the OpenKIM Repository of
+  Models or see
+  `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
+  to learn how to install the specific KIM models.
+
 ----------
 
 .. _kokkos:

doc/src/Build_package.rst

@@ -1,4 +1,5 @@
 Include packages in build
+
 =========================
 
 In LAMMPS, a package is a group of files that enable a specific set of
@@ -160,6 +161,7 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
     cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake  # change settings to use the GNU compilers by default
     cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers

doc/src/Commands_bond.rst

@@ -35,6 +35,7 @@ OPT.
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
@@ -84,6 +85,7 @@ OPT.
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
    * :doc:`harmonic (iko) <angle_harmonic>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`

doc/src/Commands_fix.rst

@@ -62,6 +62,7 @@ OPT.
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
    * :doc:`eos/cv <fix_eos_cv>`
    * :doc:`eos/table <fix_eos_table>`
@@ -195,7 +196,7 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
-   * :doc:`shake <fix_shake>`
+   * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
    * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
@@ -220,6 +221,8 @@ OPT.
    * :doc:`temp/rescale <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
+   * :doc:`tgnpt/drude <fix_tgnh_drude>`
+   * :doc:`tgnvt/drude <fix_tgnh_drude>`
    * :doc:`thermal/conductivity <fix_thermal_conductivity>`
    * :doc:`ti/spring <fix_ti_spring>`
    * :doc:`tmd <fix_tmd>`

doc/src/Commands_pair.rst

@@ -241,6 +241,7 @@ OPT.
    * :doc:`spin/dipole/long <pair_spin_dipole>`
    * :doc:`spin/dmi <pair_spin_dmi>`
    * :doc:`spin/exchange <pair_spin_exchange>`
+   * :doc:`spin/exchange/biquadratic <pair_spin_exchange>`
    * :doc:`spin/magelec <pair_spin_magelec>`
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`

doc/src/Developer.rst

@@ -13,5 +13,7 @@ of time and requests from the LAMMPS user community.
    Developer_org
    Developer_flow
    Developer_write
+   Developer_notes
+   Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_notes.rst

@@ -0,0 +1,105 @@
+Notes for Developers and Code Maintainers
+-----------------------------------------
+
+This section documents how a few large sections of code with LAMMPS
+work at a conceptual level.  Comments on code in source files
+typically document what a variable stores, what a small section of
+code does, or what a function does or its input/outputs.  The topics
+on this page are intended to document code at a higher level.
+
+KSpace PPPM FFT grids
+^^^^^^^^^^^^^^^^^^^^^
+
+The various :doc:`KSpace PPPM <kspace_style>` styles in LAMMPS use
+FFTs to solve Poisson's equation.  This subsection describes:
+
+* how FFT grids are defined
+* how they are decomposed across processors
+* how they are indexed by each processor
+* how particle charge and electric field values are mapped to/from
+  the grid
+
+An FFT grid cell is a 3d volume; grid points are corners of a grid
+cell and the code stores values assigned to grid points in vectors or
+3d arrays.  A global 3d FFT grid has points indexed 0 to N-1 inclusive
+in each dimension.
+
+Each processor owns two subsets of the grid, each subset is
+brick-shaped.  Depending on how it is used, these subsets are
+allocated as a 1d vector or 3d array.  Either way, the ordering of
+values within contiguous memory x fastest, then y, z slowest.
+
+For the ``3d decomposition`` of the grid, the global grid is
+partitioned into bricks that correspond to the sub-domains of the
+simulation box that each processor owns.  Often, this is a regular 3d
+array (Px by Py by Pz) of bricks, where P = number of processors =
+Px * Py * Pz.  More generally it can be a tiled decomposition, where
+each processor owns a brick and the union of all the bricks is the
+global grid.  Tiled decompositions are produced by load balancing with
+the RCB algorithm; see the :doc:`balance rcb <balance>` command.
+
+For the ``FFT decompostion`` of the grid, each processor owns a brick
+that spans the entire x dimension of the grid while the y and z
+dimensions are partitioned as a regular 2d array (P1 by P2), where P =
+P1 * P2.
+
+The following indices store the inclusive bounds of the brick a
+processor owns, within the global grid:
+
+.. parsed-literal::
+
+   nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
+   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
+   nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
+
+The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
+dimension, where N is the grid size.
+
+The ``out`` indices index an array which stores the ``in`` subset of
+the grid plus ghost cells that surround it.  These indices can thus be
+< 0 or >= N.
+
+The number of ghost cells a processor owns in each of the 6 directions
+is a function of:
+
+.. parsed-literal::
+
+   neighbor skin distance (since atoms can move outside a proc subdomain)
+   qdist = offset or charge from atom due to TIP4P fictitious charge
+   order = mapping stencil size
+   shift = factor used when order is an even number (see below)
+
+Here is an explanation of how the PPPM variables ``order``,
+``nlower`` / ``nupper``, ``shift``, and ``OFFSET`` work. They are the
+relevant variables that determine how atom charge is mapped to grid
+points and how field values are mapped from grid points to atoms:
+
+.. parsed-literal::
+
+   order = # of nearby grid points in each dim that atom charge/field are mapped to/from
+   nlower,nupper = extent of stencil around the grid point an atom is assigned to
+   OFFSET = large integer added/subtracted when mapping to avoid int(-0.75) = 0 when -1 is the desired result
+
+The particle_map() method assigns each atom to a grid point.
+
+If order is even, say 4:
+
+.. parsed-literal::
+
+   atom is assigned to grid point to its left (in each dim)
+   shift = OFFSET
+   nlower = -1, nupper = 2, which are offsets from assigned grid point
+   window of mapping grid pts is thus 2 grid points to left of atom, 2 to right
+
+If order is odd, say 5:
+
+.. parsed-literal::
+
+   atom is assigned to left/right grid pt it is closest to (in each dim)
+   shift = OFFSET + 0.5
+   nlower = 2, nupper = 2
+   if point is in left half of cell, then window of affected grid pts is 3 grid points to left of atom, 2 to right
+   if point is in right half of cell, then window of affected grid pts is 2 grid points to left of atom, 3 to right
+
+These settings apply to each dimension, so that if order = 5, an
+atom's charge is mapped to 125 grid points that surround the atom.

doc/src/Developer_unittest.rst

@@ -0,0 +1,523 @@
+Adding tests for unit testing
+-----------------------------
+
+This section discusses adding or expanding tests for the unit test
+infrastructure included into the LAMMPS source code distribution.
+Unlike example inputs, unit tests focus on testing the "local" behavior
+of individual features, tend to run very fast, and should be set up to
+cover as much of the added code as possible.  When contributing code to
+the distribution, the LAMMPS developers will appreciate if additions
+to the integrated unit test facility are included.
+
+Given the complex nature of MD simulations where many operations can
+only be performed when suitable "real" simulation environment has been
+set up, not all tests will be unit tests in the strict definition of
+the term.  They are rather executed on a more abstract level by issuing
+LAMMPS script commands and then inspecting the changes to the internal
+data.  For some classes of tests, generic test programs have been
+written that can be applied to parts of LAMMPS that use the same
+interface (via polymorphism) and those are driven by input files, so
+tests can be added by simply adding more of those input files.  Those
+tests should be seen more as a hybrid between unit and regression tests.
+
+When adding tests it is recommended to also :ref:`enable support for
+code coverage reporting <testing>`, and study the coverage reports
+so that it is possible to monitor which parts of the code of a given
+file are executed during the tests and which tests would need to be
+added to increase the coverage.
+
+The tests are grouped into categories and corresponding folders.
+The following sections describe how the tests are implemented and
+executed in those categories with increasing complexity of tests
+and implementation.
+
+
+Tests for utility functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These tests are driven by programs in the ``unittest/utils`` folder
+and most closely resemble conventional unit tests. There is one test
+program for each namespace or group of classes or file. The naming
+convention for the sources and executables is that they start with
+with ``test_``.  The following sources and groups of tests are currently
+available:
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+   :align: left
+
+   * - File name:
+     - Test name:
+     - Description:
+   * - ``test_fmtlib.cpp``
+     - FmtLib
+     - Tests for ``fmtlib::`` functions used by LAMMPS
+   * - ``test_math_eigen_impl.cpp``
+     - MathEigen
+     - Tests for ``MathEigen::`` classes and functions
+   * - ``test_mempool.cpp``
+     - MemPool
+     - Tests for :cpp:class:`MyPage <LAMMPS_NS::MyPage>` and :cpp:class:`MyPoolChunk <LAMMPS_NS::MyPoolChunk>`
+   * - ``test_tokenizer.cpp``
+     - Tokenizer
+     - Tests for :cpp:class:`Tokenizer <LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer <LAMMPS_NS::ValueTokenizer>`
+   * - ``test_utils.cpp``
+     - Utils
+     - Tests for ``utils::`` :doc:`functions <Developer_utils>`
+
+To add tests either an existing source file needs to be modified or a
+new source file needs to be added to the distribution and enabled for
+testing.  To add a new file suitable CMake script code needs to be added
+to the ``CMakeLists.txt`` file in the ``unittest/utils`` folder.  Example:
+
+.. code-block:: cmake
+
+   add_executable(test_tokenizer test_tokenizer.cpp)
+   target_link_libraries(test_tokenizer PRIVATE lammps GTest::GMockMain GTest::GMock GTest::GTest)
+   add_test(Tokenizer test_tokenizer)
+
+This adds instructions to build the ``test_tokenizer`` executable from
+``test_tokenizer.cpp`` and links it with the GoogleTest libraries and the
+LAMMPS library as well as it uses the ``main()`` function from the
+GoogleMock library of GoogleTest.  The third line registers the executable
+as a test program to be run from ``ctest`` under the name ``Tokenizer``.
+
+The test executable itself will execute multiple individual tests
+through the GoogleTest framework. In this case each test consists of
+creating a tokenizer class instance with a given string and explicit or
+default separator choice, and then executing member functions of the
+class and comparing their results with expected values. A few examples:
+
+.. code-block:: c++
+
+   TEST(Tokenizer, empty_string)
+   {
+       Tokenizer t("", " ");
+       ASSERT_EQ(t.count(), 0);
+   }
+
+   TEST(Tokenizer, two_words)
+   {
+       Tokenizer t("test word", " ");
+       ASSERT_EQ(t.count(), 2);
+   }
+
+   TEST(Tokenizer, default_separators)
+   {
+       Tokenizer t(" \r\n test \t word \f");
+       ASSERT_THAT(t.next(), Eq("test"));
+       ASSERT_THAT(t.next(), Eq("word"));
+       ASSERT_EQ(t.count(), 2);
+   }
+
+Each of these TEST functions will become an individual
+test run by the test program. When using the ``ctest``
+command as a front end to run the tests, their output
+will be suppressed and only a summary printed, but adding
+the '-V' option will then produce output from the tests
+above like the following:
+
+.. code-block::
+
+   [...]
+   1: [ RUN      ] Tokenizer.empty_string
+   1: [       OK ] Tokenizer.empty_string (0 ms)
+   1: [ RUN      ] Tokenizer.two_words
+   1: [       OK ] Tokenizer.two_words (0 ms)
+   1: [ RUN      ] Tokenizer.default_separators
+   1: [       OK ] Tokenizer.default_separators (0 ms)
+   [...]
+
+The MathEigen test collection has been adapted from a standalone test
+and does not use the GoogleTest framework and thus not representative.
+The other test sources, however, can serve as guiding examples for
+additional tests.
+
+Tests for individual LAMMPS commands
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The tests ``unittest/commands`` are a bit more complex as they require
+to first create a :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
+and then use the :doc:`C++ API <Cplusplus>` to pass individual commands
+to that LAMMPS instance.  For that reason these tests use a GoogleTest
+"test fixture", i.e. a class derived from ``testing::Test`` that will
+create (and delete) the required LAMMPS class instance for each set of
+tests in a ``TEST_F()`` function.  Please see the individual source files
+for different examples of setting up suitable test fixtures.  Here is an
+example for implementing a test using a fixture by first checking the
+default value and then issuing LAMMPS commands and checking whether they
+have the desired effect:
+
+.. code-block:: c++
+
+   TEST_F(SimpleCommandsTest, ResetTimestep)
+   {
+       ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       if (!verbose) ::testing::internal::CaptureStdout();
+       lmp->input->one("reset_timestep 10");
+       if (!verbose) ::testing::internal::GetCapturedStdout();
+       ASSERT_EQ(lmp->update->ntimestep, 10);
+
+       if (!verbose) ::testing::internal::CaptureStdout();
+       lmp->input->one("reset_timestep 0");
+       if (!verbose) ::testing::internal::GetCapturedStdout();
+       ASSERT_EQ(lmp->update->ntimestep, 0);
+   }
+
+Please note the use of the (global) verbose variable to control whether
+the LAMMPS command will be silent by capturing the output or not.  In
+the default case, verbose == false, the test output will be compact and
+not mixed with LAMMPS output. However setting the verbose flag (via
+setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
+helpful to understand why tests fail unexpectedly.
+
+Another complexity of these tests stems from the need to capture
+situations where LAMMPS will stop with an error, i.e. handle so-called
+"death tests".  Here the LAMMPS code will operate differently depending
+on whether it was configured to throw C++ exceptions on errors or call
+either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
+also needs to detect whether LAMMPS was compiled with the OpenMPI
+library, as OpenMPI is **only** compatible the death test options of the
+GoogleTest library when C++ exceptions are enabled; otherwise those
+"death tests" must be skipped to avoid reporting bogus failures.  The
+specifics of this step are implemented in the ``TEST_FAILURE()``
+macro. These tests operate by capturing the screen output when executing
+the failing command and then comparing that with a provided regular
+expression string pattern.  Example:
+
+.. code-block:: C++
+
+   TEST_F(SimpleCommandsTest, UnknownCommand)
+   {
+       TEST_FAILURE(".*ERROR: Unknown command.*", lmp->input->one("XXX one two"););
+   }
+
+The following test programs are currently available:
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+   :align: left
+
+   * - File name:
+     - Test name:
+     - Description:
+   * - ``test_simple_commands.cpp``
+     - SimpleCommands
+     - Tests for LAMMPS commands that do not require a box
+   * - ``test_lattice_region.cpp``
+     - LatticeRegion
+     - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
+   * - ``test_kim_commands.cpp``
+     - KimCommands
+     - Tests for several commands from the :ref:`KIM package <PKG-KIM>`
+   * - ``test_reset_ids.cpp``
+     - ResetIDs
+     - Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
+
+
+Tests for the C-style library interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Tests for validating the LAMMPS C-style library interface are in the
+``unittest/c-library`` folder.  They are implemented in either way used
+for utility functions and for LAMMPS commands, but use the functions
+implemented in the ``src/library.cpp`` file as much as possible.  There
+may be some overlap with other tests, but only in as much as is required
+to test the C-style library API.  The tests are distributed over
+multiple test programs which tries to match the grouping of the
+functions in the source code and :ref:`in the manual <lammps_c_api>`.
+
+This group of tests also includes tests invoking LAMMPS in parallel
+through the library interface, provided that LAMMPS was compiled with
+MPI support.  These include tests where LAMMPS is run in multi-partition
+mode or only on a subset of the MPI world communicator.  The CMake
+script code for adding this kind of test looks like this:
+
+.. code-block:: CMake
+
+   if (BUILD_MPI)
+     add_executable(test_library_mpi test_library_mpi.cpp)
+     target_link_libraries(test_library_mpi PRIVATE lammps GTest::GTest GTest::GMock)
+     target_compile_definitions(test_library_mpi PRIVATE ${TEST_CONFIG_DEFS})
+     add_mpi_test(NAME LibraryMPI NUM_PROCS 4 COMMAND $<TARGET_FILE:test_library_mpi>)
+   endif()
+
+Note the custom function ``add_mpi_test()`` which adapts how ``ctest``
+will execute the test so it is launched in parallel (with 4 MPI ranks).
+
+Tests for the Python module and package
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/python`` folder contains primarily tests for classes and
+functions in the LAMMPS python module but also for commands in the
+PYTHON package.  These tests are only enabled, if the necessary
+prerequisites are detected or enabled during configuration and
+compilation of LAMMPS (shared library build enabled, Python interpreter
+found, Python development files found).
+
+The Python tests are implemented using the ``unittest`` standard Python
+module and split into multiple files with similar categories as the
+tests for the C-style library interface.
+
+Tests for the Fortran interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Tests for using the Fortran module are in the ``unittest/fortran``
+folder.  Since they are also using the GoogleTest library, they require
+to also implement test wrappers in C++ that will call fortran functions
+which provide a C function interface through ISO_C_BINDINGS that will in
+turn call the functions in the LAMMPS Fortran module.  This part of the
+unit tests is incomplete since the Fortran module it is based on is
+incomplete as well.
+
+Tests for the C++-style library interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The tests in the ``unittest/cplusplus`` folder are somewhat similar to
+the tests for the C-style library interface, but do not need to test the
+several convenience and utility functions that are only available through
+the C-style interface.  Instead it can focus on the more generic features
+that are used internally.  This part of the unit tests is currently still
+mostly in the planning stage.
+
+Tests for reading and writing file formats
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/formats`` folder contains test programs for reading and
+writing files like data files, restart files, potential files or dump files.
+This covers simple things like the file i/o convenience functions in the
+``utils::`` namespace to complex tests of atom styles where creating and
+deleting of atoms with different properties is tested in different ways
+and through script commands or reading and writing of data or restart files.
+
+Tests for styles computing or modifying forces
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These are tests common configurations for pair styles, bond styles,
+angle styles, kspace styles and certain fix styles.  Those are tests
+driven by some test executables build from sources in the
+``unittest/force-styles`` folder and use LAMMPS input template and data
+files as well as input files in YAML format from the
+``unittest/force-styles/tests`` folder. The YAML file names have to
+follow some naming conventions so they get associated with the test
+programs and categorized and listed with canonical names in the list
+of tests as displayed by ``ctest -N``.  If you add a new YAML file,
+you need to re-run CMake to update the corresponding list of tests.
+
+A minimal YAML file for a (molecular) pair style test will looks
+something like the following (see ``mol-pair-zero.yaml``):
+
+.. code-block:: yaml
+
+   ---
+   lammps_version: 24 Aug 2020
+   date_generated: Tue Sep 15 09:44:21 202
+   epsilon: 1e-14
+   prerequisites: ! |
+     atom full
+     pair zero
+   pre_commands: ! ""
+   post_commands: ! ""
+   input_file: in.fourmol
+   pair_style: zero 8.0
+   pair_coeff: ! |
+     * *
+   extract: ! ""
+   natoms: 29
+   init_vdwl: 0
+   init_coul: 0
+
+   [...]
+
+The following table describes the available keys and their purpose for
+testing pair styles:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Key:
+     - Description:
+   * - lammps_version
+     - LAMMPS version used to last update the reference data
+   * - date_generated
+     - date when the file was last updated
+   * - epsilon
+     - base value for the relative precision required for tests to pass
+   * - prerequisites
+     - list of style kind / style name pairs required to run the test
+   * - pre_commands
+     - LAMMPS commands to be executed before the input template file is read
+   * - post_commands
+     - LAMMPS commands to be executed right before the actual tests
+   * - input_file
+     - LAMMPS input file template based on pair style zero
+   * - pair_style
+     - arguments to the pair_style command to be tested
+   * - pair_coeff
+     - list of pair_coeff arguments to set parameters for the input template
+   * - extract
+     - list of keywords supported by ``Pair::extract()`` and their dimension
+   * - natoms
+     - number of atoms in the input file template
+   * - init_vdwl
+     - non-Coulomb pair energy after "run 0"
+   * - init_coul
+     - Coulomb pair energy after "run 0"
+   * - init_stress
+     - stress tensor after "run 0"
+   * - init_forces
+     - forces on atoms after "run 0"
+   * - run_vdwl
+     - non-Coulomb pair energy after "run 4"
+   * - run_coul
+     - Coulomb pair energy after "run 4"
+   * - run_stress
+     - stress tensor after "run 4"
+   * - run_forces
+     - forces on atoms after "run 4"
+
+The test program will read all this data from the YAML file and then
+create a LAMMPS instance, apply the settings/commands from the YAML file
+as needed and then issue a "run 0" command, write out a restart file, a
+data file and a coeff file. The actual test will then compare computed
+energies, stresses, and forces with the reference data, issue a "run 4"
+command and compare to the second set of reference data.  This will be
+run with both the newton_pair setting enabled and disabled and is
+expected to generate the same results (allowing for some numerical
+noise). Then it will restart from the previously generated restart and
+compare with the reference and also start from the data file.  A final
+check will use multi-cutoff r-RESPA (if supported by the pair style) at
+a 1:1 split and compare to the Verlet results.  These sets of tests are
+run with multiple test fixtures for accelerated styles (OPT, USER-OMP,
+USER-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
+these tests the relative error (epsilon) is lowered by a common factor
+due to the additional numerical noise, but the tests are still comparing
+to the same reference data.
+
+Additional tests will check whether all listed extract keywords are
+supported and have the correct dimensionality and the final set of tests
+will set up a few pairs of atoms explicitly and in such a fashion that
+the forces on the atoms computed from ``Pair::compute()`` will match
+individually with the results from ``Pair::single()``, if the pair style
+does support that functionality.
+
+With this scheme a large fraction of the code of any tested pair style
+will be executed and consistent results are required for different
+settings and between different accelerated pair style variants and the
+base class, as well as for computing individual pairs through the
+``Pair::single()`` where supported.
+
+The ``test_pair_style`` tester is used with 4 categories of test inputs:
+
+- pair styles compatible with molecular systems using bonded
+  interactions and exclusions.  For pair styles requiring a KSpace style
+  the KSpace computations are disabled.  The YAML files match the
+  pattern "mol-pair-\*.yaml" and the tests are correspondingly labeled
+  with "MolPairStyle:\*"
+- pair styles not compatible with the previous input template.
+  The YAML files match the pattern "atomic-pair-\*.yaml" and the tests are
+  correspondingly labeled with "AtomicPairStyle:\*"
+- manybody pair styles.
+  The YAML files match the pattern "atomic-pair-\*.yaml" and the tests are
+  correspondingly labeled with "AtomicPairStyle:\*"
+- kspace styles.
+  The YAML files match the pattern "kspace-\*.yaml" and the tests are
+  correspondingly labeled with "KSpaceStyle:\*". In these cases a compatible
+  pair style is defined, but the computation of the pair style contributions
+  is disabled.
+
+The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
+fashion and share support functions with the pair style tester.  The final
+group of tests in this section is for fix styles that add/manipulate forces
+and velocities, e.g. for time integration, thermostats and more.
+
+Adding a new test is easiest done by copying and modifying an existing test
+for a style that is similar to one to be tested.  The file name should follow
+the naming conventions described above and after copying the file, the first
+step is to replace the style names where needed.  The coefficient values
+do not have to be meaningful, just in a reasonable range for the given system.
+It does not matter if some forces are large, for as long as they do not diverge.
+
+The template input files define a large number of index variables at the top
+that can be modified inside the YAML file to control the behavior.  For example,
+if a pair style requires a "newton on" setting, the following can be used in
+as the "pre_commands" section:
+
+.. code-block:: yaml
+
+   pre_commands: ! |
+     variable newton_pair delete
+     variable newton_pair index on
+
+And for a pair style requiring a kspace solver the following would be used as
+the "post_commands" section:
+
+.. code-block:: yaml
+
+   post_commands: ! |
+     pair_modify table 0
+     kspace_style pppm/tip4p 1.0e-6
+     kspace_modify gewald 0.3
+     kspace_modify compute no
+
+Note that this disables computing the kspace contribution, but still will run
+the setup.  The "gewald" parameter should be set explicitly to speed up the run.
+For styles with long-range electrostatics, typically two tests are added one using
+the (slower) analytic approximation of the erfc() function and the other using
+the tabulated coulomb, to test both code paths. The reference results in the YAML
+files then should be compared manually, if they agree well enough within the limits
+of those two approximations.
+
+The ``test_pair_style`` and equivalent programs have special command line options
+to update the YAML files. Running a command like
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
+
+will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
+the reference data and write a new file with to ``new.yaml``.  If this step fails,
+there are likely some (LAMMPS or YAML) syntax issues in the YAML file that need to
+be resolved and then one can compare the two files to see if the output is as expected.
+
+It is also possible to do an update in place with:
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml -u
+
+And one can finally run the full set of tests with:
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml
+
+This will just print a summary of the groups of tests.  When using the "-v" flag
+the test will also keep any LAMMPS output and when using the "-s" flag, there
+will be some statistics reported on the relative errors for the individual checks
+which can help to figure out what would be a good choice of the epsilon parameter.
+It should be as small as possible to catch any unintended side effects from changes
+elsewhere, but large enough to accommodate the numerical noise due to the implementation
+of the potentials and differences in compilers.
+
+.. note::
+
+   These kinds of tests can be very sensitive to compiler optimization and
+   thus the expectation is that they pass with compiler optimization turned
+   off. When compiler optimization is enabled, there may be some failures, but
+   one has to carefully check whether those are acceptable due to the enhanced
+   numerical noise from reordering floating-point math operations or due to
+   the compiler mis-compiling the code. That is not always obvious.
+
+
+Tests for programs in the tools folder
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/tools`` folder contains tests for programs in the
+``tools`` folder.  This currently only contains tests for the LAMMPS
+shell, which are implemented as a python scripts using the ``unittest``
+Python module and launching the tool commands through the ``subprocess``
+Python module.

doc/src/Errors_warnings.rst

@@ -119,7 +119,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
 
 *Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
-
    Since LAMMPS stores topology data with individual atoms, all atoms
    comprising a bond, angle, dihedral or improper must be present on any
    sub-domain that "owns" the atom with the information, either as a

doc/src/Howto_drude.rst

@@ -42,10 +42,11 @@ screening. It may be necessary to use the *extra/special/per/atom*
 keyword of the :doc:`read_data <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
 group.
 
-There are two ways to thermostat the Drude particles at a low
+There are three ways to thermostat the Drude particles at a low
 temperature: use either :doc:`fix langevin/drude <fix_langevin_drude>`
 for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
-thermostat. The former requires use of the command :doc:`comm_modify vel yes <comm_modify>`. The latter requires two separate integration
+thermostat, or :doc:`fix tgnvt/drude <fix_tgnh_drude>` for a temperature-grouped Nose-Hoover thermostat.
+The first and third require use of the command :doc:`comm_modify vel yes <comm_modify>`. The second requires two separate integration
 fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
 degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
 command *comm_modify vel yes*.

doc/src/Howto_drude2.rst

@@ -36,7 +36,7 @@ polarizability :math:`\alpha` by
 
 Ideally, the mass of the Drude particle should be small, and the
 stiffness of the harmonic bond should be large, so that the Drude
-particle remains close ot the core. The values of Drude mass, Drude
+particle remains close to the core. The values of Drude mass, Drude
 charge, and force constant can be chosen following different
 strategies, as in the following examples of polarizable force
 fields:
@@ -221,6 +221,14 @@ modification of forces but no position/velocity updates), the fix
 
    fix NVE all nve
 
+To avoid the flying ice cube artifact, where the atoms progressively freeze and the
+center of mass of the whole system drifts faster and faster, the *fix momentum*
+can be used. For instance:
+
+.. code-block:: LAMMPS
+
+   fix MOMENTUM all momentum 100 linear 1 1 1
+
 Finally, do not forget to update the atom type elements if you use
 them in a *dump_modify ... element ...* command, by adding the element
 type of the DPs. Here for instance
@@ -376,14 +384,7 @@ For our phenol example, the groups would be defined as
 
 Note that with the fixes *drude/transform*\ , it is not required to
 specify *comm_modify vel yes* because the fixes do it anyway (several
-times and for the forces also).  To avoid the flying ice cube artifact
-:ref:`(Lamoureux and Roux) <Lamoureux2>`, where the atoms progressively freeze and the
-center of mass of the whole system drifts faster and faster, the *fix
-momentum* can be used. For instance:
-
-.. code-block:: LAMMPS
-
-   fix MOMENTUM all momentum 100 linear 1 1 1
+times and for the forces also).
 
 It is a bit more tricky to run a NPT simulation with Nose-Hoover
 barostat and thermostat.  First, the volume should be integrated only
@@ -404,6 +405,31 @@ instructions for thermostatting and barostatting will look like
    fix NVT DRUDES nvt temp 1. 1. 20
    fix INVERSE all drude/transform/inverse
 
+Another option for thermalizing the Drude model is to use the
+temperature-grouped Nose-Hoover (TGNH) thermostat proposed by :ref:`(Son) <TGNH-SON>`.
+This is implemented as :doc:`fix tgnvt/drude <fix_tgnh_drude>` and :doc:`fix tgnpt/drude <fix_tgnh_drude>`.
+It separates the kinetic energy into three contributions:
+the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs,
+and the relative motion of atom-Drude pairs.
+An independent Nose-Hoover chain is applied to each type of motion.
+When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with :doc:`thermo_style` command.
+
+NVT simulation with TGNH thermostat
+
+.. code-block:: LAMMPS
+
+   comm_modify vel yes
+   fix TGNVT all tgnvt/drude temp 300. 300. 100 1. 20
+   thermo_style custom f_TGNVT[1] f_TGNVT[2] f_TGNVT[3]
+
+NPT simulation with TGNH thermostat
+
+.. code-block:: LAMMPS
+
+   comm_modify vel yes
+   fix TGNPT all tgnpt/drude temp 300. 300. 100 1. 20 iso 1. 1. 500
+   thermo_style custom f_TGNPT[1] f_TGNPT[2] f_TGNPT[3]
+
 ----------
 
 **Rigid bodies**
@@ -480,3 +506,7 @@ NPT ensemble using Nose-Hoover thermostat:
 
 **(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
 Let, 418, 245-249 (2006)
+
+.. _TGNH-Son:
+
+**(Son)** Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).

doc/src/Howto_github.rst

@@ -72,7 +72,7 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
 
 **Feature branches**
 
-First of all, create a clone of your version on github on your local
+First of all, create a clone of your version on GitHub on your local
 machine via HTTPS:
 
 .. code-block:: bash
@@ -155,7 +155,7 @@ useful message that explains the change.
 
 .. code-block:: bash
 
-     $ git commit -m 'Finally updated the github tutorial'
+     $ git commit -m 'Finally updated the GitHub tutorial'
 
 After the commit, the changes can be pushed to the same branch on GitHub:
 

doc/src/Howto_pylammps.rst

@@ -9,8 +9,8 @@ Overview
 ``PyLammps`` is a Python wrapper class for LAMMPS which can be created
 on its own or use an existing lammps Python object.  It creates a simpler,
 more "pythonic" interface to common LAMMPS functionality, in contrast to
-the ``lammps.py`` wrapper for the C-style LAMMPS library interface which
-is written using `Python ctypes <ctypes_>`_.  The ``lammps.py`` wrapper
+the ``lammps`` wrapper for the C-style LAMMPS library interface which
+is written using `Python ctypes <ctypes_>`_.  The ``lammps`` wrapper
 is discussed on the :doc:`Python_head` doc page.
 
 Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable

doc/src/Howto_walls.rst

@@ -67,5 +67,5 @@ rotate.
 
 The only frictional idealized walls currently in LAMMPS are flat or
 curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
-command.  At some point we plan to allow regoin surfaces to be used as
+command.  At some point we plan to allow region surfaces to be used as
 frictional walls, as well as triangulated surfaces.

doc/src/Intro_citing.rst

@@ -24,13 +24,15 @@ DOI for the LAMMPS code
 LAMMPS developers use the `Zenodo service at CERN
 <https://zenodo.org/>`_ to create digital object identifies (DOI) for
 stable releases of the LAMMPS code. There are two types of DOIs for the
-LAMMPS source code: 1) the canonical DOI for **all** versions of LAMMPS,
-which will always point to the latest stable release version is:
+LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
+which will always point to the **latest** stable release version is:
 
-  `DOI: 10.5281/zenodo.3726416 <https://dx.doi/org/10.5281/zenodo.3726416>`_
+- DOI: `10.5281/zenodo.3726416 <https://dx.doi.org/10.5281/zenodo.3726416>`_
 
-In addition there are DOIs for individual stable releases starting with
-the `3 March 2020 version, DOI:10.5281/zenodo.3726417 <https://dx.doi/org/10.5281/zenodo.3726416>`_
+In addition there are DOIs for individual stable releases. Currently there are:
+
+- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
+- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
 
 
 Home page

doc/src/Packages_details.rst

@@ -1036,9 +1036,11 @@ the usual manner via MD.  Various pair, fix, and compute styles.
 * :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
 * :doc:`pair_style spin/dmi <pair_spin_dmi>`
 * :doc:`pair_style spin/exchange <pair_spin_exchange>`
+* :doc:`pair_style spin/exchange/biquadratic <pair_spin_exchange>`
 * :doc:`pair_style spin/magelec <pair_spin_magelec>`
 * :doc:`pair_style spin/neel <pair_spin_neel>`
 * :doc:`fix nve/spin <fix_nve_spin>`
+* :doc:`fix langevin/spin <fix_langevin_spin>`
 * :doc:`fix precession/spin <fix_precession_spin>`
 * :doc:`compute spin <compute_spin>`
 * :doc:`neb/spin <neb_spin>`

doc/src/Python_ext.rst

@@ -9,7 +9,7 @@ This means you can extend the Python wrapper by following these steps:
 * Add a new interface function to ``src/library.cpp`` and
   ``src/library.h``.
 * Rebuild LAMMPS as a shared library.
-* Add a wrapper method to ``python/lammps.py`` for this interface
+* Add a wrapper method to ``python/lammps/core.py`` for this interface
   function.
 * Define the corresponding ``argtypes`` list and ``restype``
   in the ``lammps.__init__()`` function.

doc/src/Python_install.rst

@@ -8,9 +8,9 @@ module.  Because of the dynamic loading, it is required that LAMMPS is
 compiled in :ref:`"shared" mode <exe>`.  It is also recommended to
 compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
 
-Two files are necessary for Python to be able to invoke LAMMPS code:
+Two components are necessary for Python to be able to invoke LAMMPS code:
 
-* The LAMMPS Python Module (``lammps.py``) from the ``python`` folder
+* The LAMMPS Python Package (``lammps``) from the ``python`` folder
 * The LAMMPS Shared Library (``liblammps.so``, ``liblammps.dylib`` or
   ``liblammps.dll``) from the folder where you compiled LAMMPS.
 
@@ -25,10 +25,10 @@ Installing the LAMMPS Python Module and Shared Library
 ======================================================
 
 Making LAMMPS usable within Python and vice versa requires putting the
-LAMMPS Python module file (``lammps.py``) into a location where the
+LAMMPS Python package (``lammps``) into a location where the
 Python interpreter can find it and installing the LAMMPS shared library
-into a folder that the dynamic loader searches or into the same folder
-where the ``lammps.py`` file is.  There are multiple ways to achieve
+into a folder that the dynamic loader searches or inside of the installed
+``lammps`` package folder.  There are multiple ways to achieve
 this.
 
 #. Do a full LAMMPS installation of libraries, executables, selected
@@ -36,13 +36,13 @@ this.
    available via CMake), which can also be either system-wide or into
    user specific folders.
 
-#. Install both files into a Python ``site-packages`` folder, either
+#. Install both components into a Python ``site-packages`` folder, either
    system-wide or in the corresponding user-specific folder. This way no
    additional environment variables need to be set, but the shared
    library is otherwise not accessible.
 
-#. Do an installation into a virtual environment. This can either be
-   an installation of the python module only or a full installation.
+#. Do an installation into a virtual environment. This can either be an
+   installation of the Python package only or a full installation of LAMMPS.
 
 #. Leave the files where they are in the source/development tree and
    adjust some environment variables.
@@ -81,19 +81,19 @@ this.
 
       This leads to an installation to the following locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$HOME/.local/lib/`` (32bit)                           |                                                             |
-      |                        | * ``$HOME/.local/lib64/`` (64bit)                         |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$HOME/.local/bin/``                                   |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/``               | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python package  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$HOME/.local/lib/`` (32bit)                                 | Set shared loader environment variable to this path         |
+      |                        | * ``$HOME/.local/lib64/`` (64bit)                               | (see below for more info on this)                           |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``$HOME/.local/bin/``                                         |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/``                     | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       For a system-wide installation you need to set
       ``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
@@ -102,19 +102,19 @@ this.
       privilege, e.g. by using ``sudo cmake --install .``.  The
       installation folders will then by changed to:
 
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                          | Notes                                                       |
-      +========================+===================================================+=============================================================+
-      | LAMMPS Python Module   | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``/usr/lib/`` (32bit)                           |                                                             |
-      |                        | * ``/usr/lib64/`` (64bit)                         |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``/usr/bin/``                                   |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``/usr/share/lammps/potentials/``               |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                | Notes                                                       |
+      +========================+=========================================================+=============================================================+
+      | LAMMPS Python package  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``/usr/lib/`` (32bit)                                 |                                                             |
+      |                        | * ``/usr/lib64/`` (64bit)                               |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``/usr/bin/``                                         |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``/usr/share/lammps/potentials/``                     |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
 
       To be able to use the "user" installation you have to ensure that
       the folder containing the LAMMPS shared library is either included
@@ -146,7 +146,7 @@ this.
       necessary due to files installed in system folders that are loaded
       automatically when a login shell is started.
 
-   .. tab:: Python module only
+   .. tab:: Python package only
 
       Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
       :doc:`traditional make <Build_make>` procedure in :ref:`shared
@@ -157,37 +157,37 @@ this.
 
          make install-python
 
-      This will try to install (only) the shared library and the python
-      module into a system folder and if that fails (due to missing
+      This will try to install (only) the shared library and the Python
+      package into a system folder and if that fails (due to missing
       write permissions) will instead do the installation to a user
       folder under ``$HOME/.local``.  For a system-wide installation you
       would have to gain superuser privilege, e.g. though ``sudo``
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python package  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       For a system-wide installation those folders would then become.
 
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                          | Notes                                                       |
-      +========================+===================================================+=============================================================+
-      | LAMMPS Python Module   | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                | Notes                                                       |
+      +========================+=========================================================+=============================================================+
+      | LAMMPS Python package  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
 
       No environment variables need to be set for those, as those
       folders are searched by default by Python or the LAMMPS Python
-      module.
+      package.
 
       For the traditional make process you can override the python
       version to version x.y when calling ``make`` with
@@ -199,9 +199,9 @@ this.
 
       .. code-block:: bash
 
-         $ python install.py -m <python module> -l <shared library> -v <version.h file> [-d <pydir>]
+         $ python install.py -p <python package> -l <shared library> -v <version.h file> [-d <pydir>]
 
-      * The ``-m`` flag points to the ``lammps.py`` python module file to be installed,
+      * The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
       * the ``-l`` flag points to the LAMMPS shared library file to be installed,
       * the ``-v`` flag points to the ``version.h`` file in the LAMMPS source
       * and the optional ``-d`` flag to a custom (legacy) installation folder
@@ -249,38 +249,38 @@ this.
       When using CMake to build LAMMPS, you need to set
       ``CMAKE_INSTALL_PREFIX`` to the value of the ``$VIRTUAL_ENV``
       environment variable during the configuration step. For the
-      traditional make procedure, not additional steps are needed.
-      After compiling LAMMPS you can do a "Python module only"
+      traditional make procedure, no additional steps are needed.
+      After compiling LAMMPS you can do a "Python package only"
       installation with ``make install-python`` and the LAMMPS Python
-      module and the shared library file are installed into the
+      package and the shared library file are installed into the
       following locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       If you do a full installation (CMake only) with "install", this
       leads to the following installation locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/`` (32bit)                           |                                                             |
-      |                        | * ``$VIRTUAL_ENV/lib64/`` (64bit)                         |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$VIRTUAL_ENV/bin/``                                   |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/``               |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/`` (32bit)                                 | Set shared loader environment variable to this path         |
+      |                        | * ``$VIRTUAL_ENV/lib64/`` (64bit)                               | (see below for more info on this)                           |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``$VIRTUAL_ENV/bin/``                                         |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/``                     | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       In that case you need to modify the ``$HOME/myenv/bin/activate``
       script in a similar fashion you need to update your
@@ -296,15 +296,15 @@ this.
          echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
 
          # MacOS
-         echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
+         echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
 
    .. tab:: In place usage
 
       You can also :doc:`compile LAMMPS <Build>` as usual in
       :ref:`"shared" mode <exe>` leave the shared library and Python
-      module files inside the source/compilation folders. Instead of
+      package inside the source/compilation folders. Instead of
       copying the files where they can be found, you need to set the environment
-      variables ``PYTHONPATH`` (for the Python module) and
+      variables ``PYTHONPATH`` (for the Python package) and
       ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH`` on MacOS
 
       For Bourne shells (bash, ksh and similar) the commands are:
@@ -325,6 +325,10 @@ this.
       You can make those changes permanent by editing your ``$HOME/.bashrc``
       or ``$HOME/.login`` files, respectively.
 
+      .. note::
+
+         The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
+
 
 To verify if LAMMPS can be successfully started from Python, start the
 Python interpreter, load the ``lammps`` Python module and create a
@@ -346,7 +350,7 @@ output similar to the following:
 .. note::
 
    Unless you opted for "In place use", you will have to rerun the installation
-   any time you recompile LAMMPS to ensure the latest Python module and shared
+   any time you recompile LAMMPS to ensure the latest Python package and shared
    library are installed and used.
 
 .. note::

doc/src/Python_module.rst

@@ -3,12 +3,12 @@ The ``lammps`` Python module
 
 .. py:module:: lammps
 
-The LAMMPS Python interface is implemented as a module called
-:py:mod:`lammps` in the ``lammps.py`` file in the ``python`` folder of
-the LAMMPS source code distribution.  After compilation of LAMMPS, the
-module can be installed into a Python system folder or a user folder
-with ``make install-python``.  Components of the module can then loaded
-into a Python session with the ``import`` command.
+The LAMMPS Python interface is implemented as a module called :py:mod:`lammps`
+which is defined in the ``lammps`` package in the ``python`` folder of the
+LAMMPS source code distribution.  After compilation of LAMMPS, the module can
+be installed into a Python system folder or a user folder with ``make
+install-python``.  Components of the module can then loaded into a Python
+session with the ``import`` command.
 
 There are multiple Python interface classes in the :py:mod:`lammps` module:
 
@@ -44,7 +44,7 @@ functions. Below is a detailed documentation of the API.
 .. autoclass:: lammps.lammps
    :members:
 
-.. autoclass:: lammps.numpy_wrapper
+.. autoclass:: lammps.numpy::numpy_wrapper
    :members:
 
 ----------
@@ -117,8 +117,8 @@ Style Constants
    to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
 
 .. _py_type_constants:
 
@@ -132,8 +132,8 @@ Type Constants
    to request  from computes  or fixes.  See :cpp:enum:`_LMP_TYPE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
 
 .. _py_vartype_constants:
 
@@ -153,6 +153,6 @@ Classes representing internal objects
    :members:
    :no-undoc-members:
 
-.. autoclass:: lammps.NumPyNeighList
+.. autoclass:: lammps.numpy::NumPyNeighList
    :members:
    :no-undoc-members:

doc/src/Python_overview.rst

@@ -2,9 +2,9 @@ Overview
 ========
 
 The LAMMPS distribution includes a ``python`` directory with the Python
-code needed to run LAMMPS from Python.  The ``python/lammps.py``
-contains :doc:`the "lammps" Python <Python_module>` that wraps the
-LAMMPS C-library interface.  This file makes it is possible to do the
+code needed to run LAMMPS from Python.  The ``python/lammps`` package
+contains :doc:`the "lammps" Python module <Python_module>` that wraps the
+LAMMPS C-library interface.  This module makes it is possible to do the
 following either from a Python script, or interactively from a Python
 prompt:
 
@@ -20,8 +20,8 @@ have a version of Python that extends Python to enable multiple
 instances of Python to read what you type.
 
 To do all of this, you must build LAMMPS in :ref:`"shared" mode <exe>`
-and make certain that your Python interpreter can find the ``lammps.py``
-file and the LAMMPS shared library file.
+and make certain that your Python interpreter can find the ``lammps``
+Python package and the LAMMPS shared library file.
 
 .. _ctypes: https://docs.python.org/3/library/ctypes.html
 

doc/src/Python_trouble.rst

@@ -33,7 +33,7 @@ the constructor call as follows (see :ref:`python_create_lammps` for more detail
    >>> lmp = lammps(name='mpi')
 
 You can also test the load directly in Python as follows, without
-first importing from the lammps.py file:
+first importing from the ``lammps`` module:
 
 .. code-block:: python
 

doc/src/Run_options.rst

@@ -62,15 +62,18 @@ used.
 
 **-in file**
 
-Specify a file to use as an input script.  This is an optional switch
-when running LAMMPS in one-partition mode.  If it is not specified,
-LAMMPS reads its script from standard input, typically from a script
-via I/O redirection; e.g. lmp_linux < in.run.  I/O redirection should
-also work in parallel, but if it does not (in the unlikely case that
-an MPI implementation does not support it), then use the -in flag.
+Specify a file to use as an input script.  This is an optional but
+recommended switch when running LAMMPS in one-partition mode.  If it
+is not specified, LAMMPS reads its script from standard input, typically
+from a script via I/O redirection; e.g. lmp_linux < in.run.
+With many MPI implementations I/O redirection also works in parallel,
+but using the -in flag will always work.
+
 Note that this is a required switch when running LAMMPS in
 multi-partition mode, since multiple processors cannot all read from
-stdin.
+stdin concurrently.  The file name may be "none" for starting
+multi-partition calculations without reading an initial input file
+from the library interface.
 
 ----------
 
@@ -296,7 +299,7 @@ command-line option.
 **-pscreen file**
 
 Specify the base name for the partition screen file, so partition N
-writes screen information to file.N. If file is none, then no
+writes screen information to file.N. If file is "none", then no
 partition screen files are created.  This overrides the filename
 specified in the -screen command-line option.  This option is useful
 when working with large numbers of partitions, allowing the partition

doc/src/angle_gaussian.rst

@@ -0,0 +1,69 @@
+.. index:: angle_style gaussian
+
+angle_style gaussian command
+================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style gaussian
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style gaussian
+   angle_coeff 1 300.0 2 0.0128 0.375 80.0 0.0730 0.148 123.0
+
+Description
+"""""""""""
+
+The *gaussian* angle style uses the potential:
+
+.. math::
+
+   E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
+
+This analytical form is a suitable potential for obtaining
+mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
+The following coefficients must be defined for each angle type via the
+:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* T temperature at which the potential was derived
+* :math:`n` (integer >=1)
+* :math:`A_1` (-)
+* :math:`w_1` (-)
+* :math:`\theta_1` (degrees)
+* ...
+* :math:`A_n` (-)
+* :math:`w_n` (-)
+* :math:`\theta_n` (degrees)
+
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Milano1:
+
+**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

doc/src/angle_style.rst

@@ -87,6 +87,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
 * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
+* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms

doc/src/atc_output.rst

@@ -14,7 +14,7 @@ Syntax
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * *output* or *output index* = name of the AtC sub-command
 * filename_prefix = prefix for data files (for *output*)
-* frequency = frequency of output in time-steps (for *output*)
+* frequency = frequency of output in timesteps (for *output*)
 * optional keywords for *output*:
 
   - text = creates text output of index, step and nodal variable values for unique nodes

doc/src/balance.rst

@@ -78,14 +78,16 @@ or particles and thus indirectly the computational cost (load) more
 evenly across processors.  The load balancing is "static" in the sense
 that this command performs the balancing once, before or between
 simulations.  The processor sub-domains will then remain static during
-the subsequent run.  To perform "dynamic" balancing, see the :doc:`fix balance <fix_balance>` command, which can adjust processor
-sub-domain sizes and shapes on-the-fly during a :doc:`run <run>`.
+the subsequent run.  To perform "dynamic" balancing, see the :doc:`fix
+balance <fix_balance>` command, which can adjust processor sub-domain
+sizes and shapes on-the-fly during a :doc:`run <run>`.
 
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or when
 the computational cost varies significantly between different
 particles.  E.g. a model of a vapor/liquid interface, or a solid with
-an irregular-shaped geometry containing void regions, or :doc:`hybrid pair style simulations <pair_hybrid>` which combine pair styles with
+an irregular-shaped geometry containing void regions, or :doc:`hybrid
+pair style simulations <pair_hybrid>` which combine pair styles with
 different computational cost.  In these cases, the LAMMPS default of
 dividing the simulation box volume into a regular-spaced grid of 3d
 bricks, with one equal-volume sub-domain per processor, may assign
@@ -101,13 +103,14 @@ which typically induces a different number of atoms assigned to each
 processor.  Details on the various weighting options and examples for
 how they can be used are :ref:`given below <weighted_balance>`.
 
-Note that the :doc:`processors <processors>` command allows some control
-over how the box volume is split across processors.  Specifically, for
-a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
-Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
-of processors.  This is sufficient to achieve good load-balance for
-some problems on some processor counts.  However, all the processor
-sub-domains will still have the same shape and same volume.
+Note that the :doc:`processors <processors>` command allows some
+control over how the box volume is split across processors.
+Specifically, for a Px by Py by Pz grid of processors, it allows
+choice of Px, Py, and Pz, subject to the constraint that Px \* Py \*
+Pz = P, the total number of processors.  This is sufficient to achieve
+good load-balance for some problems on some processor counts.
+However, all the processor sub-domains will still have the same shape
+and same volume.
 
 The requested load-balancing operation is only performed if the
 current "imbalance factor" in particles owned by each processor
@@ -170,12 +173,12 @@ The method used to perform a load balance is specified by one of the
 listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are
 described in detail below.  There are 2 kinds of styles.
 
-The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which produce
-a logical 3d grid of processors.  They operate by changing the cutting
-planes (or lines) between processors in 3d (or 2d), to adjust the
-volume (area in 2d) assigned to each processor, as in the following 2d
-diagram where processor sub-domains are shown and particles are
-colored by the processor that owns them.
+The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which
+produce a logical 3d grid of processors.  They operate by changing the
+cutting planes (or lines) between processors in 3d (or 2d), to adjust
+the volume (area in 2d) assigned to each processor, as in the
+following 2d diagram where processor sub-domains are shown and
+particles are colored by the processor that owns them.
 
 .. |balance1| image:: img/balance_uniform.jpg
    :width: 32%
@@ -190,20 +193,20 @@ colored by the processor that owns them.
 
 The leftmost diagram is the default partitioning of the simulation box
 across processors (one sub-box for each of 16 processors); the middle
-diagram is after a "grid" method has been applied.  The *rcb* style is a
-"tiling" method which does not produce a logical 3d grid of processors.
-Rather it tiles the simulation domain with rectangular sub-boxes of
-varying size and shape in an irregular fashion so as to have equal
-numbers of particles (or weight) in each sub-box, as in the rightmost
-diagram above.
+diagram is after a "grid" method has been applied.  The *rcb* style is
+a "tiling" method which does not produce a logical 3d grid of
+processors.  Rather it tiles the simulation domain with rectangular
+sub-boxes of varying size and shape in an irregular fashion so as to
+have equal numbers of particles (or weight) in each sub-box, as in the
+rightmost diagram above.
 
-The "grid" methods can be used with either of the
-:doc:`comm_style <comm_style>` command options, *brick* or *tiled*\ .  The
-"tiling" methods can only be used with :doc:`comm_style tiled <comm_style>`.  Note that it can be useful to use a "grid"
-method with :doc:`comm_style tiled <comm_style>` to return the domain
-partitioning to a logical 3d grid of processors so that "comm_style
-brick" can afterwords be specified for subsequent :doc:`run <run>`
-commands.
+The "grid" methods can be used with either of the :doc:`comm_style
+<comm_style>` command options, *brick* or *tiled*\ .  The "tiling"
+methods can only be used with :doc:`comm_style tiled <comm_style>`.
+Note that it can be useful to use a "grid" method with
+:doc:`comm_style tiled <comm_style>` to return the domain partitioning
+to a logical 3d grid of processors so that "comm_style brick" can
+afterwords be specified for subsequent :doc:`run <run>` commands.
 
 When a "grid" method is specified, the current domain partitioning can
 be either a logical 3d grid or a tiled partitioning.  In the former
@@ -280,6 +283,14 @@ information, so that they become closer together over time.  Thus as
 the recursion progresses, the count of particles on either side of the
 plane gets closer to the target value.
 
+After the balanced plane positions are determined, if any pair of
+adjacent planes are closer together than the neighbor skin distance
+(as specified by the :doc`neigh_modify <neigh_modify>` command), then
+the plane positions are shifted to separate them by at least this
+amount.  This is to prevent particles being lost when dynamics are run
+with processor sub-domains that are too narrow in one or more
+dimensions.
+
 Once the re-balancing is complete and final processor sub-domains
 assigned, particles are migrated to their new owning processor, and
 the balance procedure ends.
@@ -293,7 +304,7 @@ the balance procedure ends.
    *Niter* is specified as 10, the cutting plane will typically be
    positioned to 1 part in 1000 accuracy (relative to the perfect target
    position).  For *Niter* = 20, it will be accurate to 1 part in a
-   million.  Thus there is no need ot set *Niter* to a large value.
+   million.  Thus there is no need to set *Niter* to a large value.
    LAMMPS will check if the threshold accuracy is reached (in a
    dimension) is less iterations than *Niter* and exit early.  However,
    *Niter* should also not be set too small, since it will take roughly
@@ -416,7 +427,8 @@ The *time* weight style uses :doc:`timer data <timer>` to estimate
 weights.  It assigns the same weight to each particle owned by a
 processor based on the total computational time spent by that
 processor.  See details below on what time window is used.  It uses
-the same timing information as is used for the :doc:`MPI task timing breakdown <Run_output>`, namely, for sections *Pair*\ , *Bond*\ ,
+the same timing information as is used for the :doc:`MPI task timing
+breakdown <Run_output>`, namely, for sections *Pair*\ , *Bond*\ ,
 *Kspace*\ , and *Neigh*\ .  The time spent in those portions of the
 timestep are measured for each MPI rank, summed, then divided by the
 number of particles owned by that processor.  I.e. the weight is an

doc/src/bond_gaussian.rst

@@ -0,0 +1,70 @@
+.. index:: bond_style gaussian
+
+bond_style gaussian command
+================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style gaussian
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style gaussian
+   bond_coeff 1 300.0 2 0.0128 0.375 3.37 0.0730 0.148 3.63
+
+Description
+"""""""""""
+
+The *gaussian* bond style uses the potential:
+
+.. math::
+
+   E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
+
+This analytical form is a suitable potential for obtaining
+mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* T temperature at which the potential was derived
+* :math:`n` (integer >=1)
+* :math:`A_1` (-)
+* :math:`w_1` (-)
+* :math:`r_1` (length)
+* ...
+* :math:`A_n` (-)
+* :math:`w_n` (-)
+* :math:`r_n` (length)
+
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the
+USER-MISC package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Milano0:
+
+**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

doc/src/bond_style.rst

@@ -87,6 +87,7 @@ accelerated styles exist.
 * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
 * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
 * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
+* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
 * :doc:`gromos <bond_gromos>` - GROMOS force field bond
 * :doc:`harmonic <bond_harmonic>` - harmonic bond
 * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond

doc/src/change_box.rst

@@ -301,9 +301,13 @@ command.
 
 .. note::
 
-   Changing a periodic boundary to a non-periodic one will also
-   cause the image flag for that dimension to be reset to 0 for
-   all atoms.  LAMMPS will print a warning message, if that happens.
+   Changing a periodic boundary to a non-periodic one will also cause
+   the image flag for that dimension of all atoms to be reset to 0.
+   LAMMPS will print a warning message, if that happens.
+   Please note that this reset can lead to undesired changes when
+   atoms are involved in bonded interactions that straddle periodic
+   boundaries and thus the values of the image flag differs for those
+   atoms.
 
 ----------
 

doc/src/comm_modify.rst

@@ -84,13 +84,15 @@ information is available, then also a heuristic based on that bond length
 is computed. It is used as communication cutoff, if there is no pair
 style present and no *comm_modify cutoff* command used. Otherwise a
 warning is printed, if this bond based estimate is larger than the
-communication cutoff used. A
+communication cutoff used.
 
 The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
 communication mode *multi* instead. Since in this case the communication
 cutoffs are determined per atom type, a type specifier is needed and
 cutoff for one or multiple types can be extended. Also ranges of types
-using the usual asterisk notation can be given.
+using the usual asterisk notation can be given. For granular pair styles,
+the default cutoff is set to the sum of the current maximum atomic radii
+for each type.
 
 These are simulation scenarios in which it may be useful or even
 necessary to set a ghost cutoff > neighbor cutoff:

doc/src/compute_reduce_chunk.rst

@@ -38,7 +38,7 @@ Description
 Define a calculation that reduces one or more per-atom vectors into
 per-chunk values.  This can be useful for diagnostic output.  Or when
 used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
-used ot create per-atom values that induce a new set of chunks with a
+used to create per-atom values that induce a new set of chunks with a
 second :doc:`compute chunk/atom <compute_chunk_atom>` command.  An
 example is given below.
 

doc/src/compute_stress_atom.rst

@@ -33,32 +33,31 @@ Examples
 Description
 """""""""""
 
-Define a computation that computes per-atom stress
-tensor for each atom in a group.  In case of compute *stress/atom*,
-the tensor for each atom is symmetric with 6
-components and is stored as a 6-element vector in the following order:
-:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
-In case of compute *centroid/stress/atom*,
-the tensor for each atom is asymmetric with 9 components
-and is stored as a 9-element vector in the following order:
-:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`,
-:math:`yx`, :math:`zx`, :math:`zy`.
-See the :doc:`compute pressure <compute_pressure>` command if you want the stress tensor
+Define a computation that computes per-atom stress tensor for each
+atom in a group.  In case of compute *stress/atom*, the tensor for
+each atom is symmetric with 6 components and is stored as a 6-element
+vector in the following order: :math:`xx`, :math:`yy`, :math:`zz`,
+:math:`xy`, :math:`xz`, :math:`yz`.  In case of compute
+*centroid/stress/atom*, the tensor for each atom is asymmetric with 9
+components and is stored as a 9-element vector in the following order:
+:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
+:math:`yz`, :math:`yx`, :math:`zx`, :math:`zy`.  See the :doc:`compute
+pressure <compute_pressure>` command if you want the stress tensor
 (pressure) of the entire system.
 
-The stress tensor for atom :math:`I` is given by the following formula,
-where :math:`a` and :math:`b` take on values :math:`x`, :math:`y`, :math:`z`
-to generate the components of the tensor:
+The stress tensor for atom :math:`I` is given by the following
+formula, where :math:`a` and :math:`b` take on values :math:`x`,
+:math:`y`, :math:`z` to generate the components of the tensor:
 
 .. math::
 
    S_{ab}  =  - m v_a v_b - W_{ab}
 
-The first term is a kinetic energy contribution for atom :math:`I`.  See
-details below on how the specified *temp-ID* can affect the velocities
-used in this calculation. The second term is the virial
-contribution due to intra and intermolecular interactions,
-where the exact computation details are determined by the compute style.
+The first term is a kinetic energy contribution for atom :math:`I`.
+See details below on how the specified *temp-ID* can affect the
+velocities used in this calculation. The second term is the virial
+contribution due to intra and intermolecular interactions, where the
+exact computation details are determined by the compute style.
 
 In case of compute *stress/atom*, the virial contribution is:
 
@@ -68,29 +67,26 @@ In case of compute *stress/atom*, the virial contribution is:
   & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
   & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
-The first term is a pairwise energy
-contribution where :math:`n` loops over the :math:`N_p`
-neighbors of atom :math:`I`, :math:`\mathbf{r}_1` and :math:`\mathbf{r}_2`
-are the positions of the 2 atoms in the pairwise interaction,
-and :math:`\mathbf{F}_1` and :math:`\mathbf{F}_2` are the forces
-on the 2 atoms resulting from the pairwise interaction.
-The second term is a bond contribution of
-similar form for the :math:`N_b` bonds which atom :math:`I` is part of.
-There are similar terms for the :math:`N_a` angle, :math:`N_d` dihedral,
-and :math:`N_i` improper interactions atom :math:`I` is part of.
-There is also a term for the KSpace
-contribution from long-range Coulombic interactions, if defined.
-Finally, there is a term for the :math:`N_f` :doc:`fixes <fix>` that apply
-internal constraint forces to atom :math:`I`. Currently, only the
-:doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>` commands
-contribute to this term.
-As the coefficients in the formula imply, a virial contribution
-produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
-atoms in a Tersoff 3-body interaction) is assigned in equal portions
-to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
-the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a water molecule via the :doc:`fix shake <fix_shake>`
-command.
+The first term is a pairwise energy contribution where :math:`n` loops
+over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1`
+and :math:`\mathbf{r}_2` are the positions of the 2 atoms in the
+pairwise interaction, and :math:`\mathbf{F}_1` and
+:math:`\mathbf{F}_2` are the forces on the 2 atoms resulting from the
+pairwise interaction.  The second term is a bond contribution of
+similar form for the :math:`N_b` bonds which atom :math:`I` is part
+of.  There are similar terms for the :math:`N_a` angle, :math:`N_d`
+dihedral, and :math:`N_i` improper interactions atom :math:`I` is part
+of.  There is also a term for the KSpace contribution from long-range
+Coulombic interactions, if defined.  Finally, there is a term for the
+:math:`N_f` :doc:`fixes <fix>` that apply internal constraint forces
+to atom :math:`I`. Currently, only the :doc:`fix shake <fix_shake>`
+and :doc:`fix rigid <fix_rigid>` commands contribute to this term.  As
+the coefficients in the formula imply, a virial contribution produced
+by a small set of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a
+Tersoff 3-body interaction) is assigned in equal portions to each atom
+in the set.  E.g. 1/4 of the dihedral virial to each of the 4 atoms,
+or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
+a water molecule via the :doc:`fix shake <fix_shake>` command.
 
 In case of compute *centroid/stress/atom*, the virial contribution is:
 
@@ -99,71 +95,69 @@ In case of compute *centroid/stress/atom*, the virial contribution is:
    W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a}  F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
   & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
-As with compute *stress/atom*, the first, second, third, fourth and fifth terms
-are pairwise, bond, angle, dihedral and improper contributions,
-but instead of assigning the virial contribution equally to each atom,
-only the force :math:`\mathbf{F}_I` acting on atom :math:`I`
-due to the interaction and the relative
-position :math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
-of the interacting atoms, i.e. centroid, is used.
-As the geometric center is different
-for each interaction, the :math:`\mathbf{r}_{I0}` also differs.
-The sixth and seventh terms, Kspace and :doc:`fix <fix>` contribution
-respectively, are computed identical to compute *stress/atom*.
-Although the total system virial is the same as compute *stress/atom*,
-compute *centroid/stress/atom* is know to result in more consistent
-heat flux values for angle, dihedrals and improper contributions
-when computed via :doc:`compute heat/flux <compute_heat_flux>`.
+As with compute *stress/atom*, the first, second, third, fourth and
+fifth terms are pairwise, bond, angle, dihedral and improper
+contributions, but instead of assigning the virial contribution
+equally to each atom, only the force :math:`\mathbf{F}_I` acting on
+atom :math:`I` due to the interaction and the relative position
+:math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
+of the interacting atoms, i.e. centroid, is used.  As the geometric
+center is different for each interaction, the :math:`\mathbf{r}_{I0}`
+also differs.  The sixth and seventh terms, Kspace and :doc:`fix
+<fix>` contribution respectively, are computed identical to compute
+*stress/atom*.  Although the total system virial is the same as
+compute *stress/atom*, compute *centroid/stress/atom* is know to
+result in more consistent heat flux values for angle, dihedrals and
+improper contributions when computed via :doc:`compute heat/flux
+<compute_heat_flux>`.
 
-If no extra keywords are listed, the kinetic contribution
-all of the virial contribution terms are
-included in the per-atom stress tensor.  If any extra keywords are
-listed, only those terms are summed to compute the tensor.  The
-*virial* keyword means include all terms except the kinetic energy
-*ke*\ .
+If no extra keywords are listed, the kinetic contribution all of the
+virial contribution terms are included in the per-atom stress tensor.
+If any extra keywords are listed, only those terms are summed to
+compute the tensor.  The *virial* keyword means include all terms
+except the kinetic energy *ke*\ .
 
 Note that the stress for each atom is due to its interaction with all
 other atoms in the simulation, not just with other atoms in the group.
 
-Details of how compute *stress/atom* obtains the virial for individual atoms for
-either pairwise or many-body potentials, and including the effects of
-periodic boundary conditions is discussed in :ref:`(Thompson) <Thompson2>`.
-The basic idea for many-body potentials is to treat each component of
-the force computation between a small cluster of atoms in the same
-manner as in the formula above for bond, angle, dihedral, etc
-interactions.  Namely the quantity :math:`\mathbf{r} \cdot \mathbf{F}`
-is summed over the atoms in
-the interaction, with the :math:`r` vectors unwrapped by periodic boundaries
-so that the cluster of atoms is close together.  The total
+Details of how compute *stress/atom* obtains the virial for individual
+atoms for either pairwise or many-body potentials, and including the
+effects of periodic boundary conditions is discussed in
+:ref:`(Thompson) <Thompson2>`.  The basic idea for many-body
+potentials is to treat each component of the force computation between
+a small cluster of atoms in the same manner as in the formula above
+for bond, angle, dihedral, etc interactions.  Namely the quantity
+:math:`\mathbf{r} \cdot \mathbf{F}` is summed over the atoms in the
+interaction, with the :math:`r` vectors unwrapped by periodic
+boundaries so that the cluster of atoms is close together.  The total
 contribution for the cluster interaction is divided evenly among those
-atoms. Details of how compute *centroid/stress/atom* obtains
-the virial for individual atoms
-is given in :ref:`(Surblys) <Surblys1>`,
-where the idea is that the virial of the atom :math:`I`
-is the result of only the force :math:`\mathbf{F}_I` on the atom due
-to the interaction
-and its positional vector :math:`\mathbf{r}_{I0}`,
-relative to the geometric center of the
-interacting atoms, regardless of the number of participating atoms.
-The periodic boundary treatment is identical to
+atoms.
+
+Details of how compute *centroid/stress/atom* obtains the virial for
+individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
+idea is that the virial of the atom :math:`I` is the result of only
+the force :math:`\mathbf{F}_I` on the atom due to the interaction and
+its positional vector :math:`\mathbf{r}_{I0}`, relative to the
+geometric center of the interacting atoms, regardless of the number of
+participating atoms.  The periodic boundary treatment is identical to
 that of compute *stress/atom*, and both of them reduce to identical
-expressions for two-body interactions,
-i.e. computed values for contributions from bonds and two-body pair styles,
-such as :doc:`Lennard-Jones <pair_lj>`, will be the same,
-while contributions from angles, dihedrals and impropers will be different.
+expressions for two-body interactions, i.e. computed values for
+contributions from bonds and two-body pair styles, such as
+:doc:`Lennard-Jones <pair_lj>`, will be the same, while contributions
+from angles, dihedrals and impropers will be different.
 
 The :doc:`dihedral_style charmm <dihedral_charmm>` style calculates
 pairwise interactions between 1-4 atoms.  The virial contribution of
 these terms is included in the pair virial, not the dihedral virial.
 
 The KSpace contribution is calculated using the method in
-:ref:`(Heyes) <Heyes2>` for the Ewald method and by the methodology described
-in :ref:`(Sirk) <Sirk1>` for PPPM.  The choice of KSpace solver is specified
-by the :doc:`kspace_style pppm <kspace_style>` command.  Note that for
-PPPM, the calculation requires 6 extra FFTs each timestep that
-per-atom stress is calculated.  Thus it can significantly increase the
-cost of the PPPM calculation if it is needed on a large fraction of
-the simulation timesteps.
+:ref:`(Heyes) <Heyes2>` for the Ewald method and by the methodology
+described in :ref:`(Sirk) <Sirk1>` for PPPM.  The choice of KSpace
+solver is specified by the :doc:`kspace_style pppm <kspace_style>`
+command.  Note that for PPPM, the calculation requires 6 extra FFTs
+each timestep that per-atom stress is calculated.  Thus it can
+significantly increase the cost of the PPPM calculation if it is
+needed on a large fraction of the simulation timesteps.
 
 The *temp-ID* argument can be used to affect the per-atom velocities
 used in the kinetic energy contribution to the total stress.  If the
@@ -189,10 +183,10 @@ See the :doc:`compute voronoi/atom <compute_voronoi_atom>` command for
 one possible way to estimate a per-atom volume.
 
 Thus, if the diagonal components of the per-atom stress tensor are
-summed for all atoms in the system and the sum is divided by :math:`dV`, where
-:math:`d` = dimension and :math:`V` is the volume of the system,
-the result should be :math:`-P`, where :math:`P`
-is the total pressure of the system.
+summed for all atoms in the system and the sum is divided by
+:math:`dV`, where :math:`d` = dimension and :math:`V` is the volume of
+the system, the result should be :math:`-P`, where :math:`P` is the
+total pressure of the system.
 
 These lines in an input script for a 3d system should yield that
 result. I.e. the last 2 columns of thermo output will be the same:
@@ -207,33 +201,43 @@ result. I.e. the last 2 columns of thermo output will be the same:
 .. note::
 
    The per-atom stress does not include any Lennard-Jones tail
-   corrections to the pressure added by the :doc:`pair_modify tail yes <pair_modify>` command, since those are contributions to the
-   global system pressure.
+   corrections to the pressure added by the :doc:`pair_modify tail yes
+   <pair_modify>` command, since those are contributions to the global
+   system pressure.
 
 Output info
 """""""""""
 
-This compute *stress/atom* calculates a per-atom array with 6 columns, which can be
-accessed by indices 1-6 by any command that uses per-atom values from
-a compute as input.
-The compute *centroid/stress/atom* produces a per-atom array with 9 columns,
-but otherwise can be used in an identical manner to compute *stress/atom*.
-See the :doc:`Howto output <Howto_output>` doc page
-for an overview of LAMMPS output options.
+Compute *stress/atom* calculates a per-atom array with 6 columns,
+which can be accessed by indices 1-6 by any command that uses per-atom
+values from a compute as input.  Compute *centroid/stress/atom*
+produces a per-atom array with 9 columns, but otherwise can be used in
+an identical manner to compute *stress/atom*.  See the :doc:`Howto
+output <Howto_output>` doc page for an overview of LAMMPS output
+options.
 
-The per-atom array values will be in pressure\*volume
-:doc:`units <units>` as discussed above.
+The per-atom array values will be in pressure\*volume :doc:`units
+<units>` as discussed above.
 
 Restrictions
 """"""""""""
 
-Currently (Spring 2020), compute *centroid/stress/atom* does not support
-pair styles with many-body interactions, such as :doc:`Tersoff
-<pair_tersoff>`, or pair styles with long-range Coulomb interactions.
-LAMMPS will generate an error in such cases.  In principal, equivalent
-formulation to that of angle, dihedral and improper contributions in the
-virial :math:`W_{ab}` formula can also be applied to the many-body pair
-styles, and is planned in the future.
+Currently, compute *centroid/stress/atom* does not support pair styles
+with many-body interactions (:doc:`EAM <pair_eam>` is an exception,
+since its computations are performed pairwise), nor granular pair
+styles with pairwise forces which are not aligned with the vector
+between the pair of particles.  All bond styles are supported.  All
+angle, dihedral, improper styles are supported with the exception of
+USER-INTEL and KOKKOS variants of specific styles.  It also does not
+support models with long-range Coulombic or dispersion forces,
+i.e. the kspace_style command in LAMMPS.  It also does not support the
+following fixes which add rigid-body constraints: :doc:`fix shake
+<fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
+<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
+
+LAMMPS will generate an error if one of these options is included in
+your model.  Extension of centroid stress calculations to these force
+and fix styles is planned for the future.
 
 Related commands
 """"""""""""""""

doc/src/fix.rst

@@ -205,6 +205,7 @@ accelerated styles exist.
 * :doc:`efield <fix_efield>` - impose electric field on system
 * :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
 * :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
+* :doc:`electron/stopping/fit <fix_electron_stopping>` - electronic stopping power as a friction force
 * :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force
 * :doc:`eos/cv <fix_eos_cv>` -
 * :doc:`eos/table <fix_eos_table>` -
@@ -363,6 +364,8 @@ accelerated styles exist.
 * :doc:`temp/rescale <fix_temp_rescale>` - temperature control by velocity rescaling
 * :doc:`temp/rescale/eff <fix_temp_rescale_eff>` - temperature control by velocity rescaling in the electron force field model
 * :doc:`tfmc <fix_tfmc>` - perform force-bias Monte Carlo with time-stamped method
+* :doc:`tgnvt/drude <fix_tgnh_drude>` - NVT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
+* :doc:`tgnpt/drude <fix_tgnh_drude>` - NPT time integration for Drude polarizable model via temperature-grouped Nose-Hoover
 * :doc:`thermal/conductivity <fix_thermal_conductivity>` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
 * :doc:`ti/spring <fix_ti_spring>` -
 * :doc:`tmd <fix_tmd>` - guide a group of atoms to a new configuration

doc/src/fix_bond_react.rst

@@ -35,8 +35,8 @@ Syntax
 * react-ID = user-assigned name for the reaction
 * react-group-ID = only atoms in this group are considered for the reaction
 * Nevery = attempt reaction every this many steps
-* Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units)
-* Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units)
+* Rmin = initiator atoms must be separated by more than Rmin to initiate reaction (distance units)
+* Rmax = initiator atoms must be separated by less than Rmax to initiate reaction (distance units)
 * template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology
 * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
 * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
@@ -55,6 +55,10 @@ Syntax
          *custom_charges* value = *no* or *fragmentID*
            no = update all atomic charges (default)
            fragmentID = ID of molecule fragment whose charges are updated
+         *molecule* value = *off* or *inter* or *intra*
+           off = allow both inter- and intramolecular reactions (default)
+           inter = search for reactions between molecules with different IDs
+           intra = search for reactions within the same molecule
 
 Examples
 """"""""
@@ -172,8 +176,8 @@ timesteps. *Nevery* can be specified with an equal-style
 integer.
 
 Three physical conditions must be met for a reaction to occur. First,
-a bonding atom pair must be identified within the reaction distance
-cutoffs. Second, the topology surrounding the bonding atom pair must
+an initiator atom pair must be identified within the reaction distance
+cutoffs. Second, the topology surrounding the initiator atom pair must
 match the topology of the pre-reaction template. Only atom types and
 bond connectivity are used to identify a valid reaction site (not bond
 types, etc.). Finally, any reaction constraints listed in the map file
@@ -181,10 +185,10 @@ types, etc.). Finally, any reaction constraints listed in the map file
 reaction site is eligible to be modified to match the post-reaction
 template.
 
-A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms I,J within the specified react-group-ID of type
-itype and jtype must be separated by a distance between *Rmin* and
-*Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
+An initiator atom pair will be identified if several conditions are
+met. First, a pair of atoms I,J within the specified react-group-ID of
+type itype and jtype must be separated by a distance between *Rmin*
+and *Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
 :doc:`variables <variable>`. For example, these reaction cutoffs can
 be a function of the reaction conversion using the following commands:
 
@@ -194,20 +198,20 @@ be a function of the reaction conversion using the following commands:
    fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt
    variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
 
-The following criteria are used if multiple candidate bonding atom
-pairs are identified within the cutoff distance: 1) If the bonding
+The following criteria are used if multiple candidate initiator atom
+pairs are identified within the cutoff distance: 1) If the initiator
 atoms in the pre-reaction template are not 1-2 neighbors (i.e. not
 directly bonded) the closest potential partner is chosen. 2)
-Otherwise, if the bonding atoms in the pre-reaction template are 1-2
+Otherwise, if the initiator atoms in the pre-reaction template are 1-2
 neighbors (i.e. directly bonded) the farthest potential partner is
 chosen. 3) Then, if both an atom I and atom J have each other as their
-bonding partners, these two atoms are identified as the bonding atom
-pair of the reaction site. Note that it can be helpful to select
-unique atom types for the bonding atoms: if a bonding atom pair is
-identified, as described in the previous steps, but does not
+initiator partners, these two atoms are identified as the initiator
+atom pair of the reaction site. Note that it can be helpful to select
+unique atom types for the initiator atoms: if an initiator atom pair
+is identified, as described in the previous steps, but does not
 correspond to the same pair specified in the pre-reaction template, an
 otherwise eligible reaction could be prevented from occurring. Once
-this unique bonding atom pair is identified for each reaction, there
+this unique initiator atom pair is identified for each reaction, there
 could be two or more reactions that involve the same atom on the same
 timestep. If this is the case, only one such reaction is permitted to
 occur. This reaction is chosen randomly from all potential reactions
@@ -217,7 +221,7 @@ with user-specified probabilities.
 
 The pre-reacted molecule template is specified by a molecule command.
 This molecule template file contains a sample reaction site and its
-surrounding topology. As described below, the bonding atom pairs of
+surrounding topology. As described below, the initiator atom pairs of
 the pre-reacted template are specified by atom ID in the map file. The
 pre-reacted molecule template should contain as few atoms as possible
 while still completely describing the topology of all atoms affected
@@ -231,18 +235,18 @@ missing topology with respect to the simulation. For example, the
 pre-reacted template may contain an atom that, in the simulation, is
 currently connected to the rest of a long polymer chain. These are
 referred to as edge atoms, and are also specified in the map file. All
-pre-reaction template atoms should be linked to a bonding atom, via at
-least one path that does not involve edge atoms. When the pre-reaction
-template contains edge atoms, not all atoms, bonds, charges, etc.
-specified in the reaction templates will be updated. Specifically,
-topology that involves only atoms that are 'too near' to template
-edges will not be updated. The definition of 'too near the edge'
-depends on which interactions are defined in the simulation. If the
-simulation has defined dihedrals, atoms within two bonds of edge atoms
-are considered 'too near the edge.' If the simulation defines angles,
-but not dihedrals, atoms within one bond of edge atoms are considered
-'too near the edge.' If just bonds are defined, only edge atoms are
-considered 'too near the edge.'
+pre-reaction template atoms should be linked to an initiator atom, via
+at least one path that does not involve edge atoms. When the
+pre-reaction template contains edge atoms, not all atoms, bonds,
+charges, etc. specified in the reaction templates will be updated.
+Specifically, topology that involves only atoms that are 'too near' to
+template edges will not be updated. The definition of 'too near the
+edge' depends on which interactions are defined in the simulation. If
+the simulation has defined dihedrals, atoms within two bonds of edge
+atoms are considered 'too near the edge.' If the simulation defines
+angles, but not dihedrals, atoms within one bond of edge atoms are
+considered 'too near the edge.' If just bonds are defined, only edge
+atoms are considered 'too near the edge.'
 
 .. note::
 
@@ -298,23 +302,23 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
 
 The body of the map file contains two mandatory sections and four
 optional sections. The first mandatory section begins with the keyword
-'BondingIDs' and lists the atom IDs of the bonding atom pair in the
-pre-reacted molecule template. The second mandatory section begins
-with the keyword 'Equivalences' and lists a one-to-one correspondence
-between atom IDs of the pre- and post-reacted templates. The first
-column is an atom ID of the pre-reacted molecule template, and the
-second column is the corresponding atom ID of the post-reacted
-molecule template. The first optional section begins with the keyword
-'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
-molecule template. The second optional section begins with the keyword
-'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
-delete. The third optional section begins with the keyword 'ChiralIDs'
-lists the atom IDs of chiral atoms whose handedness should be
-enforced. The fourth 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 five types of
-constraints available, as discussed below: 'distance', 'angle',
-'dihedral', 'arrhenius', and 'rmsd'.
+'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
+in the pre-reacted molecule template. The second mandatory section
+begins with the keyword 'Equivalences' and lists a one-to-one
+correspondence between atom IDs of the pre- and post-reacted
+templates. The first column is an atom ID of the pre-reacted molecule
+template, and the second column is the corresponding atom ID of the
+post-reacted molecule template. The first optional section begins with
+the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
+pre-reacted molecule template. The second optional section begins with
+the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
+template atoms to delete. The third optional section begins with the
+keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
+handedness should be enforced. The fourth 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
+five types of constraints available, as discussed below: 'distance',
+'angle', 'dihedral', 'arrhenius', and 'rmsd'.
 
 A sample map file is given below:
 
@@ -327,7 +331,7 @@ A sample map file is given below:
    7 equivalences
    2 edgeIDs
 
-   BondingIDs
+   InitiatorIDs
 
    3
    5
@@ -453,6 +457,23 @@ example, the molecule fragment could consist of only the backbone
 atoms of a polymer chain. This constraint can be used to enforce a
 specific relative position and orientation between reacting molecules.
 
+By default, all constraints must be satisfied for the reaction to
+occur. In other words, constraints are evaluated as a series of
+logical values using the logical AND operator "&&". More complex logic
+can be achieved by explicitly adding the logical AND operator "&&" or
+the logical OR operator "||" after a given constraint command. If a
+logical operator is specified after a constraint, it must be placed
+after all constraint parameters, on the same line as the constraint
+(one per line). Similarly, parentheses can be used to group
+constraints. The expression that results from concatenating all
+constraints should be a valid logical expression that can be read by
+the :doc:`variable <variable>` command after converting each
+constraint to a logical value. Because exactly one constraint is
+allowed per line, having a valid logical expression implies that left
+parentheses "(" should only appear before a constraint, and right
+parentheses ")" should only appear after a constraint and before any
+logical operator.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -462,7 +483,7 @@ A few capabilities to note: 1) You may specify as many *react*
 arguments as desired. For example, you could break down a complicated
 reaction mechanism into several reaction steps, each defined by its
 own *react* argument. 2) While typically a bond is formed or removed
-between the bonding atom pairs specified in the pre-reacted molecule
+between the initiator atoms specified in the pre-reacted molecule
 template, this is not required. 3) By reversing the order of the pre-
 and post- reacted molecule templates in another *react* argument, you
 can allow for the possibility of one or more reverse reactions.
@@ -491,12 +512,20 @@ situations, decreasing rather than increasing this parameter will
 result in an increase in stability.
 
 The *custom_charges* keyword can be used to specify which atoms'
-atomic charges are updated. When the value is set to 'no,' all atomic
+atomic charges are updated. When the value is set to 'no', all atomic
 charges are updated to those specified by the post-reaction template
 (default). Otherwise, the value should be the name of a molecule
 fragment defined in the pre-reaction molecule template. In this case,
 only the atomic charges of atoms in the molecule fragment are updated.
 
+The *molecule* keyword can be used to force the reaction to be
+intermolecular, intramolecular or either. When the value is set to
+'off', molecule IDs are not considered when searching for reactions
+(default). When the value is set to 'inter', the initiator atoms must
+have different molecule IDs in order to be considered for the
+reaction. When the value is set to 'intra', only initiator atoms with
+the same molecule ID are considered for the reaction.
+
 A few other considerations:
 
 Many reactions result in one or more atoms that are considered
@@ -558,7 +587,7 @@ These is 1 quantity for each react argument:
 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>`.
 
-When fix bond/react is 'unfixed,' all internally-created groups are
+When fix bond/react is 'unfixed', all internally-created groups are
 deleted. Therefore, fix bond/react can only be unfixed after unfixing
 all other fixes that use any group created by fix bond/react.
 
@@ -581,10 +610,14 @@ Default
 """""""
 
 The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
-reset_mol_ids = yes, custom_charges = no
+reset_mol_ids = yes, custom_charges = no, molecule = off
 
 ----------
 
 .. _Gissinger:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
+**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+
+.. _Gissinger2020:
+
+**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953–9961 (2020).

doc/src/fix_drude.rst

@@ -41,12 +41,12 @@ Restrictions
 """"""""""""
 
 This fix should be invoked before any other commands that implement
-the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
+the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
 
 Related commands
 """"""""""""""""
 
-:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
+:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
 
 Default
 """""""

doc/src/fix_electron_stopping.rst

@@ -1,28 +1,41 @@
 .. index:: fix electron/stopping
+.. index:: fix electron/stopping/fit
 
 fix electron/stopping command
 =============================
 
+fix electron/stopping/fit command
+=================================
+
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID electron/stopping Ecut file keyword value ...
+   fix ID group-ID style args
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* electron/stopping = style name of this fix command
-* Ecut = minimum kinetic energy for electronic stopping (energy units)
-* file = name of the file containing the electronic stopping power table
-* zero or more keyword/value pairs may be appended to args
-* keyword = *region* or *minneigh*
+* style = *electron/stopping* or *electron/stopping/fit*
 
   .. parsed-literal::
 
+   *electron/stopping* args = Ecut file keyword value ...
+     Ecut  = minimum kinetic energy for electronic stopping (energy units)
+     file  = name of the file containing the electronic stopping power table
+
+   *electron/stopping/fit* args = Ecut c1 c2 ...
+     Ecut  = minimum kinetic energy for electronic stopping (energy units)
+     c1 c2 = linear and quadratic coefficients for the fitted quadratic polynomial
+
+* zero or more keyword/value pairs may be appended to args for style = *electron/stopping*
+
+  .. parsed-literal::
+
+    keyword = *region* or *minneigh*
        *region* value = region-ID
-         region-ID = region, whose atoms will be affected by this fix
+          region-ID = region whose atoms will be affected by this fix
        *minneigh* value = minneigh
-         minneigh = minimum number of neighbors an atom to have stopping applied
+          minneigh = minimum number of neighbors an atom to have stopping applied
 
 Examples
 """"""""
@@ -32,6 +45,8 @@ Examples
    fix el all electron/stopping 10.0 elstop-table.txt
    fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
    fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk
+   fix 1 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
+   fix 1 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
 
 Description
 """""""""""
@@ -129,6 +144,19 @@ scientific publications, experimental databases or by using
 of the impact parameter of the ion; these results can be used
 to derive the stopping power.
 
+----------
+
+Style *electron/stopping/fit* calculates the electronic stopping power
+and cumulative energy lost to the electron gas via a quadratic functional
+and applies a drag force to the classical equations-of-motion for all
+atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
+These coefficients can be determined by fitting a quadratic polynomial to
+electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
+'Ecut c1 c2' values can be provided for multi-species simulations in the order
+of the atom types. There is an examples/USER/misc/electron_stopping/ directory,
+which illustrates uses of this command. Details of this implementation are
+further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -181,3 +209,11 @@ The default is no limitation by region, and minneigh = 1.
 .. _PASS:
 
 **(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS
+
+.. _Stewart2018:
+
+**(Stewart2018)** J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
+
+.. _Lee2020:
+
+**(Lee2020)** C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.

doc/src/fix_filter_corotate.rst

@@ -56,7 +56,7 @@ is slightly modified only for the computation of long-range forces. A
 good cluster decomposition constitutes in building clusters which
 contain the fastest covalent bonds inside clusters.
 
-If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer time-steps of at least 8fs.
+If the clusters are chosen suitably, the :doc:`run_style respa <run_style>` is stable for outer timesteps of at least 8fs.
 
 ----------
 

doc/src/fix_phonon.rst

@@ -121,7 +121,7 @@ A detailed description of this method can be found in
 
 The *sysdim* keyword is optional.  If specified with a value smaller
 than the dimensionality of the LAMMPS simulation, its value is used
-for the dynamical matrix calculation.  For example, using LAMMPS ot
+for the dynamical matrix calculation.  For example, using LAMMPS to
 model a 2D or 3D system, the phonon dispersion of a 1D atomic chain
 can be computed using *sysdim* = 1.
 

doc/src/fix_precession_spin.rst

@@ -62,7 +62,7 @@ with:
 
 The field value in Tesla is multiplied by the gyromagnetic
 ratio, :math:`g \cdot \mu_B/\hbar`, converting it into a precession frequency in
-rad.THz (in metal units and with :math:`\mu_B = 5.788 eV/T`).
+rad.THz (in metal units and with :math:`\mu_B = 5.788\cdot 10^{-5}` eV/T).
 
 As a comparison, the figure below displays the simulation of a
 single spin (of norm :math:`\mu_i = 1.0`) submitted to an external

doc/src/fix_rx.rst

@@ -90,10 +90,10 @@ accepted, *h* is increased by a proportional amount, and the next ODE step is be
 Otherwise, *h* is shrunk and the ODE step is repeated.
 
 Run-time diagnostics are available for the rkf45 ODE solver. The frequency
-(in time-steps) that diagnostics are reported is controlled by the last (optional)
+(in timesteps) that diagnostics are reported is controlled by the last (optional)
 12th argument. A negative frequency means that diagnostics are reported once at the
 end of each run. A positive value N means that the diagnostics are reported once
-per N time-steps.
+per N timesteps.
 
 The diagnostics report the average # of integrator steps and RHS function evaluations
 and run-time per ODE as well as the average/RMS/min/max per process. If the

doc/src/fix_shake.rst

@@ -1,9 +1,12 @@
 .. index:: fix shake
+.. index:: fix shake/kk
 .. index:: fix rattle
 
 fix shake command
 =================
 
+Accelerator Variants: *shake/kk*
+
 fix rattle command
 ==================
 

doc/src/fix_temp_csvr.rst

@@ -124,6 +124,19 @@ temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.
 
+An important feature of these thermostats is that they have an
+associated effective energy that is a constant of motion.
+The effective energy is the total energy (kinetic + potential) plus
+the accumulated kinetic energy changes due to the thermostat. The
+latter quantity is the global scalar computed by these fixes. This
+feature is useful to check the integration of the equations of motion
+against discretization errors. In other words, the conservation of
+the effective energy can be used to choose an appropriate integration
+:doc:`timestep <timestep>`. This is similar to the usual paradigm of
+checking the conservation of the total energy in the microcanonical
+ensemble.
+
+
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info

doc/src/fix_tgnh_drude.rst

@@ -0,0 +1,305 @@
+.. index:: fix tgnvt/drude
+.. index:: fix tgnpt/drude
+
+fix tgnvt/drude command
+=======================
+
+fix tgnpt/drude command
+=======================
+
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID style_name keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style_name = *tgnvt/drude* or *tgnpt/drude*
+* one or more keyword/values pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *temp* *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 *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint*
+       *temp* values = Tstart Tstop Tdamp Tdrude Tdamp_drude
+         Tstart, Tstop = external temperature at start/end of run (temperature units)
+         Tdamp = temperature damping parameter (time units)
+         Tdrude = desired temperature of Drude oscillators (temperature units)
+         Tdamp_drude = temperature damping parameter for Drude oscillators (time units)
+       *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
+         Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+         Pdamp = pressure damping parameter (time units)
+       *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp
+         Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+         Pdamp = stress damping parameter (time units)
+       *couple* = *none* or *xyz* or *xy* or *yz* or *xz*
+       *tchain* value = N
+         N = length of thermostat chain (1 = single thermostat)
+       *pchain* value = N
+         N length of thermostat chain on barostat (0 = no thermostat)
+       *mtk* value = *yes* or *no* = add in MTK adjustment term or not
+       *tloop* value = M
+         M = number of sub-cycles to perform on thermostat
+       *ploop* value = M
+         M = number of sub-cycles to perform on barostat thermostat
+       *nreset* value = reset reference cell every this many timesteps
+       *scalexy* value = *yes* or *no* = scale xy with ly
+       *scaleyz* value = *yes* or *no* = scale yz with lz
+       *scalexz* value = *yes* or *no* = scale xz with lz
+       *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
+       *fixedpoint* values = x y z
+         x,y,z = perform barostat dilation/contraction around this point (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   comm_modify vel yes
+   fix 1 all tgnvt/drude temp 300.0 300.0 100.0 1.0 20.0
+   fix 1 water tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 iso 0.0 0.0 1000.0
+   fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0
+   fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
+
+Description
+"""""""""""
+
+These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt
+<fix_nh>` and :doc:`fix npt <fix_nh>` for thermalized Drude polarizable
+models.  They apply temperature-grouped Nose-Hoover thermostat (TGNH)
+proposed by :ref:`(Son) <tgnh-Son>`.  When there are fast vibrational
+modes with frequencies close to Drude oscillators (e.g. double bonds or
+out-of-plane torsions), this thermostat can provide better kinetic
+energy equipartitioning.
+
+The difference between TGNH and the original Nose-Hoover thermostat is that,
+TGNH separates the kinetic energy of the group into three contributions:
+molecular center of mass (COM) motion,
+motion of COM of atom-Drude pairs or non-polarizable atoms relative to molecular COM,
+and relative motion of atom-Drude pairs.
+An independent Nose-Hoover chain is applied to each type of motion.
+The temperatures for these three types of motion are denoted as
+molecular translational temperature (:math:`T_\mathrm{M}`), real atomic temperature (:math:`T_\mathrm{R}`) and Drude temperature (:math:`T_\mathrm{D}`),
+which are defined in terms of their associated degrees of freedom (DOF):
+
+.. math::
+
+    T_\mathrm{M}=\frac{\Sigma_{i}^{N_\mathrm{mol}} M_i V_i^2}{3 \left ( N_\mathrm{mol} - \frac{N_\mathrm{mol}}{N_\mathrm{mol,sys}} \right ) k_\mathrm{B}}
+
+.. math::
+
+    T_\mathrm{R}=\frac{\Sigma_{i}^{N_\mathrm{real}} m_i (v_i-v_{M,i})^2}{(N_\mathrm{DOF} - 3 N_\mathrm{mol} + 3 \frac{N_\mathrm{mol}}{N_\mathrm{mol,sys}} - 3 N_\mathrm{drude}) k_\mathrm{B}}
+
+.. math::
+
+    T_\mathrm{D}=\frac{\Sigma_{i}^{N_\mathrm{drude}} m_i^{\prime} v_i^{\prime 2}}{3 N_\mathrm{drude} k_\mathrm{B}}
+
+Here :math:`N_\mathrm{mol}` and :math:`N_\mathrm{mol,sys}` are the numbers of molecules in the group and in the whole system, respectively.
+:math:`N_\mathrm{real}` is the number of atom-Drude pairs and non-polarizable atoms in the group.
+:math:`N_\mathrm{drude}` is the number of Drude particles in the group.
+:math:`N_\mathrm{DOF}` is the DOF of the group.
+:math:`M_i` and :math:`V_i` are the mass and the COM velocity of the i-th molecule.
+:math:`m_i` is the mass of the i-th atom-Drude pair or non-polarizable atom.
+:math:`v_i` is the velocity of COM of i-th atom-Drude pair or non-polarizable atom.
+:math:`v_{M,i}` is the COM velocity of the molecule the i-th atom-Drude pair or non-polarizable atom belongs to.
+:math:`m_i^\prime` and :math:`v_i^\prime` are the reduced mass and the relative velocity of the i-th atom-Drude pair.
+
+.. note::
+
+   These fixes require that each atom knows whether it is a Drude particle or
+   not.  You must therefore use the :doc:`fix drude <fix_drude>` command to
+   specify the Drude status of each atom type.
+
+   Because the TGNH thermostat thermostats the molecular COM motion,
+   all atoms belonging to the same molecule must be in the same group.
+   That is, these fixes can not be applied to a subset of a molecule.
+
+   For this fix to act correctly, ghost atoms need to know their velocity.
+   You must use the :doc:`comm_modify <comm_modify>` command to enable this.
+
+   These fixes assume that the translational DOF of the whole system is removed.
+   It is therefore recommended to invoke :doc:`fix momentum <fix_momentum>` command so that the :math:`T_\mathrm{M}` is calculated correctly.
+
+----------
+
+The thermostat parameters are specified using the *temp* keyword.
+The thermostat is applied to only the translational DOF
+for the particles.  The translational DOF can also have
+a bias velocity removed before thermostatting takes place; see the
+description below.  The desired temperature for molecular and real atomic motion 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. :math:`\tau`
+or fs or ps - see the :doc:`units <units>` command).
+The parameter *Tdrude* is the desired temperature for Drude motion at each timestep.
+Similar to *Tdamp*, the *Tdamp_drude* parameter determines the relaxation speed for Drude motion.
+Fix group are the only ones whose velocities and positions are updated
+by the velocity/position update portion of the integration.
+Other thermostat-related keywords are *tchain*\  and *tloop*\ ,
+which are detailed in :doc:`fix nvt <fix_nh>`.
+
+.. note::
+
+   A Nose-Hoover thermostat will not work well for arbitrary values
+   of *Tdamp*\ .  If *Tdamp* is too small, the temperature can fluctuate
+   wildly; if it is too large, the temperature will take a very long time
+   to equilibrate.  A good choice for many models is a *Tdamp* of around
+   100 timesteps.  A smaller *Tdamp_drude* value would be required
+   to maintain Drude motion at low temperature.
+
+.. code-block:: LAMMPS
+
+   fix 1 all nvt temp 300.0 300.0 $(100.0*dt) 1.0 $(20.0*dt)
+
+----------
+
+The barostat parameters for fix style *tgnpt/drude* is specified
+using one or more of the *iso*\ , *aniso*\ , *tri*\ , *x*\ , *y*\ , *z*\ , *xy*\ ,
+*xz*\ , *yz*\ , and *couple* keywords.  These keywords give you the
+ability to specify all 6 components of an external stress tensor, and
+to couple various of these components together so that the dimensions
+they represent are varied together during a constant-pressure
+simulation. Other barostat-related keywords are *pchain*\ , *mtk*\ , *ploop*\ ,
+*nreset*\ , *scalexy*\ , *scaleyz*\ , *scalexz*\ , *flip*\ and *fixedpoint*.
+The meaning of barostat parameters are detailed in :doc:`fix npt <fix_nh>`.
+
+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
+changed, all atoms are re-scaled to new positions.
+
+.. note::
+
+   Unlike the :doc:`fix temp/berendsen <fix_temp_berendsen>` command
+   which performs thermostatting but NO time integration, these fixes
+   perform thermostatting/barostatting AND time integration.  Thus you
+   should not use any other time integration fix, such as :doc:`fix nve <fix_nve>` on atoms to which this fix is applied.
+   Likewise, these fixes should not be used on atoms that also
+   have their temperature controlled by another fix - e.g. by :doc:`fix langevin/drude <fix_langevin_drude>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` and :doc:`Howto barostat <Howto_barostat>` doc pages for a discussion of different
+ways to compute temperature and perform thermostatting and
+barostatting.
+
+----------
+
+Like other fixes that perform thermostatting, these fixes can
+be used with :doc:`compute commands <compute>` that calculate a
+temperature after removing a "bias" from the atom velocities.
+This is not done by default, but only if the :doc:`fix_modify <fix_modify>` command
+is used to assign a temperature compute to this fix that includes such
+a bias term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal DOF, and the bias is added back in.
+
+.. note::
+
+   However, not all temperature compute commands are valid to be used with these fixes.
+   Precisely, only temperature compute that does not modify the DOF of the group can be used.
+   E.g. :doc:`compute temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos <compute_viscosity_cos>`
+   compute the kinetic energy after remove a velocity gradient without affecting the DOF of the group,
+   then they can be invoked in this way.
+   In contrast, :doc:`compute temp/partial <compute_temp_partial>` may remove the DOF at one or more dimensions,
+   therefore it cannot be used with these fixes.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+These fixes writes the state of all the thermostat and barostat
+variables to :doc:`binary restart files <restart>`.  See the
+:doc:`read_restart <read_restart>` command for 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.
+
+The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
+supported by these fixes.  You can use them to assign a
+:doc:`compute <compute>` you have defined to this fix which will be used
+in its thermostatting or barostatting procedure, as described above.
+If you do this, note that the kinetic energy derived from the compute
+temperature should be consistent with the virial term computed using
+all atoms for the pressure.  LAMMPS will warn you if you choose to
+compute temperature on a subset of atoms.
+
+.. note::
+
+   If both the *temp* and *press* keywords are used in a single
+   thermo_modify command (or in two separate commands), then the order in
+   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   an argument when it is specified.  The *temp* keyword will override
+   this (for the pressure compute being used by fix npt), but only if the
+   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   comes before the *press* keyword, then the new pressure compute
+   specified by the *press* keyword will be unaffected by the *temp*
+   setting.
+
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+fixes to add the energy change induced by Nose/Hoover thermostatting
+and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>`.
+
+These fixes compute a global scalar and a global vector of quantities,
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar value calculated by these fixes is "extensive"; the vector
+values are "intensive".
+The scalar is the cumulative energy change due to the fix.
+The vector stores the three temperatures :math:`T_\mathrm{M}`, :math:`T_\mathrm{R}` and :math:`T_\mathrm{D}`.
+
+These fixes can ramp their external temperature and pressure over
+multiple runs, using the *start* and *stop* keywords of the
+:doc:`run <run>` command.  See the :doc:`run <run>` command for details of
+how to do this.
+
+These fixes are not invoked during :doc:`energy minimization <minimize>`.
+
+----------
+
+Restrictions
+""""""""""""
+
+These fixes are only available when LAMMPS was built with the USER-DRUDE package.
+These fixes cannot be used with dynamic groups as defined by the :doc:`group <group>` command.
+These fixes cannot be used in 2D simulations.
+
+*X*\ , *y*\ , *z* cannot be barostatted if the associated dimension is not
+periodic.  *Xy*\ , *xz*\ , and *yz* can only be barostatted if the
+simulation domain is triclinic and the second dimension in the keyword
+(\ *y* dimension in *xy*\ ) is periodic.  The :doc:`create_box <create_box>`,
+:doc:`read data <read_data>`, and :doc:`read_restart <read_restart>`
+commands specify whether the simulation box is orthogonal or
+non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz
+tilt factors.
+
+For the *temp* keyword, the final *Tstop* cannot be 0.0 since it would
+make the external T = 0.0 at some timestep during the simulation which
+is not allowed in the Nose/Hoover formulation.
+
+The *scaleyz yes*\ , *scalexz yes*\ , and *scalexy yes* options
+can only be used if the second dimension in the keyword is periodic,
+and if the tilt factor is not coupled to the barostat via keywords
+*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
+
+Related commands
+""""""""""""""""
+
+:doc:`fix drude <fix_drude>`, :doc:`fix nvt <fix_nh>`, :doc:`fix_npt <fix_nh>`,
+:doc:`fix_modify <fix_modify>`
+
+Default
+"""""""
+
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
+ploop = 1, nreset = 0, couple = none,
+flip = yes, scaleyz = scalexz = scalexy = yes if periodic in second
+dimension and not coupled to barostat, otherwise no.
+
+----------
+
+.. _tgnh-Son:
+
+**(Son)** Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).

doc/src/lattice.rst

@@ -251,12 +251,16 @@ in commands that use the spacings should be decipherable.
 
 ----------
 
-Example commands for generating a Wurtzite crystal (courtesy
-of Aidan Thompson), with its 8 atom unit cell.
+Example commands for generating a Wurtzite crystal.
+The lattice constants approximate those of CdSe.
+The :math:`\sqrt{3}\times 1` orthorhombic supercell is used
+with the x, y, and z directions oriented
+along :math:`[\bar{1}\bar{2}30]`,
+:math:`[10\bar{1}0]`, and :math:`[0001]`, respectively.
 
 .. code-block:: LAMMPS
 
-   variable a equal  4.340330
+   variable a equal  4.34
    variable b equal  $a*sqrt(3.0)
    variable c equal  $a*sqrt(8.0/3.0)
 
@@ -264,8 +268,8 @@ of Aidan Thompson), with its 8 atom unit cell.
    variable five6 equal 5.0/6.0
 
    lattice custom    1.0     &
-           a1      $a       0.0     0.0     &
-           a2      0.0      $b      0.0     &
+           a1      $b       0.0     0.0     &
+           a2      0.0      $a      0.0     &
            a3      0.0      0.0     $c      &
            basis   0.0      0.0     0.0     &
            basis   0.5      0.5     0.0     &

doc/src/message.rst

@@ -34,7 +34,7 @@ Examples
    message server md file tmp.couple
 
    message client md zmq localhost:5555
-   message server md zmq \*:5555
+   message server md zmq *:5555
 
    message client md mpi/one
    message server md mpi/one

doc/src/molecule.rst

@@ -201,11 +201,12 @@ bonds between nuclear cores and Drude electrons in a different manner.
 
 Each section is listed below in alphabetic order.  The format of each
 section is described including the number of lines it must contain and
-rules (if any) for whether it can appear in the data file.  In each
-case the ID is ignored; it is simply included for readability, and
-should be a number from 1 to Nlines for the section, indicating which
-atom (or bond, etc) the entry applies to.  The lines are assumed to be
-listed in order from 1 to Nlines, but LAMMPS does not check for this.
+rules (if any) for whether it can appear in the data file.  For per-
+atom sections, entries should be numbered from 1 to Natoms (where
+Natoms is the number of atoms in the template), indicating which atom
+(or bond, etc) the entry applies to.  Per-atom sections need to
+include a setting for every atom, but the atoms can be listed in any
+order.
 
 ----------
 

doc/src/neighbor.rst

@@ -49,7 +49,9 @@ sometimes be faster.  Either style should give the same answers.
 
 The *multi* style is a modified binning algorithm that is useful for
 systems with a wide range of cutoff distances, e.g. due to different
-size particles.  For the *bin* style, the bin size is set to 1/2 of
+size particles. For granular pair styles, cutoffs are set to the
+sum of the maximum atomic radii for each atom type.
+For the *bin* style, the bin size is set to 1/2 of
 the largest cutoff distance between any pair of atom types and a
 single set of bins is defined to search over for all atom types.  This
 can be inefficient if one pair of types has a very long cutoff, but
@@ -57,8 +59,10 @@ other type pairs have a much shorter cutoff.  For style *multi* the
 bin size is set to 1/2 of the shortest cutoff distance and multiple
 sets of bins are defined to search over for different atom types.
 This imposes some extra setup overhead, but the searches themselves
-may be much faster for the short-cutoff cases.  See the :doc:`comm_modify mode multi <comm_modify>` command for a communication option
-that may also be beneficial for simulations of this kind.
+may be much faster for the short-cutoff cases.
+See the :doc:`comm_modify mode multi <comm_modify>` command for a
+communication option that may also be beneficial for simulations of
+this kind.
 
 The :doc:`neigh_modify <neigh_modify>` command has additional options
 that control how often neighbor lists are built and which pairs are

doc/src/package.rst

@@ -18,13 +18,16 @@ Syntax
        *gpu* args = Ngpu keyword value ...
          Ngpu = # of GPUs per node
          zero or more keyword/value pairs may be appended
-         keywords = *neigh* or *newton* or *binsize* or *split* or *gpuID* or *tpa* or *device* or *blocksize*
+         keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *device* or *blocksize*
            *neigh* value = *yes* or *no*
              yes = neighbor list build on GPU (default)
              no = neighbor list build on CPU
            *newton* = *off* or *on*
              off = set Newton pairwise flag off (default and required)
              on = set Newton pairwise flag on (currently not allowed)
+           *pair/only* = *off* or *on*
+             off = apply "gpu" suffix to all available styles in the GPU package (default)
+             on  - apply "gpu" suffix only pair styles
            *binsize* value = size
              size = bin size for neighbor list construction (distance units)
            *split* = fraction
@@ -65,7 +68,7 @@ Syntax
            *no_affinity* values = none
        *kokkos* args = keyword value ...
          zero or more keyword/value pairs may be appended
-         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/reverse* or *cuda/aware*
+         keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/reverse* or *cuda/aware* or *pair/only*
            *neigh* value = *full* or *half*
              full = full neighbor list
              half = half neighbor list built in thread-safe manner
@@ -91,6 +94,9 @@ Syntax
            *cuda/aware* = *off* or *on*
              off = do not use CUDA-aware MPI
              on = use CUDA-aware MPI (default)
+           *pair/only* = *off* or *on*
+             off = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default)
+             on  = use device acceleration only for pair styles (and host acceleration for others)
        *omp* args = Nthreads keyword value ...
          Nthread = # of OpenMP threads to associate with each MPI process
          zero or more keyword/value pairs may be appended
@@ -194,6 +200,14 @@ for compatibility with the package command for other accelerator
 styles.  Note that the newton setting for bonded interactions is not
 affected by this keyword.
 
+The *pair/only* keyword can change how any "gpu" suffix is applied.
+By default a suffix is applied to all styles for which an accelerated
+variant is available.  However, that is not always the most effective
+way to use an accelerator.  With *pair/only* set to *on* the suffix
+will only by applied to supported pair styles, which tend to be the
+most effective in using an accelerator and their operation can be
+overlapped with all other computations on the CPU.
+
 The *binsize* keyword sets the size of bins used to bin atoms in
 neighbor list builds performed on the GPU, if *neigh* = *yes* is set.
 If *binsize* is set to 0.0 (the default), then bins = the size of the
@@ -448,8 +462,7 @@ does not require atomic operations in the calculation of pair forces. For
 that reason, *full* is the default setting for GPUs. However, when
 running on CPUs, a *half* neighbor list is the default because it are
 often faster, just as it is for non-accelerated pair styles. Similarly,
-the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`. If not explicitly set, the value of
-*neigh/qeq* will match *neigh*\ .
+the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
 
 If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
 threads only over atoms. However, for small systems, this may not expose
@@ -535,12 +548,20 @@ available (currently only possible with OpenMPI v2.0.0 or later), then
 the *cuda/aware* keyword is automatically set to *off* by default. When
 the *cuda/aware* keyword is set to *off* while any of the *comm*
 keywords are set to *device*\ , the value for these *comm* keywords will
-be automatically changed to *host*\ . This setting has no effect if not
+be automatically changed to *no*\ . This setting has no effect if not
 running on GPUs or if using only one MPI rank. CUDA-aware MPI is available
 for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the
 "MV2_USE_CUDA" environment variable is set to "1", CrayMPI, and IBM
 Spectrum MPI when the "-gpu" flag is used.
 
+The *pair/only* keyword can change how the KOKKOS suffix "kk" is applied
+when using an accelerator device.  By default device acceleration is
+always used for all available styles.  With *pair/only* set to *on* the
+suffix setting will choose device acceleration only for pair styles and
+run all other force computations concurrently on the host CPU.
+The *comm* flags will also automatically be changed to *no*\ . This can
+result in better performance for certain configurations and system sizes.
+
 ----------
 
 The *omp* style invokes settings associated with the use of the

doc/src/pair_atm.rst

@@ -143,7 +143,7 @@ combinations, else an error will result.
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair styles do not support the :doc:`pair_modify <pair_modify>`
+This pair style do not support the :doc:`pair_modify <pair_modify>`
 mix, shift, table, and tail options.
 
 This pair style writes its information to :doc:`binary restart files

doc/src/pair_buck_long.rst

@@ -117,7 +117,7 @@ global Coulombic cutoff is allowed.
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair styles does not support mixing.  Thus, coefficients for all
+This pair style does not support mixing.  Thus, coefficients for all
 I,J pairs must be specified explicitly.
 
 This pair style supports the :doc:`pair_modify <pair_modify>` shift

doc/src/pair_gayberne.rst

@@ -160,7 +160,7 @@ For atom type pairs I,J and I != J, the epsilon and sigma coefficients
 and cutoff distance for this pair style can be mixed.  The default mix
 value is *geometric*\ .  See the "pair_modify" command for details.
 
-This pair styles supports the :doc:`pair_modify <pair_modify>` shift
+This pair style supports the :doc:`pair_modify <pair_modify>` shift
 option for the energy of the Lennard-Jones portion of the pair
 interaction, but only for sphere-sphere interactions.  There is no
 shifting performed for ellipsoidal interactions due to the anisotropic

doc/src/pair_lcbop.rst

@@ -75,14 +75,15 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This pair styles is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
 
 This pair potential requires the :doc:`newton <newton>` setting to be
 "on" for pair interactions.
 
-The C.lcbop potential file provided with LAMMPS (see the potentials
-directory) is parameterized for metal :doc:`units <units>`.  You can use
+The ``C.lcbop`` potential file provided with LAMMPS (see the potentials
+directory) is parameterized for :doc:`metal units <units>`.  You can use
 the LCBOP potential with any LAMMPS units, but you would need to
 create your own LCBOP potential file with coefficients listed in the
 appropriate units if your simulation does not use "metal" units.

doc/src/pair_meam_spline.rst

@@ -20,7 +20,7 @@ Examples
 
    pair_style meam/spline
    pair_coeff * * Ti.meam.spline Ti
-   pair_coeff * * Ti.meam.spline Ti Ti Ti
+   pair_coeff * * Ti.meam.spline Ti O
 
 Description
 """""""""""
@@ -84,23 +84,22 @@ where N is the number of LAMMPS atom types:
 See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
 to specify the path for the potential file.
 
-As an example, imagine the Ti.meam.spline file has values for Ti (old style).  If
-your LAMMPS simulation has 3 atoms types and they are all to be
-treated with this potentials, you would use the following pair_coeff
-command:
+As an example, imagine the Ti.meam.spline file has values for Ti (old style).
+In that case your LAMMPS simulation may only have one atom type which has
+to be mapped to the Ti element as follows:
 
 .. code-block:: LAMMPS
 
-   pair_coeff * * Ti.meam.spline Ti Ti Ti
+   pair_coeff * * Ti.meam.spline Ti
 
-The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
-The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
-in the potential file.  If a mapping value is specified as NULL, the
-mapping is not performed.  This can be used when a *meam/spline*
-potential is used as part of the *hybrid* pair style.  The NULL values
-are placeholders for atom types that will be used with other
-potentials. The old-style potential maps any non-NULL species named
-on the command line to that single type.
+The first 2 arguments must be \* \* and there may be only one element
+following or NULL. Systems where there would be multiple atom types
+assigned to the same element are **not** supported by this pair style
+due to limitations in its implementation.  If a mapping value is
+specified as NULL, the mapping is not performed.  This can be used when
+a *meam/spline* potential is used as part of the *hybrid* pair style.
+The NULL values are placeholders for atom types that will be used with
+other potentials.
 
 An example with a two component spline (new style) is TiO.meam.spline, where
 the command
@@ -143,6 +142,8 @@ Restrictions
 This pair style requires the :doc:`newton <newton>` setting to be "on"
 for pair interactions.
 
+This pair style does not support mapping multiple atom types to the same element.
+
 This pair style is only enabled if LAMMPS was built with the USER-MISC
 package.  See the :doc:`Build package <Build_package>` doc page for more
 info.

doc/src/pair_polymorphic.rst

@@ -298,7 +298,7 @@ described above.  For each of the F functions, nx values are listed.
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair styles does not support the :doc:`pair_modify <pair_modify>`
+This pair style does not support the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options.
 
 This pair style does not write their information to :doc:`binary restart

doc/src/pair_resquared.rst

@@ -173,7 +173,7 @@ equation for the Hamaker constant presented here.  Mixing of sigma and
 epsilon followed by calculation of the energy prefactors using the
 equations above is recommended.
 
-This pair styles supports the :doc:`pair_modify <pair_modify>` shift
+This pair style supports the :doc:`pair_modify <pair_modify>` shift
 option for the energy of the Lennard-Jones portion of the pair
 interaction, but only for sphere-sphere interactions.  There is no
 shifting performed for ellipsoidal interactions due to the anisotropic

doc/src/pair_spin_exchange.rst

@@ -1,14 +1,19 @@
 .. index:: pair_style spin/exchange
+.. index:: pair_style spin/exchange/biquadratic
 
 pair_style spin/exchange command
 ================================
 
+pair_style spin/exchange/biquadratic command
+============================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    pair_style spin/exchange cutoff
+   pair_style spin/exchange/biquadratic cutoff
 
 * cutoff = global cutoff pair (distance in metal units)
 
@@ -19,7 +24,11 @@ Examples
 
    pair_style spin/exchange 4.0
    pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
-   pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965
+   pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 offset yes
+
+   pair_style spin/exchange/biquadratic 4.0
+   pair_coeff * * biquadratic 4.0 0.05 0.03 1.48 0.05 0.03 1.48 offset no
+   pair_coeff 1 2 biquadratic 6.0 -0.01 0.0 1.9 0.0 0.1 19
 
 Description
 """""""""""
@@ -31,69 +40,163 @@ pairs of magnetic spins:
 
    H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,\vec{s}_i \cdot \vec{s}_j
 
-where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two neighboring magnetic spins of two particles,
-:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance between the two
-particles. The summation is over pairs of nearest neighbors.
-:math:`J(r_{ij})` is a function defining the intensity and the sign of the exchange
-interaction for different neighboring shells. This function is defined as:
+where :math:`\vec{s}_i` and :math:`\vec{s}_j` are two unit vectors representing
+the magnetic spins of two particles (usually atoms), and
+:math:`r_{ij} = \vert \vec{r}_i - \vec{r}_j \vert` is the inter-atomic distance
+between those two particles. The summation is over pairs of nearest neighbors.
+:math:`J(r_{ij})` is a function defining the intensity and the sign of the
+exchange interaction for different neighboring shells.
+
+Style *spin/exchange/biquadratic* computes a biquadratic exchange interaction
+between pairs of magnetic spins:
 
 .. math::
 
-    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+   H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
+                      \vec{s}_{i}\cdot \vec{s}_{j}
+                      -\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
+                      \left(\vec{s}_{i}\cdot
+                      \vec{s}_{j}\right)^2
 
-where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients defined in the associated
-"pair_coeff" command, and :math:`R_c` is the radius cutoff associated to
-the pair interaction (see below for more explanations).
+where :math:`\vec{s}_i`,  :math:`\vec{s}_j`,  :math:`r_{ij}` and
+:math:`J(r_{ij})` have the same definitions as above, and :math:`K(r_{ij})` is
+a second function, defining the intensity and the sign of the biquadratic term.
 
-The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that the function above matches with
-the value of the exchange interaction for the :math:`N` neighbor shells taken into account.
-Examples and more explanations about this function and its parameterization are reported
-in :ref:`(Tranchida) <Tranchida3>`.
+The interatomic dependence of :math:`J(r_{ij})` and :math:`K(r_{ij})` in both
+interactions above is defined by the following function:
+
+.. math::
+
+    {f}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2
+    \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right)
+    e^{-\left( \frac{r_{ij}}{d} \right)^2 }\Theta (R_c - r_{ij})
+
+where :math:`a`, :math:`b` and :math:`d` are the three constant coefficients
+defined in the associated "pair_coeff" command, and :math:`R_c` is the radius
+cutoff associated to the pair interaction (see below for more explanations).
+
+The coefficients :math:`a`, :math:`b`, and :math:`d` need to be fitted so that
+the function above matches with the value of the exchange interaction for the
+:math:`N` neighbor shells taken into account.
+Examples and more explanations about this function and its parameterization
+are reported in :ref:`(Tranchida) <Tranchida3>`.
+
+When a *spin/exchange/biquadratic* pair style is defined, six coefficients
+(three for :math:`J(r_{ij})`, and three for :math:`K(r_{ij})`) have to be
+fitted.
 
 From this exchange interaction, each spin :math:`i` will be submitted
-to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
-force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
-such as:
+to a magnetic torque :math:`\vec{\omega}_{i}`, and its associated atom can be
+submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
+:doc:`fix nve/spin <fix_nve_spin>`), such as:
 
 .. math::
 
    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
    \left(r_{ij} \right)\,\vec{s}_{j}
    ~~{\rm and}~~
-   \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
+   \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
+   \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
 
-with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij} = \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
+with :math:`\hbar` the Planck constant (in metal units), and :math:`\vec{e}_{ij}
+= \frac{\vec{r}_i - \vec{r}_j}{\vert \vec{r}_i-\vec{r}_j \vert}` the unit
 vector between sites :math:`i` and :math:`j`.
+Equivalent forces and magnetic torques are generated for the biquadratic term
+when a *spin/exchange/biquadratic* pair style is defined.
 
 More details about the derivation of these torques/forces are reported in
 :ref:`(Tranchida) <Tranchida3>`.
 
-For the *spin/exchange* pair style, the following coefficients must be defined
-for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
-the examples above, or in the data file or restart files read by the
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands, and
-set in the following order:
+For the *spin/exchange* and *spin/exchange/biquadratic* pair styles, the
+following coefficients must be defined for each pair of atoms types via the
+:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
+file or restart files read by the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands, and set in the following order:
 
 * :math:`R_c` (distance units)
 * :math:`a`  (energy units)
 * :math:`b`  (adim parameter)
 * :math:`d`  (distance units)
 
-Note that :math:`R_c` is the radius cutoff of the considered exchange interaction,
-and :math:`a`, :math:`b` and :math:`d` are the three coefficients performing the parameterization
-of the function :math:`J(r_{ij})` defined above.
+for the *spin/exchange* pair style, and:
+
+* :math:`R_c` (distance units)
+* :math:`a_j`  (energy units)
+* :math:`b_j`  (adim parameter)
+* :math:`d_j`  (distance units)
+* :math:`a_k`  (energy units)
+* :math:`b_k`  (adim parameter)
+* :math:`d_k`  (distance units)
+
+for the *spin/exchange/biquadratic* pair style.
+
+Note that :math:`R_c` is the radius cutoff of the considered exchange
+interaction, and :math:`a`, :math:`b` and :math:`d` are the three coefficients
+performing the parameterization of the function :math:`J(r_{ij})` defined
+above (in the *biquadratic* style, :math:`a_j`, :math:`b_j`, :math:`d_j` and
+:math:`a_k`, :math:`b_k`, :math:`d_k` are the coefficients of :math:`J(r_{ij})`
+and :math:`K(r_{ij})` respectively).
+
 
 None of those coefficients is optional. If not specified, the
 *spin/exchange* pair style cannot be used.
 
 ----------
 
+**Offsetting magnetic forces and energies**\ :
+
+For spin-lattice simulation, it can be useful to offset the
+mechanical forces and energies generated by the exchange
+interaction.
+The *offset* keyword allows to apply this offset.
+By setting *offset* to *yes*, the energy definitions above are
+replaced by:
+
+.. math::
+
+   H_{ex} = -\sum_{i,j}^N J_{ij} (r_{ij}) \,[ \vec{s}_i \cdot \vec{s}_j-1 ]
+
+for the *spin/exchange* pair style, and:
+
+.. math::
+
+   H_{bi} = -\sum_{i, j}^{N} {J}_{ij} \left(r_{ij} \right)\,
+                      [ \vec{s}_{i}\cdot \vec{s}_{j} -1 ]
+                      -\sum_{i, j}^{N} {K}_{ij} \left(r_{ij} \right)\,
+                      [ \left(\vec{s}_{i}\cdot
+                      \vec{s}_{j}\right)^2 -1]
+
+for the *spin/exchange/biquadratic* pair style.
+
+Note that this offset only affects the calculation of the energy
+and mechanical forces. It does not modify the calculation of the
+precession vectors (and thus does no impact the purely magnetic
+properties).
+This ensures that when all spins are aligned, the magnetic energy
+and the associated mechanical forces (and thus the pressure
+generated by the magnetic potential) are null.
+
+.. note::
+  This offset term can be very important when calculations such as
+  equations of state (energy vs volume, or energy vs pressure) are
+  being performed. Indeed, setting the *offset* term ensures that
+  at the ground state of the crystal and at the equilibrium magnetic
+  configuration (typically ferromagnetic), the pressure is null,
+  as expected.
+  Otherwise, magnetic forces could generate a residual pressure.
+
+When the *offset* option is set to *no*, no offset is applied
+(also corresponding to the default option).
+
+----------
+
 Restrictions
 """"""""""""
 
 All the *pair/spin* styles are part of the SPIN package.  These styles
 are only enabled if LAMMPS was built with this package, and if the
-atom_style "spin" was declared.  See the :doc:`Build package <Build_package>` doc page for more info.
+atom_style "spin" was declared.
+See the :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""
@@ -105,7 +208,7 @@ Default
 """""""
 
 
-none
+The default *offset* keyword value is *no*.
 
 ----------
 

doc/src/pair_srp.rst

@@ -124,7 +124,7 @@ at the cutoff distance :math:`r_c`.
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This pair styles does not support mixing.
+This pair style does not support mixing.
 
 This pair style does not support the :doc:`pair_modify <pair_modify>`
 shift option for the energy of the pair interaction. Note that as

doc/src/pair_style.rst

@@ -305,6 +305,7 @@ accelerated styles exist.
 * :doc:`spin/dipole/long <pair_spin_dipole>` -
 * :doc:`spin/dmi <pair_spin_dmi>` -
 * :doc:`spin/exchange <pair_spin_exchange>` -
+* :doc:`spin/exchange/biquadratic <pair_spin_exchange>` -
 * :doc:`spin/magelec <pair_spin_magelec>` -
 * :doc:`spin/neel <pair_spin_neel>` -
 * :doc:`srp <pair_srp>` -

doc/src/python.rst

@@ -323,8 +323,8 @@ Python function is as follows:
 
 The function definition must include a variable (lmpptr in this case)
 which corresponds to SELF in the python command.  The first line of the
-function imports the Python module lammps.py in the python directory of
-the distribution.  The second line creates a Python object "lmp" which
+function imports the :doc:`"lammps" Python module <Python_module>`.
+The second line creates a Python object ``lmp`` which
 wraps the instance of LAMMPS that called the function.  The "ptr=lmpptr"
 argument is what makes that happen.  The third line invokes the
 command() function in the LAMMPS library interface.  It takes a single
@@ -502,18 +502,16 @@ Python library on your system.  Settings to enable this are in the
 lib/python/Makefile.lammps file.  See the lib/python/README file for
 information on those settings.
 
-If you use Python code which calls back to LAMMPS, via the SELF input
-argument explained above, there is an extra step required when
-building LAMMPS.  LAMMPS must also be built as a shared library and
-your Python function must be able to load the Python module in
-python/lammps.py that wraps the LAMMPS library interface.  These are
-the same steps required to use Python by itself to wrap LAMMPS.
-Details on these steps are explained on the :doc:`Python <Python_head>`
-doc page.  Note that it is important that the stand-alone LAMMPS
-executable and the LAMMPS shared library be consistent (built from the
-same source code files) in order for this to work.  If the two have
-been built at different times using different source files, problems
-may occur.
+If you use Python code which calls back to LAMMPS, via the SELF input argument
+explained above, there is an extra step required when building LAMMPS.  LAMMPS
+must also be built as a shared library and your Python function must be able to
+load the :doc:`"lammps" Python module <Python_module>` that wraps the LAMMPS
+library interface.  These are the same steps required to use Python by itself
+to wrap LAMMPS.  Details on these steps are explained on the :doc:`Python
+<Python_head>` doc page.  Note that it is important that the stand-alone LAMMPS
+executable and the LAMMPS shared library be consistent (built from the same
+source code files) in order for this to work.  If the two have been built at
+different times using different source files, problems may occur.
 
 Related commands
 """"""""""""""""

doc/src/read_data.rst

@@ -345,10 +345,11 @@ Similarly, the z dimension should be periodic if xz or yz is non-zero.
 LAMMPS does not require this periodicity, but you may lose atoms if
 this is not the case.
 
-Also note that if your simulation will tilt the box, e.g. via the :doc:`fix deform <fix_deform>` command, the simulation box must be setup to
-be triclinic, even if the tilt factors are initially 0.0.  You can
-also change an orthogonal box to a triclinic box or vice versa by
-using the :doc:`change box <change_box>` command with its *ortho* and
+Also note that if your simulation will tilt the box, e.g. via the
+:doc:`fix deform <fix_deform>` command, the simulation box must be setup
+to be triclinic, even if the tilt factors are initially 0.0.  You can
+also change an orthogonal box to a triclinic box or vice versa by using
+the :doc:`change box <change_box>` command with its *ortho* and
 *triclinic* options.
 
 For 2d simulations, the *zlo zhi* values should be set to bound the z
@@ -364,24 +365,53 @@ periodic remapping will be performed using simulation box bounds that
 are the union of the existing box and the box boundaries in the new
 data file.
 
+If the system is non-periodic (in a dimension), then an image flag for
+that direction has no meaning, since there cannot be periodic images
+without periodicity and the data file is therefore - technically speaking
+- invalid.  This situation would happen when a data file was written
+with periodic boundaries and then read back for non-periodic boundaries.
+Accepting a non-zero image flag can lead to unexpected results for any
+operations and computations in LAMMPS that internally use unwrapped
+coordinates (for example computing the center of mass of a group of
+atoms). Thus all non-zero image flags for non-periodic dimensions will
+be be reset to zero on reading the data file and LAMMPS will print a
+warning message, if that happens.  This is equivalent to wrapping atoms
+individually back into the principal unit cell in that direction.  This
+operation is equivalent to the behavior of the :doc:`change_box command
+<change_box>` when used to change periodicity.
+
+
+If those atoms with non-zero image flags are involved in bonded
+interactions, this reset can lead to undesired changes, when the image
+flag values differ between the atoms, i.e. the bonded interaction
+straddles domain boundaries.  For example a bond can become stretched
+across the unit cell if one of its atoms is wrapped to one side of the
+cell and the second atom to the other. In those cases the data file
+needs to be pre-processed externally to become valid again.  This can be
+done by first unwrapping coordinates and then wrapping entire molecules
+instead of individual atoms back into the principal simulation cell and
+finally expanding the cell dimensions in the non-periodic direction as
+needed, so that the image flag would be zero.
+
 .. note::
 
-   If the system is non-periodic (in a dimension), then all atoms
-   in the data file must have coordinates (in that dimension) that are
-   "greater than or equal to" the lo value and "less than or equal to"
-   the hi value.  If the non-periodic dimension is of style "fixed" (see
-   the :doc:`boundary <boundary>` command), then the atom coords must be
+   If the system is non-periodic (in a dimension), then all atoms in the
+   data file must have coordinates (in that dimension) that are "greater
+   than or equal to" the lo value and "less than or equal to" the hi
+   value.  If the non-periodic dimension is of style "fixed" (see the
+   :doc:`boundary <boundary>` command), then the atom coords must be
    strictly "less than" the hi value, due to the way LAMMPS assign atoms
    to processors.  Note that you should not make the lo/hi values
    radically smaller/larger than the extent of the atoms.  For example,
    if your atoms extend from 0 to 50, you should not specify the box
-   bounds as -10000 and 10000.  This is because LAMMPS uses the specified
-   box size to layout the 3d grid of processors.  A huge (mostly empty)
-   box will be sub-optimal for performance when using "fixed" boundary
+   bounds as -10000 and 10000 unless you also use the :doc:`processors
+   command <processors>`.  This is because LAMMPS uses the specified box
+   size to layout the 3d grid of processors.  A huge (mostly empty) box
+   will be sub-optimal for performance when using "fixed" boundary
    conditions (see the :doc:`boundary <boundary>` command).  When using
    "shrink-wrap" boundary conditions (see the :doc:`boundary <boundary>`
-   command), a huge (mostly empty) box may cause a parallel simulation to
-   lose atoms when LAMMPS shrink-wraps the box around the atoms.  The
+   command), a huge (mostly empty) box may cause a parallel simulation
+   to lose atoms when LAMMPS shrink-wraps the box around the atoms.  The
    read_data command will generate an error in this case.
 
 The "extra bond per atom" setting (angle, dihedral, improper) is only

doc/src/read_dump.rst

@@ -370,6 +370,8 @@ needed to generate absolute, unscaled coordinates.
 Restrictions
 """"""""""""
 
+The *native* dump file reader does not support binary .bin dump files.
+
 To read gzipped dump files, you must compile LAMMPS with the
 -DLAMMPS_GZIP option.  See the :doc:`Build settings <Build_settings>`
 doc page for details.

doc/src/rerun.rst

@@ -99,14 +99,15 @@ files do not match the specified output frequency.
 ----------
 
 If more than one dump file is specified, the dump files are read one
-after the other.  It is assumed that snapshot timesteps will be in
-ascending order.  If a snapshot is encountered that is not in
-ascending order, it will skip the snapshot until it reads one that is.
+after the other in the order specified.  It is assumed that snapshot
+timesteps will be in ascending order.  If a snapshot is encountered that
+is not in ascending order, it will skip the snapshot until it reads one
+that is.
 This allows skipping of a duplicate snapshot (same timestep),
 e.g. that appeared at the end of one file and beginning of the next.
 However if you specify a series of dump files in an incorrect order
 (with respect to the timesteps they contain), you may skip large
-numbers of snapshots
+numbers of snapshots.
 
 Note that the dump files specified as part of the *dump* keyword can be
 parallel files, i.e. written as multiple files either per processor
@@ -118,17 +119,24 @@ and write parallel dump files.
 
 The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
 snapshots are read from the dump file(s).  Snapshots are skipped until
-they have a timestamp >= *Nfirst*\ .  When a snapshot with a timestamp >
-*Nlast* is encountered, the rerun command finishes.  Note below that
+they have a timestep >= *Nfirst*\ .  When a snapshot with a timestep >
+*Nlast* is encountered, the rerun command finishes.  Note that
 the defaults for *first* and *last* are to read all snapshots.  If the
 *every* keyword is set to a value > 0, then only snapshots with
-timestamps that are a multiple of *Nevery* are read (the first
+timesteps that are a multiple of *Nevery* are read (the first
 snapshot is always read).  If *Nevery* = 0, then this criterion is
 ignored, i.e. every snapshot is read that meets the other criteria.
 If the *skip* keyword is used, then after the first snapshot is read,
 every Nth snapshot is read, where N = *Nskip*\ .  E.g. if *Nskip* = 3,
 then only 1 out of every 3 snapshots is read, assuming the snapshot
-timestamp is also consistent with the other criteria.
+timestep is also consistent with the other criteria.
+
+.. note::
+
+   Not all dump formats contain the timestep and not all dump readers
+   support reading it.  In that case individual snapshots are assigned
+   consecutive timestep numbers starting at 1.
+
 
 The *start* and *stop* keywords do not affect which snapshots are read
 from the dump file(s).  Rather, they have the same meaning that they
@@ -205,9 +213,8 @@ thermodynamic output or new dump file output.
 Restrictions
 """"""""""""
 
-To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option.  See the :doc:`Build settings <Build_settings>`
-doc page for details.
+The *rerun* command is subject to all restrictions of
+the :doc:`read_dump <read_dump>` command.
 
 Related commands
 """"""""""""""""

doc/src/set.rst

@@ -13,7 +13,16 @@ Syntax
 * style = *atom* or *type* or *mol* or *group* or *region*
 * ID = atom ID range or type range or mol ID range or group ID or region ID
 * one or more keyword/value pairs may be appended
-* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or           *charge* or *dipole* or *dipole/random* or *quat* or           *spin* or *spin/random* or *quat* or           *quat/random* or *diameter* or *shape* or           *length* or *tri* or *theta* or *theta/random* or           *angmom* or *omega* or           *mass* or *density* or *density/disc* or *volume* or *image* or           *bond* or *angle* or *dihedral* or *improper* or           *sph/e* or *sph/cv* or *sph/rho* or           *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or           *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name*
+* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol*
+  or *x* or *y* or *z* or *vx* or *vy* or *vz*
+  or *charge* or *dipole* or *dipole/random* or *spin* or *spin/random*
+  or *quat* *quat/random* or *diameter* or *shape* or *length* or *tri*
+  or *theta* or *theta/random* or *angmom* or *omega* or *mass*
+  or *density* or *density/disc* or *volume* or *image*
+  or *bond* or *angle* or *dihedral* or *improper*
+  or *sph/e* or *sph/cv* or *sph/rho* or *smd/contact/radius* or *smd/mass/density*
+  or *dpd/theta* or *edpd/temp* or *edpd/cv* or *cc*
+  or *i_name* or *d_name*
 
   .. parsed-literal::
 

doc/src/units.rst

@@ -66,11 +66,15 @@ generality, LAMMPS sets the fundamental quantities mass, :math:`\sigma`,
 masses, distances, energies you specify are multiples of these
 fundamental values.  The formulas relating the reduced or unitless
 quantity (with an asterisk) to the same quantity with units is also
-given.  Thus you can use the mass & :math:`\sigma` & :math:`\epsilon`
+given.  Thus you can use the mass, :math:`\sigma`, and :math:`\epsilon`
 values for a specific material and convert the results from a unitless
-LJ simulation into physical quantities.
+LJ simulation into physical quantities.  Please note that using
+these three properties as base, your unit of time has to conform
+to the relation :math:`\epsilon = \frac{m \sigma^2}{\tau^2}` since
+energy is a derived unit (in SI units you equivalently have the relation
+:math:`1\mathsf{J} = 1\frac{\mathsf{kg}\cdot\mathsf{m}^2}{\mathsf{s}^2}`).
 
-* mass = mass or *m*
+* mass = mass or :math:`m`, where :math:`M^* = \frac{M}{m}`
 * distance = :math:`\sigma`, where :math:`x^* = \frac{x}{\sigma}`
 * time = :math:`\tau`, where :math:`\tau^* = \tau \sqrt{\frac{\epsilon}{m \sigma^2}}`
 * energy = :math:`\epsilon`, where :math:`E^* = \frac{E}{\epsilon}`

doc/utils/sphinx-config/false_positives.txt

@@ -148,6 +148,7 @@ athomps
 atm
 atomeye
 atomfile
+AtomicPairStyle
 atomID
 atomistic
 attogram
@@ -240,6 +241,7 @@ bigint
 Bij
 bilayer
 bilayers
+biquadratic
 binsize
 binstyle
 binutils
@@ -277,7 +279,6 @@ Boltzman
 BondAngle
 BondBond
 bondchk
-BondingIDs
 bondmax
 bondtype
 Bonet
@@ -532,6 +533,7 @@ cuda
 Cuda
 CUDA
 CuH
+Cui
 cuFFT
 Cummins
 Curk
@@ -868,6 +870,7 @@ equilibrating
 equilibration
 Equilibria
 equilization
+equipartitioning
 Ercolessi
 Erdmann
 eradius
@@ -1118,12 +1121,15 @@ gmail
 gmake
 gmask
 Gmask
+GMock
 gneb
 GNEB
 Goldfarb
 Gonzalez-Melchor
 googlemail
+googletest
 Gordan
+Goudeau
 GPa
 gpu
 gpuID
@@ -1324,6 +1330,7 @@ inhomogeneous
 init
 initialdelay
 initializations
+InitiatorIDs
 initio
 InP
 inregion
@@ -1542,6 +1549,7 @@ ksh
 kspace
 Kspace
 KSpace
+KSpaceStyle
 Kspring
 kT
 kTequil
@@ -1882,6 +1890,7 @@ mie
 Mie
 Mij
 Mikami
+Milano
 Militzer
 Minary
 mincap
@@ -1927,6 +1936,7 @@ mol
 Mol
 molfile
 Molfile
+MolPairStyle
 moltemplate
 momb
 Monaghan
@@ -1984,6 +1994,7 @@ multi
 multibody
 Multibody
 multicenter
+multicentered
 multicmd
 multicomponent
 multicore
@@ -2004,6 +2015,7 @@ muVT
 mux
 muy
 muz
+Müller
 mv
 mV
 Mvapich
@@ -2301,7 +2313,6 @@ ortho
 orthonormal
 orthorhombic
 oso
-ot
 Otype
 Ouldridge
 outfile
@@ -2452,6 +2463,7 @@ polydispersity
 polyelectrolyte
 polyhedra
 polymorphism
+Polym
 popen
 Popov
 popstore
@@ -2614,7 +2626,6 @@ Ree
 refactored
 refactoring
 reflectionstyle
-regoin
 Reinders
 reinit
 relaxbox
@@ -2784,6 +2795,7 @@ Schulten
 Schunk
 Schuring
 Schwen
+Sci
 screenshot
 screenshots
 Scripps
@@ -2979,6 +2991,8 @@ Subclassed
 subcutoff
 subcycle
 subcycling
+subhi
+sublo
 Subramaniyan
 subscripted
 subscripting
@@ -2989,6 +3003,7 @@ Sukumaran
 Sulc
 sumsq
 Sunderland
+supercell
 superset
 supersphere
 Supinski
@@ -3058,9 +3073,11 @@ tex
 tfac
 tfmc
 tfMC
-th
+tgnpt
+tgnvt
 Thakkar
 Thaokar
+th
 thb
 thei
 Theodorou
@@ -3287,6 +3304,7 @@ vdfmax
 vdim
 vdisplace
 vdW
+vdwl
 vec
 vectorial
 vectorization
@@ -3454,6 +3472,7 @@ xyz
 xz
 xzhou
 yaff
+yaml
 YAFF
 Yamada
 Yaser
@@ -3464,6 +3483,7 @@ Yc
 ycm
 Yeh
 yellowgreen
+Yethiraj
 yflag
 yhi
 yi

examples/COUPLE/fortran2/Makefile

@@ -14,7 +14,7 @@ CXXLIB = -lstdc++    # replace with your C++ runtime libs
 # Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
 FFLAGS = -O2 -fPIC
 CXXFLAGS = -O2 -fPIC
-CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
+CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX -DLAMMPS_LIB_MPI
 
 all : liblammps_fortran.a liblammps_fortran.so
 

examples/COUPLE/python/example.py

@@ -1,4 +1,4 @@
-# this example requires the LAMMPS Python package (lammps.py) to be installed
+# this example requires the LAMMPS Python package (python/lammps) to be installed
 # and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH
 
 import lammps

examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

@@ -26,7 +26,7 @@ velocity 	all create 100 4928459 rot yes dist gaussian
 #pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
 pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
 pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.064568567
+pair_coeff 	* * spin/exchange exchange 4.0 -0.3593 1.135028015e-05 1.0645 offset yes
 #pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
 
 neighbor 	0.1 bin

examples/SPIN/iron/in.spin.iron

@@ -25,7 +25,7 @@ velocity 	all create 100 4928459 rot yes dist gaussian
 
 pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
 pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841 offset yes
 
 neighbor 	0.1 bin
 neigh_modify 	every 10 check yes delay 20

examples/SPIN/iron/in.spin.iron_cubic

@@ -21,9 +21,9 @@ mass		1 55.845
 set 		group all spin 2.2 -1.0 0.0 0.0
 velocity 	all create 100 4928459 rot yes dist gaussian
 
-pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_style 	hybrid/overlay eam/alloy spin/exchange/biquadratic 3.5
 pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
-pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+pair_coeff 	* * spin/exchange/biquadratic biquadratic 3.4 0.02726 0.2171 1.841 0.0 0.0 2.0 offset yes
 neighbor 	0.1 bin
 neigh_modify 	every 10 check yes delay 20
 

examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py

@@ -6,9 +6,17 @@ import matplotlib.pyplot as plt
 import mpmath as mp
 
 hbar=0.658212           # Planck's constant (eV.fs/rad)
-J0=0.05                 # per-neighbor exchange interaction (eV)
+# J0=0.05                 # per-neighbor exchange interaction (eV)
+
+# exchange interaction parameters
+J1 = 11.254 # in eV 
+J2 = 0.0    # adim
+J3 = 1.0    # in Ang.
+
+# initial spins
 S1 = np.array([1.0, 0.0, 0.0])
 S2 = np.array([0.0, 1.0, 0.0])
+
 alpha=0.01              # damping coefficient
 pi=math.pi
 
@@ -30,6 +38,14 @@ def rotation_matrix(axis, theta):
       [2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
       [2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
 
+#Definition of the Bethe-Slater function
+def func_BS(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
+#Definition of the derivative of the Bethe-Slater function
+def func_dBS(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
 # calculating precession field of spin Sr
 def calc_rot_vector(Sr,Sf):
   rot = (J0/hbar)*(Sf-alpha*np.cross(Sf,Sr))/(1.0+alpha**2)
@@ -65,6 +81,6 @@ for t in range (0,N):
   # calc. average magnetization
   Sm = (S1+S2)*0.5
   # calc. energy
-  en = -2.0*J0*(np.dot(S1,S2))
+  en = -J0*(np.dot(S1,S2))
   # print res. in ps for comparison with LAMMPS
   print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en)

examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh

@@ -13,7 +13,7 @@ en="$(echo "$en-$in" | bc -l)"
 tail -n +$in log.lammps | head -n $en > res_lammps.dat
 
 # compute Langevin
-python3 -m llg_exchange.py > res_llg.dat
+python3 llg_exchange.py > res_llg.dat
 
 # plot results
-python3 -m plot_precession.py res_lammps.dat res_llg.dat
+python3 plot_precession.py res_lammps.dat res_llg.dat

examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in

@@ -5,22 +5,24 @@ atom_style      spin
 atom_modify     map array
 boundary        f f f 
 
-read_data	two_spins.data
+atom_modify 	map array 
+lattice 	sc 3.0
+region 		box block 0 2 0 1 0 1 
+create_box 	1 box
+create_atoms 	1 box
+
+mass		1 55.845
+set 		atom 1 spin 2.0 1.0 0.0 0.0
+set 		atom 2 spin 2.0 0.0 1.0 0.0
 
 pair_style      spin/exchange 3.1
 pair_coeff	* * exchange 3.1 11.254 0.0 1.0
 
-group bead      type 1  
- 
-variable        H equal 0.0
-variable        Kan equal 0.0
 variable        Temperature equal 0.0 
 variable        RUN equal 30000
 
-fix             1 all nve/spin lattice no
-fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
-fix_modify      2 energy yes
-fix             3 all langevin/spin ${Temperature} 0.01 12345
+fix             1 all nve/spin lattice frozen
+fix             2 all langevin/spin ${Temperature} 0.01 12345
 
 compute		out_mag    all spin
 compute		out_pe     all pe
@@ -34,6 +36,9 @@ variable	emag      equal c_out_mag[5]
 thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
 thermo          10
 
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 10 dump.data type x y z c_outsp[1] c_outsp[2] c_outsp[3] fx fy fz
+
 timestep	0.0001
 
 run             ${RUN}

examples/SPIN/test_problems/validation_damped_exchange/two_spins.data

@@ -1,22 +0,0 @@
-LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0
-
-2 atoms
-1 atom types
-
-0.0 6.0 xlo xhi
-0.0 3.0 ylo yhi
-0.0 3.0 zlo zhi
-
-Masses
-
-1 1
-
-Atoms # spin
-
-1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0
-2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0
-
-Velocities
-
-1 0.0 0.0 0.0
-2 0.0 0.0 0.0

examples/SPIN/test_problems/validation_nve/run-test-nve.sh

@@ -13,4 +13,4 @@ en="$(echo "$en-$in" | bc -l)"
 tail -n +$in log.lammps | head -n $en > res_lammps.dat
 
 # plot results
-python3 -m plot_nve.py res_lammps.dat res_llg.dat
+python3 plot_nve.py res_lammps.dat res_llg.dat

examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice

@@ -30,7 +30,7 @@ neighbor 	0.1 bin
 neigh_modify 	every 10 check yes delay 20
 
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix             2 all langevin 200.0 200.0 10.0 48279
+fix             2 all langevin 200.0 200.0 1.0 48279
 fix 		3 all langevin/spin 0.0 0.00001 321
 fix 		4 all nve/spin lattice moving
 timestep	0.001

examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin

@@ -29,7 +29,7 @@ neighbor 	0.1 bin
 neigh_modify 	every 10 check yes delay 20
 
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 200.0 0.1 321
+fix 		2 all langevin/spin 200.0 0.01 321
 fix 		3 all nve/spin lattice moving
 timestep	0.001
 

examples/SPIN/test_problems/validation_nvt/plot_nvt.py

@@ -39,5 +39,5 @@ plt.xlabel('Time (in ps)')
 plt.legend()
 plt.show()
 
-fig.savefig(os.path.join(os.getcwd(), "nve_spin_lattice.pdf"), bbox_inches="tight")
+fig.savefig(os.path.join(os.getcwd(), "nvt_spin_lattice.pdf"), bbox_inches="tight")
 plt.close(fig)

examples/USER/drude/README

@@ -1,8 +1,8 @@
 Example simulations of polarizable systems using Drude oscillators
 ==================================================================
 
-Each example comes in two versions for demonstrating the use of
-Nosé-Hoover or Langevin thermostats.
+Each example comes in several versions for demonstrating the use of
+Langevin, Nosé-Hoover and temperature-grouped Nosé-Hoover thermostats.
 
 * `butane` -- simulation in NVT ensemble with Thole damping
 

examples/USER/drude/butane/in.butane.tgnh

@@ -0,0 +1,57 @@
+# 250 butane system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.butane
+
+comm_modify vel yes
+
+group gBUTANE molecule 1:250
+group gCORES type 1 2 3
+group gDRUDES type 4 5
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    * thole 1.368000
+pair_coeff    2    * thole 1.368000
+pair_coeff    4    * thole 1.368000
+pair_coeff    5    * thole 1.368000
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+
+fix fDRUDE all drude C C N D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
+
+fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
+thermo 50
+
+timestep 0.5
+run 2000

examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.1

@@ -0,0 +1,203 @@
+LAMMPS (29 Oct 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# 250 butane system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.butane
+Reading data file ...
+  orthogonal box = (-19.099988 -19.099913 -19.099998) to (19.099998 19.099999 19.099987)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  5 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  9 = max dihedrals/atom
+  reading bonds ...
+  4250 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6750 dihedrals
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.0      0.0      0.5     
+  special bond factors coul:  0.0      0.0      0.5     
+     5 = max # of 1-2 neighbors
+     8 = max # of 1-3 neighbors
+    12 = max # of 1-4 neighbors
+    17 = max # of special neighbors
+  special bonds CPU = 0.005 seconds
+  read_data CPU = 0.107 seconds
+
+comm_modify vel yes
+
+group gBUTANE molecule 1:250
+4500 atoms in group gBUTANE
+group gCORES type 1 2 3
+3500 atoms in group gCORES
+group gDRUDES type 4 5
+1000 atoms in group gDRUDES
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    * thole 1.368000
+pair_coeff    2    * thole 1.368000
+pair_coeff    4    * thole 1.368000
+pair_coeff    5    * thole 1.368000
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C N D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
+       0 = # of size 2 clusters
+     500 = # of size 3 clusters
+     500 = # of size 4 clusters
+       0 = # of frozen angles
+  find clusters CPU = 0.002 seconds
+
+fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 ${vTEMP} 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 260 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 260 100.0 1 20.0
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
+  G vector (1/distance) = 0.36786669
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.031353958
+  estimated relative force accuracy = 9.4421513e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 79507 46656
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 17
+New max number of 1-2 to 1-4 neighbors: 17 (+0)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair thole, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+TGNHC thermostat for Drude model
+  DOFs of molecules, atoms and dipoles: 747.0 7250.0 3000.0
+Per MPI rank memory allocation (min/avg/max) = 26.74 | 26.74 | 26.74 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3] 
+       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    4439.7916    55742.797    334.61375    18.435655    235.53872    344.96036    18.435655 
+      50    3.1687763    2088.2827    1463.7181    133.95847    624.56452    190.24602    660.52157    113.41252            0   -767.94561    595300.94   -594872.61    2824.2625    55742.797    183.94884    0.5168738    309.18564    171.12124    0.5168738 
+     100     6.392197     2119.741     1619.097    148.17863    500.64399    180.00042    696.41212    164.28885            0   -972.75524    595305.17   -594872.47    1212.6136    55742.797    203.63725   0.14080733    399.49069    183.54186   0.14080733 
+     150    9.5800587    2141.3837    1671.6283    152.98627    469.75531     135.1638     703.8743     168.6738            0   -966.11416    595300.45   -594872.29    4391.1694    55742.797    210.25781   0.10918071    418.15558    188.92417   0.10918071 
+     200    12.853705    2171.9506    1663.8326    152.27281    508.11794    189.68939    718.42616     166.2915            0   -990.53041    595295.36   -594871.12    2071.4055    55742.797    209.24314   0.19965091    435.49843    186.01763   0.19965091 
+     250    16.067977    2208.7064    1678.7069     153.6341    529.99951    152.56393    831.36872    167.05009            0   -1047.6813    595297.24   -594870.54    1092.2375    55742.797    210.84693   0.91289443    438.53468    187.47449   0.91289443 
+     300    19.290601    2251.9246    1764.9742    161.52921    486.95043    145.17235    805.81497    155.39025            0   -1045.9572    595297.21   -594870.68    2438.7801    55742.797    220.85043     3.177778    427.70756     199.6284     3.177778 
+     350    22.523101    2270.9632    1684.9306    154.20368    586.03264    186.29543    828.98436    164.45539            0   -1016.9035    595293.56   -594870.36    2804.0926    55742.797    211.53678    1.1611927    408.91355     191.2877    1.1611927 
+     400    25.747934     2299.236    1742.1505    159.44041     557.0855    171.75438    844.97783    181.89643            0   -1068.3059    595296.85   -594870.09    346.86959    55742.797    219.02792   0.38093991    392.66374    201.22808   0.38093991 
+     450    28.921993    2335.9622    1666.2461    152.49369    669.71602     137.8956    986.46039    179.59582            0    -1060.189    595295.82   -594869.86   -125.83593    55742.797    209.50259   0.31748182    376.15783    192.41804   0.31748182 
+     500    32.312988     2377.923    1744.8977    159.69183    633.02533    192.86619    865.11335    173.23166            0   -1020.1061    595291.45   -594869.53    3306.7537    55742.797    219.29509   0.59010722    361.05703    204.77946   0.59010722 
+     550    36.691992    2428.1816     1631.766    149.33809    796.41562    183.75276    1043.9175    175.64604            0   -1030.3844    595293.08    -594869.6    1566.0362    55742.797    204.67411    1.6260367    344.40559    190.36165    1.6260367 
+     600    41.042781    2475.0304     1615.769    147.87406    859.26146    195.35951    1102.8743    185.82441            0   -1049.7179    595293.93      -594869    751.07631    55742.797     202.5711    1.8674049     324.5681    190.08503    1.8674049 
+     650    45.328915    2516.5445    1706.6033    156.18716    809.94113    177.34479    1029.3219    186.91492            0   -1005.4619     595290.9   -594869.08    2456.1336    55742.797    214.42466   0.73094758    306.66872    205.00907   0.73094758 
+     700    49.764606    2566.0671    1658.8261    151.81461    907.24102    186.97528    1088.6916    184.51371            0   -976.01174    595292.41   -594869.33    403.91053    55742.797    208.52534   0.43420426    292.04619     200.0061   0.43420426 
+     750    54.232008    2621.7889    1798.1047     164.5613    823.68424    181.39689    1029.9425    187.40871            0   -1005.4402    595300.06   -594869.68    93.345406    55742.797    226.01979   0.50741755    278.62961    220.69269   0.50741755 
+     800    58.691111    2682.2116    1697.0698    155.31465    985.14182    215.09199    1113.1134      201.785            0   -975.13212    595300.04   -594869.76   -978.97822    55742.797    213.08116     1.115316    269.45572    207.36081     1.115316 
+     850    63.191067    2745.8302    1887.0667    172.70304    858.76349    213.25376    980.55106    184.54859            0   -948.21117    595298.22    -594869.6   -1842.9661    55742.797    236.69142    1.8946563    265.28903    233.84282    1.8946563 
+     900    68.297608    2799.3194    1855.1338    169.78056     944.1856    201.04167    1103.4608     183.6645            0   -978.27382    595303.89   -594869.59   -1771.6573    55742.797    232.95614    1.1425454    262.10904    230.04879    1.1425454 
+     950    72.791466    2852.8885    1809.5899    165.61241    1043.2986     249.1926    1129.6516     191.5705            0   -961.04118     595303.8   -594869.88   -2342.8998    55742.797    227.44427   0.56184866    253.71617    224.83147   0.56184866 
+    1000    77.035667    2910.6565    1900.2429    173.90892    1010.4136    196.79043     1117.444    178.94619            0   -911.75161    595298.72   -594869.74   -30.451099    55742.797    238.87602   0.48940683    245.53211    238.28906   0.48940683 
+    1050    81.411119     2970.473    1950.8452       178.54    1019.6278    226.17987    1113.3407    186.50456            0   -935.79287    595298.24   -594868.85   -835.03656    55742.797    245.11923   0.81684119    243.27893    245.41028   0.81684119 
+    1100    85.352255    3032.1777    1913.2921    175.10317    1118.8856    252.39337    1183.7624    209.49478            0   -958.58165    595300.89   -594869.07   -2339.7573    55742.797    240.10633    1.5863163    244.29251    239.77436    1.5863163 
+    1150    88.542324    3088.7233    2015.1572     184.4258    1073.5661    215.84757    1132.2268    209.14846            0   -912.58909    595297.76   -594868.83    53.404069    55742.797    252.92982    1.5639609     247.6541    253.57807    1.5639609 
+    1200    92.122601    3137.9447    1895.1546    173.44324    1242.7901    238.97673     1266.308    207.46165            0   -898.18367    595297.09   -594868.86   -940.55827    55742.797    238.13441   0.75999751    245.44164    237.48006   0.75999751 
+    1250    95.311451    3187.5696    2117.7204    193.81231    1069.8492    181.35781    1173.5116    216.10446            0   -933.15422    595300.81   -594868.78     -1638.23    55742.797    266.21428   0.54658889    243.60628    268.65384   0.54658889 
+    1300    98.511654    3238.1405    2050.9414    187.70074    1187.1991    249.20898    1196.3016    223.50078            0    -909.6591     595296.3   -594868.46   -1547.4617    55742.797    257.76705    0.6695258    252.14097     258.4534    0.6695258 
+    1350    101.52721    3288.0387    2035.6917     186.3051     1252.347    218.31874     1254.421    222.85512            0   -868.43705    595293.49    -594868.3    390.90212    55742.797    255.64252    1.2189872    257.21253    255.58654    1.2189872 
+    1400    104.52829    3334.0324    2200.7086    201.40733    1133.3238      203.591    1213.1272    225.86605            0   -936.79465    595295.53      -594868    1372.2474    55742.797    276.25415    1.6144005    265.70225    277.45567    1.6144005 
+    1450    107.57536    3365.7397     2053.535     187.9381    1312.2047    229.27407    1349.3993    233.25524            0   -924.22271    595292.17   -594867.67   -836.52213    55742.797    257.94919     1.053914     270.4816    256.76466     1.053914 
+    1500    110.67807    3391.6801    2142.1349    196.04671    1249.5452    216.36803     1271.289    236.65847            0     -894.899    595287.51   -594867.38    1789.6923    55742.797    269.25236   0.63559736    274.68538    268.80398   0.63559736 
+    1550    113.65872    3411.9839    2115.0942    193.57196    1296.8897    192.92659    1363.4027    230.98652            0   -914.70137    595291.47   -594867.19    2191.6084    55742.797    265.85125   0.63359087    272.59399    265.26653   0.63359087 
+    1600    116.66477    3424.9783    2002.6546    183.28156    1422.3237    261.62038    1419.7862    242.17905            0   -928.05995    595294.38   -594867.58   -1278.1217    55742.797    251.58666   0.95135757    265.94171     250.2117   0.95135757 
+    1650    119.69122    3429.9661    2102.8573    192.45205    1327.1088    253.88883    1296.8164    239.01537            0   -888.25345    595293.11   -594867.47    948.16575    55742.797    263.99864    1.4686915    261.93718    264.32028    1.4686915 
+    1700    122.69838     3421.465    2141.4791    195.98669    1279.9859    181.31236     1326.081    226.54243            0   -878.86521    595292.19   -594867.28    241.93125    55742.797     268.9293    1.2770595    262.79349    269.67278    1.2770595 
+    1750    125.70436    3402.5396    2090.1999    191.29365    1312.3397    263.74025    1296.4274    228.60032            0   -905.54661    595296.37   -594867.25   -1707.3557    55742.797    262.65583   0.80319616    257.84463    263.26023   0.80319616 
+    1800    128.64288    3381.1607    2133.1735    195.22657    1247.9872    234.93738     1242.035    231.34689            0   -887.78079    595295.05    -594867.6   -6.7713651    55742.797    268.11425   0.66416955    258.06107    269.26102   0.66416955 
+    1850    131.64553    3358.3375    2097.2908     191.9426    1261.0467    207.32514    1269.9582    225.83462            0   -867.84477    595293.05   -594867.28    1032.3077    55742.797    263.55741   0.77783532    261.21918    263.90739   0.77783532 
+    1900    134.66459    3335.0634    2130.3209    194.96549    1204.7425    244.28549    1208.9691    209.87044            0   -885.54671     595293.8   -594866.63   -302.54262    55742.797    267.53309    1.2569444    256.95232    268.73397    1.2569444 
+    1950    137.77487    3309.5009     2065.148    189.00092    1244.3529    244.25407    1240.7976    222.92873            0   -891.58467    595294.86    -594866.9   -2000.0789    55742.797    259.29344    1.3652015    254.19331    259.92622    1.3652015 
+    2000    140.88126    3284.0767    2005.7474    183.56462    1278.3292    226.17277    1236.5565    225.16671            0   -837.57878    595295.52   -594867.51    942.09961    55742.797    251.97128   0.96329477     250.4516    252.23212   0.96329477 
+Loop time of 140.882 on 1 procs for 2000 steps with 4500 atoms
+
+Performance: 0.613 ns/day, 39.134 hours/ns, 14.196 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 90.189     | 90.189     | 90.189     |   0.0 | 64.02
+Bond    | 5.0432     | 5.0432     | 5.0432     |   0.0 |  3.58
+Kspace  | 39.478     | 39.478     | 39.478     |   0.0 | 28.02
+Neigh   | 2.4322     | 2.4322     | 2.4322     |   0.0 |  1.73
+Comm    | 0.62876    | 0.62876    | 0.62876    |   0.0 |  0.45
+Output  | 0.021652   | 0.021652   | 0.021652   |   0.0 |  0.02
+Modify  | 2.9918     | 2.9918     | 2.9918     |   0.0 |  2.12
+Other   |            | 0.09631    |            |       |  0.07
+
+Nlocal:        4500.00 ave        4500 max        4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        9440.00 ave        9440 max        9440 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:       811251.0 ave      811251 max      811251 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 811251
+Ave neighs/atom = 180.27800
+Ave special neighs/atom = 13.333333
+Neighbor list builds = 31
+Dangerous builds = 0
+Total wall time: 0:02:21

examples/USER/drude/butane/log.12Nov20.butane.tgnh.g++.4

@@ -0,0 +1,203 @@
+LAMMPS (29 Oct 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# 250 butane system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.butane
+Reading data file ...
+  orthogonal box = (-19.099988 -19.099913 -19.099998) to (19.099998 19.099999 19.099987)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  5 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  9 = max dihedrals/atom
+  reading bonds ...
+  4250 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6750 dihedrals
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.0      0.0      0.5     
+  special bond factors coul:  0.0      0.0      0.5     
+     5 = max # of 1-2 neighbors
+     8 = max # of 1-3 neighbors
+    12 = max # of 1-4 neighbors
+    17 = max # of special neighbors
+  special bonds CPU = 0.002 seconds
+  read_data CPU = 0.135 seconds
+
+comm_modify vel yes
+
+group gBUTANE molecule 1:250
+4500 atoms in group gBUTANE
+group gCORES type 1 2 3
+3500 atoms in group gCORES
+group gDRUDES type 4 5
+1000 atoms in group gDRUDES
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    * thole 1.368000
+pair_coeff    2    * thole 1.368000
+pair_coeff    4    * thole 1.368000
+pair_coeff    5    * thole 1.368000
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C N D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
+       0 = # of size 2 clusters
+     500 = # of size 3 clusters
+     500 = # of size 4 clusters
+       0 = # of frozen angles
+  find clusters CPU = 0.003 seconds
+
+fix fNVT all tgnvt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 ${vTEMP} 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 260 100.0 ${vTEMP_D} 20.0
+fix fNVT all tgnvt/drude temp 260 260 100.0 1 20.0
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
+  G vector (1/distance) = 0.36786669
+  grid = 36 36 36
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.031353958
+  estimated relative force accuracy = 9.4421513e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 26875 11664
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 17
+New max number of 1-2 to 1-4 neighbors: 17 (+0)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair thole, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+TGNHC thermostat for Drude model
+  DOFs of molecules, atoms and dipoles: 747.0 7250.0 3000.0
+Per MPI rank memory allocation (min/avg/max) = 17.33 | 17.61 | 17.71 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNVT[1] f_fNVT[2] f_fNVT[3] 
+       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    4439.7916    55742.797    334.61375    18.435655    235.53872    344.96036    18.435655 
+      50    1.2808116    2088.3442    1463.7416    133.96062    624.60259    190.28732    660.54143    113.40785            0   -767.95454    595300.93   -594872.61    2824.0523    55742.797     183.9497   0.52468068    309.23594    171.11764   0.52468068 
+     100    2.5584104    2119.7471    1619.1466    148.18318    500.60051     180.0129    696.37693    164.27736            0   -972.76956    595305.17   -594872.47    1212.1148    55742.797    203.64285   0.14251823    399.52878    183.54411   0.14251823 
+     150    3.8010236    2141.3696    1671.6877    152.99171    469.68182     135.1764    703.84494     168.6598            0   -966.14516    595300.44   -594872.29     4390.752    55742.797    210.26485   0.11034179    418.18146    188.92927   0.11034179 
+     200    5.1283429    2171.9547    1663.9057     152.2795    508.04901    189.69207    718.41361    166.26728            0   -990.56316    595295.36   -594871.12    2071.2788    55742.797    209.25133   0.20233224    435.53114     186.0233   0.20233224 
+     250    6.4042978    2208.7763    1678.8339    153.64571    529.94239    152.60724    831.35366    166.99449            0   -1047.7147    595297.24   -594870.54      1092.02    55742.797    210.85827    0.9252592    438.54342     187.4861    0.9252592 
+     300    7.6759895    2251.8197     1764.844     161.5173    486.97577    145.12518    805.82891    155.36767            0   -1045.8941    595297.22   -594870.68    2440.3181    55742.797    220.83898    3.1684561    427.70245    199.61611    3.1684561 
+     350    8.9352416    2270.8953    1684.8322    154.19468    586.06305    186.26267     828.9806    164.47014            0   -1016.8664    595293.58   -594870.36    2805.0915    55742.797    211.52748     1.151954    408.90784    191.27829     1.151954 
+     400    10.226474    2299.1993    1742.2608     159.4505    556.93851    171.73982    844.94626    181.87018            0   -1068.3641    595296.84   -594870.09    346.42411    55742.797    219.04152   0.38166821    392.61871    201.24772   0.38166821 
+     450    11.460384     2335.947    1666.1971     152.4892    669.74994    137.90858    986.43107    179.60302            0   -1060.1348    595295.81   -594869.87   -124.88535    55742.797    209.49545   0.32005879    376.11474    192.41461   0.32005879 
+     500    12.727526    2377.9345    1744.9374    159.69546    632.99715     192.8966    865.02273    173.24203            0   -1020.0569    595291.42   -594869.52    3307.6909    55742.797    219.29743   0.59718599    361.06132    204.78161   0.59718599 
+     550    14.002285    2428.2193    1631.8271    149.34369     796.3922    183.78402    1043.8511    175.66575            0   -1030.3885    595293.08    -594869.6    1565.6449    55742.797     204.6776    1.6372397    344.46071    190.35982    1.6372397 
+     600    15.309195    2474.8599    1615.6237    147.86076    859.23616    195.26628    1102.8384    185.89393            0   -1049.6659    595293.91   -594869.01    751.15809    55742.797    202.55856    1.8521167    324.58977    190.06895    1.8521167 
+     650    16.528946    2516.5107    1706.7483    156.20043    809.76241    177.33665    1029.1545     186.8922            0   -1005.4741    595290.93   -594869.08    2457.4736    55742.797    214.44458   0.72647262    306.69821    205.02801   0.72647262 
+     700    17.788857    2566.0306    1658.7538      151.808    907.27687     187.0133    1088.6084    184.61388            0   -976.00491    595292.38   -594869.33    403.14977    55742.797    208.51586   0.43547213    292.00328    200.00013   0.43547213 
+     750    19.056136    2621.8108    1798.0665     164.5578    823.74429    181.38067    1030.1211    187.24746            0   -1005.3911    595300.06   -594869.68    92.552993    55742.797    226.01327   0.51200863    278.52415    220.69636   0.51200863 
+     800    20.328816    2682.2638    1697.1503    155.32202    985.11349    215.11037    1113.1057    201.61206            0   -974.97574    595300.02   -594869.76   -976.02218    55742.797    213.08709    1.1265124    269.37146    207.37604    1.1265124 
+     850    21.675028    2745.7956    1887.1133    172.70731    858.68222    213.20281    980.38605    184.58101            0   -948.10772    595298.22    -594869.6    -1838.829    55742.797    236.69968    1.8882632    265.22854    233.85817    1.8882632 
+     900    22.973234    2799.2121    1855.3963    169.80459    943.81573    200.99559    1103.2167    183.64073            0   -978.26954    595303.83   -594869.59   -1773.6417    55742.797    232.99302    1.1323134    262.06588    230.09392    1.1323134 
+     950    24.248459    2852.9103    1809.6345     165.6165    1043.2758    249.23659    1129.5155    191.54177            0   -960.95833    595303.82   -594869.88   -2343.6579    55742.797    227.45041   0.56047502    253.63589    224.84652   0.56047502 
+    1000    25.536354    2910.7011    1900.5669    173.93856    1010.1343    196.76213    1117.2835    179.06956            0    -911.9529    595298.71   -594869.74   -33.375682    55742.797    238.91568   0.49230975    245.54917    238.33106   0.49230975 
+    1050    27.032801     2970.593    1950.7545    178.53171    1019.8385    226.09391    1113.2803    186.61907            0   -935.59614    595298.29   -594868.85   -832.86686    55742.797    245.10467   0.82528071    243.25364    245.39681   0.82528071 
+    1100    28.276849     3032.248    1914.0097    175.16884    1118.2383     252.4222    1183.4081    209.13741            0   -958.53105    595300.88   -594869.07   -2341.1239    55742.797    240.19374    1.5939531     244.2841    239.87168    1.5939531 
+    1150    29.492505    3088.6987    2014.6006    184.37485    1074.0982    215.76487    1132.4575    209.01044            0   -912.08646    595297.78   -594868.83    59.335425    55742.797    252.86479    1.5506297    247.67435    253.50422    1.5506297 
+    1200    30.792128     3137.976    1895.5574     173.4801    1242.4187    239.01663    1266.2435    206.94828            0   -898.01399    595297.09   -594868.87   -935.85119    55742.797    238.18675   0.75585601    245.80184    237.50082   0.75585601 
+    1250    32.351654    3187.6007    2118.7576    193.90723    1068.8431    181.27841    1173.4284    215.72666            0   -933.61935    595300.82   -594868.79   -1641.4966    55742.797    266.34429   0.54783845    244.09536    268.74691   0.54783845 
+    1300    34.279555    3238.1339    2050.9128    187.69812    1187.2212    249.09831    1195.8579    223.95802            0   -909.52255    595296.29   -594868.46   -1548.7665    55742.797    257.76137   0.67507496    252.48992    258.41118   0.67507496 
+    1350    36.142639    3287.8996    2035.6486    186.30115     1252.251    218.35091    1254.3488    223.36318            0   -868.93347    595293.43   -594868.31    385.64561    55742.797    255.63367    1.2281317    257.51447    255.54567    1.2281317 
+    1400    37.680265    3333.7702    2200.7264    201.40895    1133.0439    203.40304     1213.391    225.99045            0   -937.20521    595295.47   -594868.01    1368.2351    55742.797    276.25818    1.6096154    265.82263    277.44771    1.6096154 
+    1450    38.930719    3365.4323     2053.468    187.93197    1311.9643    229.10608    1350.1009    232.99574            0   -924.67313    595292.11   -594867.67   -844.05749    55742.797    257.94445    1.0440927    270.14303    256.79431    1.0440927 
+    1500    40.161434    3391.3707    2141.7727    196.01356     1249.598     216.2106    1271.1542    236.52415            0   -894.39832    595287.52   -594867.41    1800.4964    55742.797    269.20769   0.63415006    273.93125    268.83182   0.63415006 
+    1550    41.331434    3411.6894    2114.0335    193.47488    1297.6559     192.9656     1363.167    231.27359            0   -913.98645    595291.45   -594867.21    2209.1641    55742.797    265.71649   0.63741948    271.92193    265.18682   0.63741948 
+    1600    42.514856    3424.7938    2003.2634    183.33728    1421.5305    261.67378     1419.189    241.66354            0   -927.77417    595294.37    -594867.6   -1282.8296    55742.797     251.6594   0.96160577    265.79668    250.30691   0.96160577 
+    1650    43.712954    3429.9764    2104.4785    192.60041    1325.4979    253.75783    1296.7732    237.25083            0   -887.95744    595293.15   -594867.48    966.66903    55742.797    264.20211    1.4699573    262.83185    264.45262    1.4699573 
+    1700    44.988869    3421.4427    2141.3199    195.97211    1280.1228    180.56711    1326.1422    227.27194            0   -878.75929     595292.2    -594867.3    269.33339    55742.797    268.91342    1.2659937    264.28353    269.50173    1.2659937 
+    1750     46.32512    3402.6047    2089.4689    191.22675    1313.1357    263.71155    1295.9383    229.85515            0   -905.40883     595296.3   -594867.26   -1711.6299    55742.797    262.56648   0.79625261    258.49733    263.09439   0.79625261 
+    1800    47.626741    3381.3633    2132.4465    195.16003    1248.9167    234.45582    1241.8128    232.64927            0   -887.43322    595295.06   -594867.63    6.1750563    55742.797    268.02308   0.66339407    257.61935    269.20593   0.66339407 
+    1850    48.859097    3358.9769    2090.1997    191.29363    1268.7772    207.84877    1271.8504    229.08032            0   -865.66614    595292.95   -594867.29    1046.4693    55742.797    262.66189   0.78698303    260.47063    262.99635   0.78698303 
+    1900    50.086851     3336.417    2129.6659    194.90555    1206.7511    244.28118    1211.1819    208.93923            0   -884.87319    595293.88   -594866.65   -289.20276    55742.797    267.44697    1.2668343      256.868    268.64764    1.2668343 
+    1950    51.245913    3311.0369    2068.2384    189.28375    1242.7985    243.85893    1242.1317    220.07989            0   -891.04779    595294.68   -594866.91   -1991.6618    55742.797     259.6859    1.3553911    254.54251     260.3233    1.3553911 
+    2000    52.444694    3285.8337    2003.2382    183.33497    1282.5955    227.01654    1237.0479    227.77755            0   -837.34967     595295.6   -594867.49    937.91227    55742.797    251.65869   0.95505158    250.48617    251.88363   0.95505158 
+Loop time of 52.4449 on 4 procs for 2000 steps with 4500 atoms
+
+Performance: 1.647 ns/day, 14.568 hours/ns, 38.135 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 26.398     | 27.961     | 29.034     |  18.3 | 53.31
+Bond    | 1.3959     | 1.5762     | 1.7169     |   9.5 |  3.01
+Kspace  | 17.592     | 18.436     | 19.757     |  18.9 | 35.15
+Neigh   | 0.8492     | 0.85015    | 0.85101    |   0.1 |  1.62
+Comm    | 1.311      | 1.6626     | 2.0789     |  22.0 |  3.17
+Output  | 0.010571   | 0.011494   | 0.013821   |   1.3 |  0.02
+Modify  | 1.8078     | 1.8237     | 1.8372     |   0.8 |  3.48
+Other   |            | 0.1236     |            |       |  0.24
+
+Nlocal:        1125.00 ave        1220 max        1043 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:        5813.50 ave        5907 max        5699 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:       202807.0 ave      217353 max      190808 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 811227
+Ave neighs/atom = 180.27267
+Ave special neighs/atom = 13.333333
+Neighbor list builds = 31
+Dangerous builds = 0
+Total wall time: 0:00:52

examples/USER/drude/ethanol/in.ethanol.tgnh

@@ -0,0 +1,79 @@
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
+kspace_style pppm 1.0e-4
+
+comm_modify vel yes
+read_data data.ethanol
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    1    4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
+pair_coeff    1    5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # CTO H
+pair_coeff    2    4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
+pair_coeff    2    5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    3    4 lj/cut/coul/long 0.071413 2.792848 # H OH
+pair_coeff    3    5 lj/cut/coul/long 0.000000 0.000000 # H HO
+pair_coeff    4    4 lj/cut/coul/long 0.169996 3.120000 # OH OH
+pair_coeff    4    5 lj/cut/coul/long 0.000000 0.000000 # OH HO
+pair_coeff    5    5 lj/cut/coul/long 0.000000 0.000000 # HO HO
+pair_coeff    *  6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    1 thole 2.051000
+pair_coeff    1    2 thole 1.580265
+pair_coeff    1    4 thole 1.416087
+pair_coeff    1    6 thole 2.051000
+pair_coeff    1    7 thole 1.580265
+pair_coeff    1    8 thole 1.416087
+pair_coeff    2    2 thole 1.217570
+pair_coeff    2    4 thole 1.091074
+pair_coeff    2    6 thole 1.580265
+pair_coeff    2    7 thole 1.217570
+pair_coeff    2    8 thole 1.091074
+pair_coeff    4    4 thole 0.977720
+pair_coeff    4    6 thole 1.416087
+pair_coeff    4    7 thole 1.091074
+pair_coeff    4    8 thole 0.977720
+pair_coeff    6    6 thole 2.051000
+pair_coeff    6    7 thole 1.580265
+pair_coeff    6    8 thole 1.416087
+pair_coeff    7    7 thole 1.217570
+pair_coeff    7    8 thole 1.091074
+pair_coeff    8    8 thole 0.977720
+
+group gETHANOL molecule 1:250
+group gATOMS type 1 2 3 4 5
+group gDRUDES type 6 7 8
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 300.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gATOMS  create ${vTEMP} 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+
+fix fDRUDE all drude C C N C N D D D
+
+fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
+
+fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
+thermo 20
+
+timestep 0.5
+run 2000

examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.1

@@ -0,0 +1,287 @@
+LAMMPS (29 Oct 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
+kspace_style pppm 1.0e-4
+
+comm_modify vel yes
+read_data data.ethanol
+Reading data file ...
+  orthogonal box = (-14.013845 -14.027809 -14.018882) to (14.016930 14.017730 14.085730)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  3000 atoms
+  scanning bonds ...
+  5 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  9 = max dihedrals/atom
+  reading bonds ...
+  2750 bonds
+  reading angles ...
+  3250 angles
+  reading dihedrals ...
+  3000 dihedrals
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.0      0.0      0.5     
+  special bond factors coul:  0.0      0.0      0.5     
+     5 = max # of 1-2 neighbors
+     6 = max # of 1-3 neighbors
+    10 = max # of 1-4 neighbors
+    11 = max # of special neighbors
+  special bonds CPU = 0.003 seconds
+  read_data CPU = 0.062 seconds
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    1    4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
+pair_coeff    1    5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # CTO H
+pair_coeff    2    4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
+pair_coeff    2    5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    3    4 lj/cut/coul/long 0.071413 2.792848 # H OH
+pair_coeff    3    5 lj/cut/coul/long 0.000000 0.000000 # H HO
+pair_coeff    4    4 lj/cut/coul/long 0.169996 3.120000 # OH OH
+pair_coeff    4    5 lj/cut/coul/long 0.000000 0.000000 # OH HO
+pair_coeff    5    5 lj/cut/coul/long 0.000000 0.000000 # HO HO
+pair_coeff    *  6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    1 thole 2.051000
+pair_coeff    1    2 thole 1.580265
+pair_coeff    1    4 thole 1.416087
+pair_coeff    1    6 thole 2.051000
+pair_coeff    1    7 thole 1.580265
+pair_coeff    1    8 thole 1.416087
+pair_coeff    2    2 thole 1.217570
+pair_coeff    2    4 thole 1.091074
+pair_coeff    2    6 thole 1.580265
+pair_coeff    2    7 thole 1.217570
+pair_coeff    2    8 thole 1.091074
+pair_coeff    4    4 thole 0.977720
+pair_coeff    4    6 thole 1.416087
+pair_coeff    4    7 thole 1.091074
+pair_coeff    4    8 thole 0.977720
+pair_coeff    6    6 thole 2.051000
+pair_coeff    6    7 thole 1.580265
+pair_coeff    6    8 thole 1.416087
+pair_coeff    7    7 thole 1.217570
+pair_coeff    7    8 thole 1.091074
+pair_coeff    8    8 thole 0.977720
+
+group gETHANOL molecule 1:250
+3000 atoms in group gETHANOL
+group gATOMS type 1 2 3 4 5
+2250 atoms in group gATOMS
+group gDRUDES type 6 7 8
+750 atoms in group gDRUDES
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 300.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gATOMS  create ${vTEMP} 12345
+velocity gATOMS  create 300 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C N C N D D D
+
+fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
+     250 = # of size 2 clusters
+     250 = # of size 3 clusters
+     250 = # of size 4 clusters
+       0 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 1 1000
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
+thermo 20
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
+  G vector (1/distance) = 0.37973843
+  grid = 30 30 30
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.028997858
+  estimated relative force accuracy = 8.7326188e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 50653 27000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 11
+New max number of 1-2 to 1-4 neighbors: 11 (+0)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair thole, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+TGNHC thermostat for Drude model
+  DOFs of molecules, atoms and dipoles: 747.0 4500.0 2250.0
+Per MPI rank memory allocation (min/avg/max) = 22.99 | 22.99 | 22.99 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3] 
+       0            0    13868.828    2013.3852    270.28772    11855.443     3145.896    51.880809 0.00019113234            0    8481.5109    514734.14   -514557.98    170210.19    22094.109    381.62759    10.134301    291.07893    396.91308    10.134301 
+      20     1.299002    9802.0013    5175.0939     694.7326    4626.9074    1138.6388    2334.7257    132.32135            0    1890.1205    514082.52   -514951.42    83148.665    22175.038    987.97886    9.5650257    2458.1912    744.58226    9.5650257 
+      40    2.6585262    9235.2784    5579.5869    749.03392    3655.6915    905.50827    1897.9797    277.48003            0    1696.6242    513843.84   -514965.74    60300.581    22359.787    1068.9505    1.5632512    2851.9591    773.68368    1.5632512 
+      60    4.0767848    8671.8892    5504.7567    738.98831    3167.1326    829.06537    2052.5827    330.50295            0    997.94126    513948.25    -514991.2    48878.532    22600.438    1054.9063    0.8609188    3046.3154     725.0357    0.8609188 
+      80    5.4198065    8041.4551    5718.4601    767.67701    2322.9951    733.58679    1714.9273    332.16847            0    607.45721    513906.05   -514971.19      46156.9    22855.703    1095.9536   0.67476425    2911.1504    795.36156   0.67476425 
+     100    6.8445274    7424.1846    5485.2445    736.36888    1938.9402    725.61122    1556.2473    334.28427            0    311.33112    513993.29   -514981.82    35649.376    23094.997    1051.3109    0.5222695    2722.3778    774.61471    0.5222695 
+     120    8.1987147    6864.2981    5106.0869    685.46872    1758.2112    639.80517    1608.9702     330.7119            0    225.63755    513930.12   -514977.04    28592.139    23302.575    978.67156   0.41481306    2531.1524    721.61219   0.41481306 
+     140    9.6125531    6355.2419    4782.2344    641.99302    1573.0074     692.8178    1572.2236    329.75157            0    62.526757    513879.29   -514963.61    24166.914    23482.684    916.61358   0.35571984    2382.5955    673.87165   0.35571984 
+     160    10.981043    5871.6552    4610.4861     618.9366     1261.169    680.52384    1414.3474    329.28182            0   -159.78058    513987.52   -514990.72    27542.211    23647.419    883.68752   0.35918951    2123.8994    678.40147   0.35918951 
+     180    12.332621    5435.5691    4279.3184    574.47885    1156.2507    684.91656    1423.9511    309.44801            0   -233.41405    513945.61   -514974.26    18688.318    23808.753    820.22155   0.31322062    1867.6728    646.89147   0.31322062 
+     200    13.684023    5063.6933     3974.692    533.58416    1089.0012    610.82746    1398.9423    299.55778            0   -238.71277    514006.42   -514988.03    14346.596    23962.516    761.81108   0.34323344    1649.6269    614.94153   0.34323344 
+     220    15.025737    4729.6345    3862.1044    518.46979    867.53006    589.15408    1361.5835    291.68077            0   -382.15023    514000.76    -514993.5    14084.228    24106.002    740.21384   0.37572015    1480.8499    617.76172   0.37572015 
+     240    16.361954      4425.17    3701.2817    496.88008    723.88831    584.37459     1295.507    282.13297            0   -468.19466    514014.29   -514984.22    13175.309    24240.893    709.36164   0.42725973    1335.0379    605.97228   0.42725973 
+     260    17.686205    4147.8236    3444.1814    462.36555     703.6422    561.69812    1304.6664    277.46507            0   -505.18688    514062.51   -514997.51    9960.5444    24367.441    660.03654   0.51674844    1202.6787    570.39815   0.51663293 
+     280    19.001433    3906.0499    3263.3789    438.09363    642.67099    612.03629    1258.9736    278.79088            0   -503.36734     513978.2   -514981.97    5911.2321    24482.777    625.29586   0.70431199     1076.194    550.86363   0.70431199 
+     300    20.239475    3688.6521    3138.7761    421.36628    549.87595    589.66541    1229.0183    274.52568            0   -529.41366    513980.02   -514993.93    8818.9035        24585    601.19081    1.2138917    967.42544    540.79666    1.2138917 
+     320     21.55208    3484.9768    3041.6682    408.32999    443.30859    581.36133     1221.761    276.40415            0   -581.91733    513938.29   -514992.59    9181.7725    24679.377    582.27807    1.9067083    865.20562    535.70028    1.9067083 
+     340    22.866527     3301.111    2892.7326    388.33607     408.3784    575.39496    1150.6761    289.75308            0   -522.13929    513897.14   -514982.44    7705.6777    24768.367    553.48144    2.4790842    782.86323    515.77305    2.4790842 
+     360    24.169391     3134.601    2727.1786    366.11121    407.42236    560.04836    1167.7896     290.8151            0   -534.37256    513917.26   -514994.12    5173.1603    24851.201    521.90957    2.0935593     720.9275    489.22054    2.0935593 
+     380    25.499891    2978.9742    2626.4574    352.58985    352.51679    565.92745    1159.8532    276.01665            0   -574.15206    513906.53   -514981.66    5406.7601     24926.52    502.85217    1.5076664    663.92569    476.44959    1.5078823 
+     400    26.749513    2830.4515    2571.0905    345.15709    259.36106    608.49648    1122.7921    254.35509            0   -631.46578    513898.27   -514993.09    6598.5441    24996.189    492.43661    1.0446762    619.49263    471.67242    1.0443567 
+     420    28.295841    2690.9016    2510.0923    336.96837    180.80925    579.44132    1054.4508    246.41333            0   -619.58628    513907.01   -514986.92     3344.148    25062.431    480.89086   0.69994647     565.8201    467.11319   0.69994647 
+     440    29.740652    2568.0899    2415.0979     324.2158    152.99201    549.56174    1062.4133     248.3112            0   -625.52103    513895.56   -514977.34    1508.2507    25122.432    462.77313    0.4830629     522.5615    453.15678    0.4830629 
+     460    31.033999    2452.8301    2374.2562    318.73299    78.573926    560.62424    1025.2699    241.11159            0   -664.87807    513904.81   -514988.36    2645.1623    25175.119    454.98091   0.39620035      489.058    449.62743   0.39620035 
+     480    32.287371    2343.6513    2309.9229    310.09654    33.728418    543.67605     1036.735     236.6691            0   -646.19525    513846.07   -514983.23    4840.3297    25223.454    442.64176   0.41089885    466.91678    438.90721   0.41089885 
+     500    33.575452    2237.0869    2186.7578    293.56219    50.329153    569.29753     1077.789    237.78011            0    -644.2024    513802.59   -514992.93     3147.641    25270.717    419.03821   0.39338041    448.26725    414.46511   0.39352695 
+     520    34.882586    2139.9267    2184.6613    293.28075   -44.734618    598.44589    949.76187    230.75426            0   -639.80829    513811.79   -514995.68    89.417432    25315.104    418.62009   0.43123772    424.93066    417.85161   0.43123772 
+     540    36.099168    2047.6906    2096.7059    281.47314   -49.015331    603.23512    994.03336    236.23878            0   -642.85411    513760.61   -515000.28    2488.0247    25353.845     401.6824    0.6095642    402.80198    401.76434    0.6095642 
+     560    37.392444    1959.8223    2108.0902    283.00143   -148.26783    556.77844    933.83445    228.23222            0   -640.71325    513772.73   -514999.13    3943.0471    25390.643    403.78476   0.79631768    387.29154    406.79182   0.79631768 
+     580    38.599277    1877.9441    2032.3004      272.827   -154.35632    567.35925    915.88654      217.432            0   -638.21268    513777.18      -514994    990.21765    25427.432    389.08915     1.184871    380.81536    390.72199     1.184871 
+     600    39.880662    1802.0089    2025.4302    271.90471   -223.42134    546.62696    900.79592    214.83879            0   -668.01506    513782.41   -515000.08    13.167029    25461.023    387.51997    1.7732181    375.29493    389.80736     1.773544 
+     620    41.151704    1729.2181    1934.4658    259.69315   -205.24769    550.82063    913.19495    217.45935            0   -675.32746    513791.35   -515002.74    241.52954    25490.189    369.99117    1.9848435    365.94576    370.90937    1.9848435 
+     640    42.367107    1658.2621    1869.4172    250.96067   -211.15505    560.62227    911.72129    213.95368            0   -665.21833    513766.85   -514999.08     3632.223    25516.498    357.58414    1.8379694      353.567    358.48938    1.8379694 
+     660    43.641386    1588.4137    1852.2333    248.65382    -263.8196    577.15612    856.06817     203.8208            0   -643.32076    513743.58   -515001.12    1748.9053    25544.141    354.40947    1.5590879    342.18406    356.67449    1.5598187 
+     680    44.916294    1522.8833    1803.3756     242.0949    -280.4923     569.2594    868.20962    207.92742            0   -667.28233    513741.85   -515000.45   -707.71197    25570.844    345.28497   0.99527257    329.41069    348.14899   0.99572941 
+     700    46.126721    1461.9096    1769.8128    237.58924   -307.90315     542.7914    861.81473    203.22264            0   -674.68634    513754.76    -514995.8    1167.0096    25593.851    338.95839   0.74443058    320.56652    342.23742   0.74427874 
+     720    47.342692    1403.7901    1774.9009     238.2723   -371.11079    533.63282     871.2916    186.94204            0   -661.24368    513696.56   -514998.29    1734.2343    25615.595    339.99734   0.59618884    315.31635    344.32074   0.59612251 
+     740    48.606886    1347.7019    1788.1767    240.05451   -440.47482    551.44173    832.07818    173.00046            0   -679.31011    513685.34   -515003.03    1108.3607    25637.321    342.57548   0.51883795    311.99896    347.87957   0.51883795 
+     760    49.886167    1294.2014    1732.3399    232.55868   -438.13849      563.187    825.18662    175.50788            0   -672.34818    513677.51   -515007.18   -2118.7763    25657.738    331.88911   0.47758368    305.31362    336.52173   0.47757969 
+     780    51.181176    1243.7936      1720.77    231.00547    -476.9764    565.28094     800.5385    187.89263            0    -663.7818    513643.08   -515009.99     142.9942    25673.523    329.66915   0.48221433    293.10673    335.95739   0.48257178 
+     800    52.501053    1195.7584    1713.4482    230.02255    -517.6898    575.29743    793.40588    182.96177            0    -652.3437    513594.18   -515011.19    2569.2035    25687.829    328.22734   0.57136512    282.06342    336.10937   0.57136512 
+     820    53.730285    1149.3704    1688.6401    226.69218   -539.26966    566.02535    783.51259    170.42752            0   -645.21365    513596.56   -515010.58    158.43243    25703.753    323.41372   0.70633792    274.90722     331.6814   0.70633792 
+     840    55.059346    1107.3402    1626.7277    218.38072   -519.38749    557.00463    817.13283    161.18356            0    -661.6802    513616.64   -515009.67   -859.99932    25718.477    311.42538   0.98533165    274.36623    317.78482   0.98533165 
+     860     56.26804    1067.0989    1619.5401    217.41582   -552.44114    567.51474    819.44456    157.01002            0   -653.65749    513563.92   -515006.67   -110.22037    25730.521    309.90587    1.3158099    279.28284     315.1959    1.3158099 
+     880    57.552129    1028.7737    1622.6482    217.83307   -593.87455     579.7559    769.38822    163.25737            0   -641.48094    513545.77   -515010.56    2044.3918    25741.489    310.33341    1.7085038    277.85767    315.93127    1.7085038 
+     900    58.752011    990.85148    1635.8709    219.60816   -645.01941    590.07687    741.99946    160.20976            0   -648.65733    513521.95    -515010.6   -616.21441    25753.742    312.82551    1.8081896    279.97773    318.48679    1.8081896 
+     920     60.02342    953.65737     1657.228    222.47525   -703.57061     574.2732    734.42873     151.5283            0   -657.51865    513506.29   -515012.57   -2391.2196    25763.907    316.97803    1.6721323    286.84832     322.1911    1.6717714 
+     940    61.246864     917.3708    1532.2653    205.69958   -614.89448     576.8991     775.3663    162.78532            0   -639.35069    513524.45   -515015.04    564.89367    25770.107    293.21271    1.2280076    293.75433    293.31884    1.2282942 
+     960    62.520232    883.18364    1537.9463    206.46223   -654.76268    563.51425    761.32405    161.47799            0   -631.38061    513503.44   -515013.14    1374.3226    25776.278    294.40866    0.9786147    300.31219    293.62423   0.97818807 
+     980     63.72859    851.43088    1538.0246    206.47273   -686.59368    565.62724    756.61795    152.08723            0   -645.22417    513500.66   -515016.36   -203.76984    25783.711    294.53876   0.71003563    300.78246    293.69924   0.71029723 
+    1000    65.325249    822.29342    1546.1186    207.55932   -723.82514    573.24707    705.27714    145.40402            0    -627.3824    513491.87   -515012.24   -1482.5195    25790.098    296.12917   0.61958842    301.40343    295.45106   0.61958842 
+    1020    67.066265    795.41337    1551.6368    208.30012   -756.22343    597.40466    700.03219    143.14559            0   -631.02663    513445.32    -515011.1    748.62224    25794.159    297.21498    0.5543604    297.93873    297.29299    0.5543604 
+    1040    68.784411    769.92029    1548.9081     207.9338    -778.9878    581.53993    723.87795    137.61133            0   -624.63041    513420.31    -515017.7    1356.2174    25798.811     296.7141   0.50251818    294.64447    297.25547   0.50251818 
+    1060    70.531164    745.98628    1514.0024    203.24787    -768.0161    590.02417    718.13714    148.25485            0   -620.67061    513412.77   -515016.53   -984.90789    25804.672    289.98962   0.57944566    296.06714    289.17408   0.57944566 
+    1080    72.339286    724.41988    1468.7378    197.17131   -744.31795    587.12574    750.82761    166.43289            0   -611.54088    513376.94    -515014.1   -1369.9774    25808.741    281.26901   0.68044534    297.86474    278.70146   0.68043227 
+    1100    74.081078     705.1492    1475.7507    198.11275   -770.60147    596.03939    703.74275    166.87407            0   -604.94878    513382.71   -515015.02    322.11458    25810.632    282.54351   0.84350846     304.3263    279.11613   0.84359917 
+    1120     75.92559    688.04772    1517.3948    203.70329   -829.34708    589.83314    688.24666     158.8665            0   -610.41803    513358.01   -515013.88    1171.4548    25812.799    290.41298    1.1090646    307.74167    287.73002    1.1090646 
+    1140    77.724149    672.36504    1512.4831    203.04391   -840.11804     611.8019    686.11567     154.1589            0    -600.4798    513325.18    -515016.9   -1129.2791    25816.098    289.32063    1.4608372    307.70226    286.46216    1.4608372 
+    1160    79.533442    657.64948    1524.9394    204.71611    -867.2899    614.09367    686.86805    145.77079            0   -587.50349    513287.47   -515013.99   -1405.9783    25817.666    291.61223    1.6855491    302.37391    290.02089    1.6855106 
+    1180    81.243201    643.07936    1483.2148    199.11478   -840.13545    607.70554    729.46823    145.73396            0   -581.12793     513268.2   -515010.11    951.82863    25817.313    283.62844    1.6507547    296.31179     281.7127    1.6507678 
+    1200    83.124235    628.84892     1508.103    202.45591   -879.25413    610.27958    699.47204    146.65751            0   -581.22705    513258.98   -515013.42     845.8635    25818.085    288.47775    1.4683346    288.26595    288.70552    1.4687429 
+    1220    84.861868    615.48595    1506.3938    202.22645   -890.90781    640.61601    705.74981    149.24915            0   -568.44006    513197.45   -515015.53   -989.87699    25819.897     288.2897    1.1425522    284.47457    289.11499    1.1433225 
+    1240    86.657973    603.46611       1521.8    204.29466    -918.3339    627.93094     681.9999    147.50604            0   -563.03024    513206.69   -515019.43   -1294.0886    25820.275    291.33208   0.93495852    284.52005    292.65658   0.93566845 
+    1260    88.527368    592.83025    1550.0222    208.08336   -957.19193    638.74876    684.27892    144.10419            0   -567.28292    513161.98   -515019.02    366.82518     25818.88    296.84123   0.70423253    289.40784    298.27306   0.70423253 
+    1280     90.26083    583.62238    1500.3203    201.41111   -916.69791    658.39007    717.40575    149.49357            0   -560.74831    513138.12   -515019.36    468.99306    25817.909    287.36089   0.59306602    294.54267    286.36029   0.59306602 
+    1300     92.13165    575.42151    1519.3082    203.96014   -943.88664    655.72041    704.25181    141.32573            0   -550.47558     513125.5   -515020.21   -1022.3924    25817.559    291.00356   0.58689962    300.73954    289.58167   0.58691655 
+    1320    93.894194     568.3477    1518.4074    203.83922   -950.05966    670.96379    726.82052    139.93925            0   -527.97883    513058.34   -515018.15   -972.06273    25815.822    290.83615   0.57457637    307.54777      288.256   0.57459152 
+    1340    95.719114    562.07892    1523.1375    204.47422   -961.05857    677.25051    688.02873    138.64793            0   -528.35304     513081.3   -515017.94    1058.9949    25813.039    291.70253   0.66885112    312.02785    288.52311   0.66873042 
+    1360    97.524416    556.93389    1560.3959    209.47598    -1003.462    665.73523    686.80959    139.77318            0   -523.04289    513045.29   -515018.03    937.16072    25811.796     298.7948    0.7861094    312.82634    296.66456   0.78666076 
+    1380    99.357452    553.33396    1516.3062    203.55714   -962.97224    678.04454    713.74957    137.42774            0   -517.91272    513044.03   -515018.31   -292.99291    25811.915    290.25807   0.98357958    308.02329    287.50255   0.98357958 
+    1400    101.09848    550.59887    1532.5676    205.74016    -981.9687    668.87709    700.85053    135.12927            0   -539.20798    513074.89   -515022.51   -1158.8487    25811.561    293.25245    1.2705054     302.5546    291.90379    1.2705054 
+    1420    102.92972    548.73321    1476.7658    198.24903   -928.03261    677.96546    739.35433    145.56163            0   -552.34431    513084.77   -515023.34    9.5625031     25809.75    282.48418     1.436009    300.29464    279.71597     1.436009 
+    1440    104.66752    547.12666    1527.8761    205.11036   -980.74947    650.61377     711.8671    147.59824            0   -556.66671    513090.53   -515024.69    1019.1836    25808.157    292.23402    1.5483375    300.12772    291.11848    1.5483375 
+    1460    106.50314    545.65053    1490.3999    200.07935   -944.74941    670.75445     719.7737    150.18449            0   -549.39105    513087.25   -515023.32   -1319.4425    25807.672    285.07809    1.4821899    301.34029    282.56847    1.4823299 
+    1480    108.28741    544.77516     1526.097    204.87152   -981.32183     652.3433    696.79415    149.20209            0    -556.6563    513098.18   -515021.18   -742.16174    25805.656    292.01497    1.2636175    302.51451     290.4664    1.2639932 
+    1500    110.12511    545.19541     1545.583    207.48742   -1000.3876    645.73389    715.44716     136.9985            0   -567.26011    513090.87   -515022.18   -400.28471    25802.486    295.86865     0.987897    302.34922    294.99013     0.987897 
+    1520    111.89057     546.1418    1523.2045    204.48322   -977.06274    643.78664    737.65713    128.87884            0    -556.6123    513087.83   -515018.61     382.6378    25799.004    291.65193   0.81691637    299.79434    290.49472   0.81691637 
+    1540    113.68915    548.12322    1532.5317    205.73534   -984.40845    662.00085    713.14115    141.83628            0   -546.54637    513065.85   -515020.69   -558.02865    25796.128    293.49257   0.69415483    292.07299    293.92389   0.69415483 
+    1560    115.74426    551.58749    1524.0291    204.59391   -972.44159    662.89347    709.62799    163.91089            0   -538.91833    513050.59   -515020.55   -1648.6737    25792.534     291.9015   0.60340834    283.91962    293.42109   0.60340834 
+    1580    118.02455    556.31359    1557.1932    209.04604   -1000.8797    650.22504    703.18471    164.34921            0   -547.76291    513048.79   -515019.67    218.40066    25787.071    298.26162   0.59762744    279.75915    301.53187   0.59762744 
+    1600    119.98362     561.8489    1536.2864     206.2394    -974.4375     650.4012    725.52549    152.37926            0    -524.6233    513039.24   -515017.36    724.91327    25782.038    294.23674   0.63726972    276.89513    297.31161   0.63726972 
+    1620    121.24569    568.29298    1516.8518     203.6304   -948.55886    669.43634    758.17152    141.59579            0   -508.64869    513005.84   -515014.95    305.45057    25778.393    290.46698   0.74019001    276.01771     293.0592   0.74019001 
+    1640    122.52086    575.42679    1531.3719    205.57965   -955.94515    683.26836    731.47049    143.09022            0   -504.62735    513005.89   -515015.04   -1258.1839    25775.243    293.18351   0.89655264    276.95868    296.07228   0.89655264 
+    1660    123.85319    583.33428     1520.971    204.18338   -937.63676      670.138    752.36615    158.20486            0   -497.10065    512993.63   -515014.87     990.4476    25771.018    291.11283    1.0757415     276.8874    293.66833    1.0757415 
+    1680    125.13263    591.99646    1532.4661    205.72654   -940.46967    689.25478    743.16987    168.03522            0    -502.0189     512975.1   -515014.01    1349.4251    25768.301     293.2049    1.3360644    279.26444    295.71449    1.3360644 
+    1700    126.41729    600.72595     1576.928    211.69534   -976.20204    698.82384    728.20266    164.32429            0   -509.63109    512960.78   -515018.71   -714.74537    25767.499    301.65964    1.4963853    288.03969    304.12166    1.4963853 
+    1720     127.8002    608.72776    1572.2293    211.06457   -963.50155    686.50487     751.5254    162.66596            0   -520.30848     512974.4   -515018.29   -1233.7505    25765.895    300.75432     1.507047    296.46478    301.66689     1.507047 
+    1740    129.05369    615.86972    1571.5987    210.97992   -955.72903    672.03255    760.03518    170.57691            0   -531.78859    512987.74   -515014.32   -5.6954413    25762.646    300.66959     1.422713    303.78613    300.35269     1.422713 
+    1760    130.46587    622.55796    1579.5377    212.04568   -956.97974    706.80226    734.80437    178.63803            0   -529.02192    512966.71   -515014.91    1439.5408    25759.728    302.30266    1.1633531    310.55359    301.13515    1.1641118 
+    1780    131.77476    628.52662    1584.4407    212.70388   -955.91404    676.79766    773.29727    172.22703            0   -534.56221    512976.35   -515020.03   -1144.3707    25758.632    303.36936   0.86750014    314.93649     301.6529   0.86760316 
+    1800    133.12003    634.21603    1614.4896    216.73781   -980.27353    677.17437    758.17735    157.86038            0   -522.96761    512972.14   -515022.66   -952.36111    25756.246    309.15671   0.80472277    318.00054    307.89448   0.80488217 
+    1820    134.41588    639.49479    1633.2745     219.2596   -993.77971    706.25176    736.76382    153.75695            0   -523.32693    512955.21   -515022.44    534.27821    25752.618     312.8094   0.68438418    326.33448    310.77281   0.68437053 
+    1840    135.69809    643.87101    1634.8429    219.47015   -990.97185    701.84421    766.76216    151.35177            0   -502.94871    512911.91   -515019.89    654.67154    25749.912    313.13395   0.62866073    330.35595    310.48258   0.62856511 
+    1860    137.01849     646.9769    1624.5262    218.08519   -977.54933    717.81093    788.02881    151.94179            0   -495.90915    512881.92   -515021.34   -1064.2782    25748.146    311.14125   0.66359764    330.55161    308.12656   0.66359764 
+    1880    138.29577    648.32991    1639.5616    220.10361   -991.23166    726.93665    759.79041    159.81907            0   -493.81895    512873.87   -515017.83   -1411.6366    25744.916    313.99078   0.74007658     329.3198    311.65549   0.74007658 
+    1900    139.67366    648.89417    1644.4291    220.75706   -995.53493    724.72865    762.39029    163.96612            0   -495.61342    512866.53   -515017.54    1351.1833    25740.228    314.85836   0.89300573    324.54001    313.46241   0.89316115 
+    1920    140.93714    648.51479    1660.4204    222.90381   -1011.9056     683.6849    759.17365    164.85228            0   -494.26512    512891.03   -515016.38    401.57284    25737.361    317.86954    1.0199045    319.35529    317.83552    1.0202343 
+    1940    142.29997    646.69169    1612.2108    216.43189   -965.51908    714.97385    778.57354    175.15205            0    -508.7717    512893.53   -515018.97   -1076.6986    25735.181    308.53939    1.2258299    312.47436    308.09188    1.2258299 
+    1960     143.5485    643.66804    1612.4723      216.467   -968.80423    729.94319    778.86473    177.62474            0   -483.88964    512849.44   -515020.79   -696.10678    25731.708    308.50602    1.4206534    300.71602    310.00483    1.4206534 
+    1980    144.89715    639.49991    1600.0251    214.79602   -960.52514    725.68053     773.8468    176.16615            0   -469.86188    512851.09   -515017.45    822.18174    25727.586    306.08335    1.5058554    291.63271    308.68799     1.505066 
+    2000    146.15013    633.86554    1648.9263    221.36078   -1015.0607    703.29388    761.03433    170.08933            0   -468.34451    512835.81   -515016.94    763.74636    25724.778    315.51687    1.3681009    284.57812    320.86295    1.3683497 
+Loop time of 146.15 on 1 procs for 2000 steps with 3000 atoms
+
+Performance: 0.591 ns/day, 40.597 hours/ns, 13.685 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 92.462     | 92.462     | 92.462     |   0.0 | 63.26
+Bond    | 2.9377     | 2.9377     | 2.9377     |   0.0 |  2.01
+Kspace  | 28.493     | 28.493     | 28.493     |   0.0 | 19.50
+Neigh   | 4.3811     | 4.3811     | 4.3811     |   0.0 |  3.00
+Comm    | 0.86167    | 0.86167    | 0.86167    |   0.0 |  0.59
+Output  | 0.040132   | 0.040132   | 0.040132   |   0.0 |  0.03
+Modify  | 16.886     | 16.886     | 16.886     |   0.0 | 11.55
+Other   |            | 0.08886    |            |       |  0.06
+
+Nlocal:        3000.00 ave        3000 max        3000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        10696.0 ave       10696 max       10696 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:       737603.0 ave      737603 max      737603 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 737603
+Ave neighs/atom = 245.86767
+Ave special neighs/atom = 10.500000
+Neighbor list builds = 59
+Dangerous builds = 0
+Total wall time: 0:02:26

examples/USER/drude/ethanol/log.12Nov20.ethanol.tgnh.g++.4

@@ -0,0 +1,287 @@
+LAMMPS (29 Oct 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0
+kspace_style pppm 1.0e-4
+
+comm_modify vel yes
+read_data data.ethanol
+Reading data file ...
+  orthogonal box = (-14.013845 -14.027809 -14.018882) to (14.016930 14.017730 14.085730)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  3000 atoms
+  scanning bonds ...
+  5 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  9 = max dihedrals/atom
+  reading bonds ...
+  2750 bonds
+  reading angles ...
+  3250 angles
+  reading dihedrals ...
+  3000 dihedrals
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.0      0.0      0.5     
+  special bond factors coul:  0.0      0.0      0.5     
+     5 = max # of 1-2 neighbors
+     6 = max # of 1-3 neighbors
+    10 = max # of 1-4 neighbors
+    11 = max # of special neighbors
+  special bonds CPU = 0.003 seconds
+  read_data CPU = 0.115 seconds
+
+pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
+pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO
+pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
+pair_coeff    1    4 lj/cut/coul/long 0.105921 3.304542 # C3H OH
+pair_coeff    1    5 lj/cut/coul/long 0.000000 0.000000 # C3H HO
+pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO
+pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # CTO H
+pair_coeff    2    4 lj/cut/coul/long 0.105921 3.304542 # CTO OH
+pair_coeff    2    5 lj/cut/coul/long 0.000000 0.000000 # CTO HO
+pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
+pair_coeff    3    4 lj/cut/coul/long 0.071413 2.792848 # H OH
+pair_coeff    3    5 lj/cut/coul/long 0.000000 0.000000 # H HO
+pair_coeff    4    4 lj/cut/coul/long 0.169996 3.120000 # OH OH
+pair_coeff    4    5 lj/cut/coul/long 0.000000 0.000000 # OH HO
+pair_coeff    5    5 lj/cut/coul/long 0.000000 0.000000 # HO HO
+pair_coeff    *  6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
+pair_coeff    1    1 thole 2.051000
+pair_coeff    1    2 thole 1.580265
+pair_coeff    1    4 thole 1.416087
+pair_coeff    1    6 thole 2.051000
+pair_coeff    1    7 thole 1.580265
+pair_coeff    1    8 thole 1.416087
+pair_coeff    2    2 thole 1.217570
+pair_coeff    2    4 thole 1.091074
+pair_coeff    2    6 thole 1.580265
+pair_coeff    2    7 thole 1.217570
+pair_coeff    2    8 thole 1.091074
+pair_coeff    4    4 thole 0.977720
+pair_coeff    4    6 thole 1.416087
+pair_coeff    4    7 thole 1.091074
+pair_coeff    4    8 thole 0.977720
+pair_coeff    6    6 thole 2.051000
+pair_coeff    6    7 thole 1.580265
+pair_coeff    6    8 thole 1.416087
+pair_coeff    7    7 thole 1.217570
+pair_coeff    7    8 thole 1.091074
+pair_coeff    8    8 thole 0.977720
+
+group gETHANOL molecule 1:250
+3000 atoms in group gETHANOL
+group gATOMS type 1 2 3 4 5
+2250 atoms in group gATOMS
+group gDRUDES type 6 7 8
+750 atoms in group gDRUDES
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 300.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gATOMS  create ${vTEMP} 12345
+velocity gATOMS  create 300 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C N C N D D D
+
+fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5
+     250 = # of size 2 clusters
+     250 = # of size 3 clusters
+     250 = # of size 4 clusters
+       0 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+
+fix fNPT all tgnpt/drude temp ${vTEMP} ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 ${vTEMP} 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 ${vTEMP_D} 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso ${vPRESS} ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 ${vPRESS} 1000
+fix fNPT all tgnpt/drude temp 300 300 100.0 1 20.0 iso 1 1 1000
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3]
+thermo 20
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
+  G vector (1/distance) = 0.37973843
+  grid = 30 30 30
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.028997858
+  estimated relative force accuracy = 8.7326188e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 17908 7200
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 11
+New max number of 1-2 to 1-4 neighbors: 11 (+0)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair thole, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+TGNHC thermostat for Drude model
+  DOFs of molecules, atoms and dipoles: 747.0 4500.0 2250.0
+Per MPI rank memory allocation (min/avg/max) = 16.30 | 16.32 | 16.34 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] f_fNPT[1] f_fNPT[2] f_fNPT[3] 
+       0            0    13868.828    2013.3852    270.28772    11855.443     3145.896    51.880809 0.00019113234            0    8481.5109    514734.14   -514557.98    170210.19    22094.109    381.62759    10.134301    291.07893    396.91308    10.134301 
+      20    0.5489804    9803.4819    5175.7976    694.82706    4627.6843    1139.1179    2334.7381    132.32214            0    1890.1377    514082.74   -514951.37    83147.098    22175.037    987.97841    9.8830686    2458.1459    744.58371    9.8830686 
+      40    1.1305859    9235.5604     5579.723     749.0522    3655.8374    905.64066    1897.9743    277.47993            0    1696.6152    513843.93    -514965.8    60300.791    22359.784    1068.9531    1.6180875    2851.9045    773.69577    1.6180875 
+      60    1.7763265    8672.0018    5504.7529    738.98781    3167.2488    829.16747    2052.5807    330.50296            0    997.97233    513948.23    -514991.2    48877.822    22600.434    1054.8974    0.8814188    3046.2785     725.0302    0.8814188 
+      80    2.3974232    8041.5241    5718.5668    767.69134    2322.9573    733.63486    1714.8909    332.16188            0    607.44872    513906.01   -514971.19    46157.199    22855.699    1095.9682   0.68487797    2911.1669    795.37545   0.68487797 
+     100    3.0302813    7424.2386    5485.3388    736.38155    1938.8999    725.65842    1556.2309    334.30067            0    311.29882    513993.24   -514981.83    35648.625    23094.994    1051.3251   0.52778467    2722.3899    774.63067   0.52778467 
+     120    3.6273007    6864.3426    5106.0771    685.46741    1758.2655    639.83956    1608.9962    330.73079            0    225.62345    513930.12   -514977.04    28591.458    23302.572    978.66797   0.41866327    2531.1648     721.6052   0.41866327 
+     140     4.196656    6355.3019    4782.0272     641.9652    1573.2747    692.74007     1572.242    329.76251            0    62.485696    513879.64    -514963.6    24167.635     23482.68    916.57384   0.35834425     2382.631    673.81858   0.35834425 
+     160     4.779717    5871.7118    4610.7111     618.9668    1261.0006    680.57069    1414.3177    329.24321            0   -159.81123    513987.38    -514990.7    27541.231    23647.415    883.72945   0.36200572    2123.9268    678.44584   0.36200572 
+     180     5.338641    5435.6217    4279.7314     574.5343    1155.8903    684.86021    1423.9782    309.42239            0   -233.49805    513945.42   -514974.29    18687.102    23808.747    820.29876   0.31648848    1867.6601    646.98347   0.31648848 
+     200    5.9102262    5063.7313    3974.8766    533.60893    1088.8548     610.8373    1399.1355    299.45065            0   -238.66713    514006.14   -514988.04    14346.964    23962.508    761.84531   0.34591369     1649.624    614.98194   0.34591369 
+     220    6.4670983    4729.6679    3862.1203    518.47192    867.54758    589.19356    1361.7383    291.57325            0   -382.16606    514000.72   -514993.51    14083.524    24105.992    740.21525   0.37963928    1480.8429    617.76448   0.37963928 
+     240    7.0337756    4425.2126    3701.4126    496.89765    723.79998     584.3439    1295.3888    282.13205            0   -468.28082    514014.44   -514984.22    13173.086    24240.879    709.38377   0.43418988    1335.0115    606.00249   0.43418988 
+     260    7.6151553    4147.9089    3443.8677    462.32342    704.04123    561.65864    1304.8745    277.43914            0   -505.26328    514062.78   -514997.45    9958.5179    24367.421    659.97189   0.52765671    1202.5793    570.33937   0.52753359 
+     280    8.1803862    3906.1678    3262.9801     438.0401    643.18765    611.98615    1259.2636    278.89902            0   -503.31011     513978.3   -514981.95    5914.4091    24482.749    625.21285    0.7191852    1076.0582    550.78956    0.7191852 
+     300    8.7043311    3688.7789    3139.2097    421.42449    549.56918    589.70836    1228.8579    274.66549            0   -529.44562    513979.71   -514993.93    8820.6294    24584.968     601.2678    1.2327257    967.30569     540.9051    1.2327257 
+     320    9.2828722    3485.0301    3041.6251    408.32421    443.40492      581.268    1221.8962    276.57911            0   -581.90861     513938.2   -514992.63     9180.621    24679.345    582.26671    1.9139563    865.07721    535.70848    1.9139563 
+     340    9.8440863    3301.0782    2892.3054    388.27872    408.77286    575.63973    1150.7154    289.94072            0   -522.07034    513896.97   -514982.42    7703.8271    24768.334    553.40856    2.4558958    782.77492    515.70254    2.4558958 
+     360    10.398275     3134.468     2727.432    366.14522    407.03603    560.03929    1167.6565    290.68699            0   -534.30813    513917.05   -514994.09    5177.6501    24851.165    521.97249    2.0603668     720.8089    489.31359    2.0603668 
+     380    10.971208    2978.8927    2626.9512    352.65614    351.94143    566.26677    1159.7933    275.53948            0   -574.10697    513905.99   -514981.54    5406.9463    24926.487    502.95796    1.4831172    663.80755    476.59194    1.4833313 
+     400    11.487591    2830.3779    2572.5528     345.3534    257.82518    609.13682     1122.447    253.59547            0   -631.51589    513897.17   -514993.01    6594.5632    24996.158    492.72116    1.0347263    619.38728    472.02151    1.0352452 
+     420    12.147771    2690.8114    2511.4485    337.15043    179.36289    580.62912    1054.4972    245.98614            0   -619.15187    513904.39   -514986.98    3340.3887    25062.398    481.15102   0.69884987    565.60536    467.45245   0.69884987 
+     440    12.683915    2567.8386    2417.1223    324.48758    150.71626    550.84021    1061.6154    248.79898            0   -625.11745    513892.15   -514977.57    1516.8529    25122.396    463.15967   0.48668891    522.23117    453.66261   0.48668891 
+     460    13.219765    2452.4983    2377.8819    319.21973    74.616329    562.85065    1024.1437    240.77499            0   -664.71238    513899.97   -514988.41    2625.4899    25175.085     455.6735   0.40127583    488.72927    450.48999   0.40127583 
+     480    13.734817    2343.3317    2306.9816    309.70169     36.35008    544.98865    1036.7003    239.14437            0    -646.5969    513844.75   -514982.63    4826.9949    25223.402    442.07562   0.41558073    466.54905    438.30802   0.41558073 
+     500      14.2704     2236.968    2183.0006     293.0578    53.967445    569.68824    1077.5153    241.06612            0   -644.36418    513802.58   -514992.52    3137.1149    25270.633    418.31485   0.39923526    447.67208    413.72065   0.39935381 
+     520    14.830149    2139.9757    2184.3136    293.23408   -44.337922    598.68848    949.68592    231.65813            0   -640.55841    513811.34   -514995.15    74.532539    25314.977    418.54937   0.44074429    424.27621    417.87775   0.44074429 
+     540    15.342945    2047.7713    2097.3453    281.55898   -49.574068    603.65225    992.19405    234.95516            0   -644.08949     513763.2   -514999.49    2503.1827    25353.667    401.80131   0.61813129    402.19428    402.00395   0.61813129 
+     560    15.876281    1959.9733    2106.7002    282.81483   -146.72689    554.39132    933.09924    226.68229            0   -642.41154    513779.76   -514998.25    3929.9055    25390.434     403.5098   0.81842484    386.57171    406.59055   0.81842484 
+     580     16.38257    1878.3658    2030.0966    272.53115    -151.7308    563.56362    914.74758    216.22925            0   -639.68928    513785.76   -514992.34    1013.3048    25427.188    388.65548    1.2108332    381.10541    390.16777    1.2108332 
+     600    16.920685     1802.551    2017.1476     270.7928   -214.59656    542.55586    900.05624    215.01335            0   -670.18556    513796.03   -514998.07    18.493782    25460.775    385.93337    1.7700661    377.13463    387.65116    1.7700661 
+     620    17.474131    1730.0309    1927.5545    258.76534   -197.52353    548.09305    912.68313    219.66229            0   -677.86412    513801.32   -515001.42    211.58879    25489.947     368.6727    1.9725715    368.40356    368.96285    1.9725715 
+     640    17.983631    1659.1463    1874.5489    251.64958   -215.40256    560.91381    910.47755    215.67628            0   -668.88025    513765.74   -514999.33    3576.6139    25516.217    358.58525    1.8035012    356.22593    359.21531    1.8035012 
+     660    18.557287    1589.2837    1850.4075    248.40872   -261.12386     578.2925    854.48492    205.27001            0   -645.94735    513747.59   -515000.82    1704.7835    25543.749     354.0776    1.5147284    344.22319    355.94967    1.5157289 
+     680    19.099188    1523.7572    1809.2809    242.88766   -285.52371    571.10597    870.42753    209.32749            0   -670.04285    513734.83   -515001.17   -730.02178    25570.285    346.40935     1.010892    331.62309    349.09523     1.010892 
+     700    19.606934     1462.426    1781.0971    239.10411   -318.67111     547.9598    858.22372     204.5839            0   -674.26004    513742.06   -514997.24    1193.1019    25593.123    341.12225   0.74301975    322.22823    344.48583   0.74301975 
+     720    20.138988     1403.965    1772.7176     237.9792   -368.75257    537.38813    872.15383    187.31368            0   -658.83726    513691.57   -514998.34    1717.9835    25614.736    339.57934   0.59520661    315.58412    343.78893   0.59520661 
+     740    20.654731    1347.9142    1778.2063    238.71603   -430.29207    554.12065    833.24568    175.13397            0   -676.57227    513685.79   -515002.01    1164.2855     25636.35    340.66194   0.52336173    311.70411    345.69611   0.52336173 
+     760     21.20085    1294.8201    1727.5363    231.91382   -432.71627    562.83637    826.41881    177.39944            0   -670.89859    513677.68   -515006.15   -2179.3296    25656.719    330.96325   0.48927201    305.61756    335.39128   0.48927201 
+     780    21.736798    1244.1479     1729.459    232.17193   -485.31103    563.29093    800.45744    179.65918            0   -660.60078     513641.9   -515010.01    140.35372    25672.399    331.32725   0.49993893    293.14787    337.88591   0.49993893 
+     800    22.313875    1195.9276    1716.8118    230.47411    -520.8842    572.20526    790.59915    174.22123            0   -646.04585    513597.21   -515009.08    2706.2932     25686.61     328.8596   0.60065349    282.54175     336.7676   0.60065349 
+     820    22.880819    1149.3267     1681.646    225.75325   -532.31925    564.24784    783.06404    168.40012            0   -638.53799     513598.2   -515007.69     291.5994    25702.646    322.07401   0.70343079    279.53588    329.34955   0.70332477 
+     840    23.400356    1107.2877    1640.6002    220.24304   -533.31252    558.56409    815.12167    157.71519            0   -653.87313    513597.92   -515008.76   -762.24777    25717.669    314.07832    1.0007715    278.89623    320.12842    1.0010942 
+     860    23.930137    1066.5896    1621.3757    217.66224   -554.78609    569.30332    821.05893    152.83409            0   -645.45431    513552.23   -515004.75    100.50325    25730.157    310.25167    1.3271389    283.08497    314.96823    1.3271389 
+     880    24.425549    1027.6567    1624.8454    218.12803   -597.18868    587.96681    765.45362    159.91238            0   -628.42404    513525.88   -515007.98    2270.6911    25741.827    310.74777    1.7225758    280.31191    316.00736    1.7225758 
+     900    24.945527    989.67183    1619.7368    217.44223   -630.06494    605.34666    753.15286    166.12808            0   -637.67643    513491.85   -515008.87   -504.34781     25755.03    309.75098    1.7673447    280.95321    314.73839    1.7673447 
+     920    25.481976    952.75609    1646.0573    220.97563   -693.30118    586.10824    737.80362    161.44982            0   -645.91448    513480.65    -515013.4   -2245.0436     25766.26    314.83888    1.6620102    286.24272    319.79545    1.6618169 
+     940    26.009417    916.27341    1558.2262    209.18472   -641.95282    584.88671    784.61327    161.29551            0   -636.55462    513482.98   -515019.17    351.20595     25773.56    298.17626    1.2572795    293.25423    299.19214    1.2573671 
+     960     26.54868    881.26579    1570.5631    210.84088   -689.29727    567.48803    757.85558    154.89763            0   -628.37927    513476.62   -515017.78    1224.7198    25780.472    300.67272   0.95167357    297.40913    301.41483   0.95167357 
+     980    27.082306    848.00567    1563.3504    209.87262   -715.34478    576.51161    766.15302     148.2325            0   -637.27495    513450.83   -515019.79   -304.57224    25788.336    299.38564   0.72910884    295.89994    300.16415   0.72910884 
+    1000    27.619404    817.47747    1553.8221    208.59349   -736.34466    586.86696    709.60783    150.55877            0   -608.57994     513440.8    -515015.6   -1422.5332    25794.968    297.60262   0.62762006    294.24682    298.35812   0.62773318 
+    1020     28.12313     789.1786    1563.9655    209.95519   -774.78691    608.04057    694.03517    152.80101            0   -605.61567    513386.72   -515010.76    1005.4938    25799.349    299.58342   0.54306229    290.32557    301.31971   0.54293571 
+    1040    28.647646    762.65087    1534.0005    205.93252    -771.3496    587.61838    735.74998    150.09823            0   -603.04152    513371.63    -515013.4    1470.8094    25804.634    293.84005   0.54036941    291.28531    294.46003   0.54036941 
+    1060    29.166844    737.77923    1518.4576    203.84597   -780.67842    594.18573    720.72071    149.63679            0   -601.17736    513365.82   -515009.86   -729.10372    25811.329    290.84548   0.57532052    295.86391    290.20631   0.57532052 
+    1080    29.694185    715.33941    1497.4861    201.03063   -782.14665    601.83156    732.61956    157.72044            0   -593.12281    513331.09   -515012.29    -1329.475    25816.507    286.76945   0.70534246    298.86373    284.95298   0.70534246 
+    1100    30.187888    694.69953    1511.5454    202.91803   -816.84589    616.66719    703.13897    158.99611            0   -577.76244    513295.95   -515013.83    324.57282    25819.509    289.39998   0.85625823    302.74025    287.37843   0.85625823 
+    1120     30.72232    675.80012     1511.985    202.97705   -836.18488    604.64779    695.06693     153.9432            0   -584.60486    513304.31   -515009.54    1125.7488    25822.677     289.3669    1.1300709    304.44007     287.0563    1.1300629 
+    1140    31.225571    658.36551    1521.8389    204.29988   -863.47335    629.12728    674.88861    150.24405            0   -590.89933    513286.66   -515013.49   -980.39731    25826.849    291.15043     1.376207    307.33908    288.65717    1.3761333 
+    1160    31.744542    641.31431    1531.9582    205.65836   -890.64389    626.42495    680.62653    148.56061            0   -577.09298    513242.55   -515011.72   -1275.5851    25829.398    292.96469    1.6693561     303.6583    291.38487    1.6693561 
+    1180    32.314241    624.85166    1471.4431    197.53448   -846.59145     617.3346    711.86666    153.07391            0   -572.06725    513251.25   -515008.05    1129.9547    25830.175    281.38976    1.6087801    294.57721    279.38824    1.6087801 
+    1200    32.836834    609.19491    1498.3739    201.14982   -889.17902    629.25511    684.67985    160.94667            0    -569.8543    513217.89    -515012.1    714.83828    25832.193    286.64705    1.3880783    283.02115    287.44058    1.3888122 
+    1220    33.330996    594.74278    1478.8355    198.52688   -884.09277    636.92004    698.39685    160.32561            0   -562.35565    513195.99   -515013.37   -758.81758    25835.054    283.01514    1.1229017    278.46407    283.95841    1.1229296 
+    1240    33.860993    582.31866    1493.1918    200.45414   -910.87313    618.74977    681.25809    152.31533            0   -562.54483     513217.1   -515017.75   -1008.5931    25836.703     285.8671   0.88995954     281.0699    286.85402   0.88995954 
+    1260    34.359886    571.65412    1485.3064    199.39557    -913.6523    627.02685    698.36302    149.47819            0   -579.83549    513207.17   -515015.85   -191.59975    25836.765    284.43438   0.70581205    287.41841    284.12865   0.70581205 
+    1280    34.886036    563.01807    1489.0976    199.90452   -926.07957     639.7656    697.32018    156.99221            0   -585.76217    513181.62   -515016.02    169.07813     25836.47    285.20229   0.61087596    293.46017    284.02179   0.61087596 
+    1300     35.37543    555.84411    1527.2006    205.01966   -971.35646    641.09274     662.1865    159.13537            0   -579.97157    513161.92   -515015.72   -1463.4981    25836.182    292.51734   0.58590366    295.34409    292.24276   0.58590366 
+    1320    35.905183    550.05933    1490.5448    200.09879   -940.48543    625.52991    696.21744    165.64927            0   -566.29494     513152.4   -515013.99   -1001.3282    25833.961    285.49188   0.58134778    295.28397    284.05681   0.58136859 
+    1340    36.400304    545.82552    1477.3653     198.3295   -931.53974    649.76738    698.13673    166.18782            0   -561.79356    513131.65   -515015.49    256.39573    25830.414    282.92884    0.6685389    293.55866    281.35291   0.66910289 
+    1360    36.922034    543.45958     1491.565    200.23575   -948.10541    625.58496    716.94864    163.71131            0   -571.55519    513134.22   -515017.02    297.35038    25827.363    285.59777   0.79202277    296.88495     283.9144   0.79202277 
+    1380    37.451357    542.88076    1508.4282    202.49956   -965.54741    646.84583    717.12486    157.01613            0    -570.9963    513101.79   -515017.33   -727.70264    25824.817    288.73715    1.0078391    299.43294    287.15417    1.0078391 
+    1400    37.973437    543.25917    1541.9768    207.00331   -998.71768    642.88473    676.64442    147.18972            0   -575.45961    513127.78   -515017.75   -1351.9224    25821.311    295.05395    1.2758201    298.33888    294.70535    1.2758201 
+    1420    38.477087    544.25328     1494.226    200.59298   -949.97275    637.44698    691.08413    146.44269            0   -570.05548     513163.4   -515018.29   -270.25101    25816.213    285.82275      1.45608    293.72434    284.70163      1.45608 
+    1440    39.004978    546.23983    1496.1396    200.84988   -949.89981    631.74619      738.457    152.80933            0    -573.9543    513118.44   -515017.39    211.73327    25811.001    286.12443      1.60978    287.34634    286.11175      1.60978 
+    1460    39.506582    548.84457    1466.6766     196.8946   -917.83206    633.37692    721.14643    162.99807            0   -556.88904    513139.89   -515018.35   -423.45238    25806.343    280.53109    1.4808771    287.46457    279.56727    1.4808771 
+    1480    40.013021    551.95616     1529.776     205.3654   -977.81982     643.3714    687.91646    168.45052            0   -559.19128    513096.53    -515014.9   -1060.0608    25801.347    292.71931    1.2657554    295.62549    292.43217    1.2657554 
+    1500    40.538129    555.97974    1537.2966    206.37501   -981.31688    625.22061    717.66026    158.35427            0   -572.42591    513106.71   -515016.83   -521.38973    25795.193    294.26369    1.0278009    305.22402    292.64051    1.0278009 
+    1520    41.025889    561.04463    1546.2574    207.57796   -985.21278    635.77714    721.02166    143.98506            0    -562.3667    513090.07    -515013.7    480.66458    25788.679    296.07983   0.80049966    308.03207    294.29295   0.80049966 
+    1540     41.55805    566.68767    1533.2704    205.83452   -966.58278    654.42171    733.05018    143.06827            0   -536.78594    513051.91   -515012.25   -13.266306    25783.154    293.62787   0.70845158     300.7356    292.64315   0.70845158 
+    1560    42.081834    573.47741    1545.9514    207.53687   -972.47397    667.35837    705.11749    148.50883            0   -511.03863     513035.3   -515017.72   -1128.9314    25777.865      296.082   0.65411382    299.13367    295.77283   0.65411382 
+    1580    42.665773    580.84578    1594.8648    214.10328   -1014.0191    665.14281    711.19644    150.09976            0   -528.59268    513008.73    -515020.6    202.40236    25771.588    305.48503   0.59346496    305.13087    305.74762   0.59346496 
+    1600    43.198806    587.93053    1593.0533     213.8601   -1005.1228    667.00914    717.18229    154.08514            0   -518.43498    512998.02   -515022.99     1129.067     25765.95    305.11474   0.64754135    305.66863    305.22598   0.64754135 
+    1620    43.714818    594.73059    1540.0228    206.74099   -945.29217    676.98346    739.79112    155.99494            0   -494.24155    512994.51   -515018.33    526.11962    25762.249    294.90314   0.75499506     297.8325     294.6134   0.75499506 
+    1640    44.259458    602.01816    1574.0462    211.30848   -972.02805     663.3896    727.17417    151.24073            0    -494.0956    513000.57    -515020.3   -575.47503    25759.514    301.37613   0.86690808    296.74738    302.34638   0.86686227 
+    1660    44.764134     609.8688    1585.4465    212.83891   -975.57766    664.90151    754.20462    143.39975            0   -512.60013    512995.21   -515020.69    120.01767    25756.288    303.44799    1.1375937    302.29356     303.8427    1.1375483 
+    1680    45.295079     617.0121    1599.4294    214.71606   -982.41735    673.71348    740.31978    139.29744            0   -523.39592    513004.17   -515016.52     1018.995    25753.537    306.06349    1.2857605    306.24911    306.23701    1.2851446 
+    1700    45.797194     622.7816    1587.5062    213.11542   -964.72461    681.14985     737.5354    142.64373            0   -527.89471    513016.69   -515014.85   -762.54382    25752.152    303.67113    1.5346092    313.56414     302.2316    1.5344941 
+    1720    46.320299     627.3514    1607.6889    215.82486   -980.33755    664.85413    752.47086    151.63477            0   -558.53514    513025.83   -515016.59   -1533.2781    25749.855     307.5455    1.5204255    324.85436     304.8785    1.5204255 
+    1740    46.830115    630.51695    1598.6908     214.6169   -968.17382    653.58364    747.05167    160.79211            0   -580.54509    513063.86   -515012.91   -682.94257    25745.444    305.87278    1.3989272     333.2609     301.5297    1.3989272 
+    1760    47.394788    632.38111     1593.237    213.88475   -960.85589    650.78705    764.11644     167.2889            0   -573.51639    513045.53   -515015.07    563.26755    25740.336    304.94629    1.1225547    334.94227    300.17035    1.1225547 
+    1780    47.922889    633.30997    1598.6499    214.61141   -965.33996    653.54119    765.83593    164.00427            0   -562.23222    513033.51      -515020   -1327.8381    25735.912    306.08499   0.88668411    334.15679    301.62884   0.88668411 
+    1800    48.463113    633.70382    1649.9701    221.50091   -1016.2663    659.96781    745.28779    159.23213            0   -549.62971    512990.43   -515021.55   -1220.9829    25730.022    315.99137   0.72802345    326.79654    314.40852   0.72802345 
+    1820    48.984029    633.58292     1659.156    222.73407    -1025.573    665.57877    731.85128    149.46328            0   -533.84488    512983.77   -515022.39    259.29033    25722.788    317.77089   0.68459607    313.70692    318.65732   0.68459607 
+    1840    49.535432    632.84896    1602.3796     215.1121   -969.53059    677.68273    790.85762    153.52845            0   -510.95603    512938.27   -515018.91    271.83168     25716.16    306.91304   0.62307528    301.73642    307.97704   0.62193772 
+    1860    50.131212    631.44034    1614.3342    216.71695   -982.89384    704.07775    755.95641     164.4832            0   -496.35082    512910.85   -515021.91    193.91175    25710.384     309.1988   0.63700741    295.94067    311.60525   0.63654587 
+    1880    50.855644    629.18958    1597.9323    214.51508   -968.74275    705.91154    777.10222    163.27419            0   -490.72673    512895.73   -515020.04   -974.53867    25705.004    306.00767   0.74633313    296.65573     307.7641   0.74633313 
+    1900    51.442767    625.97644    1641.4591    220.35835   -1015.4827    686.52567    770.03702    156.74058            0   -497.98541    512884.62   -515015.42    634.14021    25698.897    314.30703   0.85093529    303.58173    316.29697   0.85093529 
+    1920    52.143124    621.81199    1629.0055    218.68651   -1007.1935    697.66793    744.88149    154.37261            0   -496.80305    512905.46   -515012.77    706.77423    25693.859    311.83949    1.0371868    309.16955    312.48998    1.0372355 
+    1940    52.903306    616.46004    1627.6423    218.50351   -1011.1823    701.93564    779.10792     151.5545            0    -486.4562    512854.72   -515012.04   -356.74685    25690.093    311.50393    1.2116518    310.99764    311.79486    1.2113866 
+    1960    53.626542    609.78344    1638.9504    220.02157    -1029.167     696.4213    776.28011    154.35764            0   -474.71134    512832.29   -515013.81   -303.73538    25686.165    313.59711    1.3852662     315.5116    313.48837    1.3852662 
+    1980     54.31028    600.96661     1637.173    219.78295   -1036.2064    718.42192     759.0789     153.6092            0   -472.50282    512815.84   -515010.66    -151.6766     25681.92    313.21609    1.4792586    321.24113    312.09275    1.4792586 
+    2000    54.986641    589.81965    1648.0734    221.24629   -1058.2538    690.75922    747.98481    160.84305            0   -487.54224     512840.7      -515011    980.73982    25677.907    315.36457    1.3399431    321.77651    314.51049    1.3399431 
+Loop time of 54.9868 on 4 procs for 2000 steps with 3000 atoms
+
+Performance: 1.571 ns/day, 15.274 hours/ns, 36.372 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.901     | 28.34      | 29.027     |   7.9 | 51.54
+Bond    | 0.92918    | 0.94546    | 0.97217    |   1.7 |  1.72
+Kspace  | 14.647     | 15.356     | 15.836     |  11.2 | 27.93
+Neigh   | 1.6543     | 1.6584     | 1.6622     |   0.2 |  3.02
+Comm    | 1.5279     | 1.6227     | 1.7184     |   5.6 |  2.95
+Output  | 0.022354   | 0.027337   | 0.040941   |   4.8 |  0.05
+Modify  | 5.7813     | 6.226      | 6.5243     |  12.2 | 11.32
+Other   |            | 0.8108     |            |       |  1.47
+
+Nlocal:        750.000 ave         763 max         736 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost:        6184.00 ave        6204 max        6165 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:       185088.0 ave      189615 max      180533 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 740354
+Ave neighs/atom = 246.78467
+Ave special neighs/atom = 10.500000
+Neighbor list builds = 63
+Dangerous builds = 0
+Total wall time: 0:00:55

examples/USER/misc/electron_stopping/in.cascade_AlCu

@@ -0,0 +1,38 @@
+# ***
+# Example input for including electronic stopping effects using fix electron/stopping/fit
+# Al lattice with a single incident Cu atom - multiple species simulation
+# ***
+
+units            metal
+boundary         p p p
+
+lattice          fcc 4.0495
+
+region           box block -10 10 -10 10 -10 10
+create_box       2 box
+create_atoms     1 box
+
+pair_style	 eam/alloy
+pair_coeff	 * * ../../../../potentials/AlCu.eam.alloy Al Cu
+
+mass             1 26.982
+mass             2 63.546
+
+velocity         all create 300 42534 mom yes rot yes
+
+set              atom 1 type 2
+group            pka id 1
+velocity         pka set 1120 1620 400
+
+fix              1 all nve
+fix              2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
+fix              3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
+
+thermo           5
+thermo_style     custom step dt time temp pe ke f_3
+thermo_modify    lost warn flush yes
+
+#dump             0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
+#dump_modify      0 first yes
+
+run              100

examples/USER/misc/electron_stopping/in.cascade_SiSi

@@ -0,0 +1,36 @@
+# ***
+# Example input for including electronic stopping effects using fix electron/stopping/fit
+# Si lattice with one primary knock-on atom (PKA) - single species simulation
+# ***
+
+units            metal
+boundary         p p p
+
+lattice          diamond 5.431
+
+region           box block -10 10 -10 10 -10 10
+create_box       1 box
+create_atoms     1 box
+
+pair_style       tersoff/zbl
+pair_coeff       * * ../../../../potentials/SiC.tersoff.zbl Si
+
+mass             1 28.0855
+
+velocity         all create 300 42534 mom yes rot yes
+
+group            pka id 1
+velocity         pka set 1120 1620 400
+
+fix              1 all nve
+fix              2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
+fix              3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
+
+thermo           5
+thermo_style     custom step dt time temp pe ke f_3
+thermo_modify    lost warn flush yes
+
+#dump             0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
+#dump_modify      0 first yes
+
+run              100